PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deelman, Ewa; Carothers, Christopher; Mandal, Anirban

Here we report that computational science is well established as the third pillar of scientific discovery and is on par with experimentation and theory. However, as we move closer toward the ability to execute exascale calculations and process the ensuing extreme-scale amounts of data produced by both experiments and computations alike, the complexity of managing the compute and data analysis tasks has grown beyond the capabilities of domain scientists. Therefore, workflow management systems are absolutely necessary to ensure current and future scientific discoveries. A key research question for these workflow management systems concerns the performance optimization of complex calculation andmore » data analysis tasks. The central contribution of this article is a description of the PANORAMA approach for modeling and diagnosing the run-time performance of complex scientific workflows. This approach integrates extreme-scale systems testbed experimentation, structured analytical modeling, and parallel systems simulation into a comprehensive workflow framework called Pegasus for understanding and improving the overall performance of complex scientific workflows.« less

PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows

DOE PAGES

Deelman, Ewa; Carothers, Christopher; Mandal, Anirban; ...

2015-07-14

Here we report that computational science is well established as the third pillar of scientific discovery and is on par with experimentation and theory. However, as we move closer toward the ability to execute exascale calculations and process the ensuing extreme-scale amounts of data produced by both experiments and computations alike, the complexity of managing the compute and data analysis tasks has grown beyond the capabilities of domain scientists. Therefore, workflow management systems are absolutely necessary to ensure current and future scientific discoveries. A key research question for these workflow management systems concerns the performance optimization of complex calculation andmore » data analysis tasks. The central contribution of this article is a description of the PANORAMA approach for modeling and diagnosing the run-time performance of complex scientific workflows. This approach integrates extreme-scale systems testbed experimentation, structured analytical modeling, and parallel systems simulation into a comprehensive workflow framework called Pegasus for understanding and improving the overall performance of complex scientific workflows.« less

Modelling and analysis of workflow for lean supply chains

NASA Astrophysics Data System (ADS)

Ma, Jinping; Wang, Kanliang; Xu, Lida

2011-11-01

Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

An Auto-management Thesis Program WebMIS Based on Workflow

NASA Astrophysics Data System (ADS)

Chang, Li; Jie, Shi; Weibo, Zhong

An auto-management WebMIS based on workflow for bachelor thesis program is given in this paper. A module used for workflow dispatching is designed and realized using MySQL and J2EE according to the work principle of workflow engine. The module can automatively dispatch the workflow according to the date of system, login information and the work status of the user. The WebMIS changes the management from handwork to computer-work which not only standardizes the thesis program but also keeps the data and documents clean and consistent.

Workflow Automation: A Collective Case Study

ERIC Educational Resources Information Center

Harlan, Jennifer

2013-01-01

Knowledge management has proven to be a sustainable competitive advantage for many organizations. Knowledge management systems are abundant, with multiple functionalities. The literature reinforces the use of workflow automation with knowledge management systems to benefit organizations; however, it was not known if process automation yielded…

Development of a novel imaging informatics-based system with an intelligent workflow engine (IWEIS) to support imaging-based clinical trials

PubMed Central

Wang, Ximing; Liu, Brent J; Martinez, Clarisa; Zhang, Xuejun; Winstein, Carolee J

2015-01-01

Imaging based clinical trials can benefit from a solution to efficiently collect, analyze, and distribute multimedia data at various stages within the workflow. Currently, the data management needs of these trials are typically addressed with custom-built systems. However, software development of the custom- built systems for versatile workflows can be resource-consuming. To address these challenges, we present a system with a workflow engine for imaging based clinical trials. The system enables a project coordinator to build a data collection and management system specifically related to study protocol workflow without programming. Web Access to DICOM Objects (WADO) module with novel features is integrated to further facilitate imaging related study. The system was initially evaluated by an imaging based rehabilitation clinical trial. The evaluation shows that the cost of the development of system can be much reduced compared to the custom-built system. By providing a solution to customize a system and automate the workflow, the system will save on development time and reduce errors especially for imaging clinical trials. PMID:25870169

Workflow technology: the new frontier. How to overcome the barriers and join the future.

PubMed

Shefter, Susan M

2006-01-01

Hospitals are catching up to the business world in the introduction of technology systems that support professional practice and workflow. The field of case management is highly complex and interrelates with diverse groups in diverse locations. The last few years have seen the introduction of Workflow Technology Tools, which can improve the quality and efficiency of discharge planning by the case manager. Despite the availability of these wonderful new programs, many case managers are hesitant to adopt the new technology and workflow. For a myriad of reasons, a computer-based workflow system can seem like a brick wall. This article discusses, from a practitioner's point of view, how professionals can gain confidence and skill to get around the brick wall and join the future.

Flexible Early Warning Systems with Workflows and Decision Tables

NASA Astrophysics Data System (ADS)

Riedel, F.; Chaves, F.; Zeiner, H.

2012-04-01

An essential part of early warning systems and systems for crisis management are decision support systems that facilitate communication and collaboration. Often official policies specify how different organizations collaborate and what information is communicated to whom. For early warning systems it is crucial that information is exchanged dynamically in a timely manner and all participants get exactly the information they need to fulfil their role in the crisis management process. Information technology obviously lends itself to automate parts of the process. We have experienced however that in current operational systems the information logistics processes are hard-coded, even though they are subject to change. In addition, systems are tailored to the policies and requirements of a certain organization and changes can require major software refactoring. We seek to develop a system that can be deployed and adapted to multiple organizations with different dynamic runtime policies. A major requirement for such a system is that changes can be applied locally without affecting larger parts of the system. In addition to the flexibility regarding changes in policies and processes, the system needs to be able to evolve; when new information sources become available, it should be possible to integrate and use these in the decision process. In general, this kind of flexibility comes with a significant increase in complexity. This implies that only IT professionals can maintain a system that can be reconfigured and adapted; end-users are unable to utilise the provided flexibility. In the business world similar problems arise and previous work suggested using business process management systems (BPMS) or workflow management systems (WfMS) to guide and automate early warning processes or crisis management plans. However, the usability and flexibility of current WfMS are limited, because current notations and user interfaces are still not suitable for end-users, and workflows are usually only suited for rigid processes. We show how improvements can be achieved by using decision tables and rule-based adaptive workflows. Decision tables have been shown to be an intuitive tool that can be used by domain experts to express rule sets that can be interpreted automatically at runtime. Adaptive workflows use a rule-based approach to increase the flexibility of workflows by providing mechanisms to adapt workflows based on context changes, human intervention and availability of services. The combination of workflows, decision tables and rule-based adaption creates a framework that opens up new possibilities for flexible and adaptable workflows, especially, for use in early warning and crisis management systems.

Lessons from implementing a combined workflow-informatics system for diabetes management.

PubMed

Zai, Adrian H; Grant, Richard W; Estey, Greg; Lester, William T; Andrews, Carl T; Yee, Ronnie; Mort, Elizabeth; Chueh, Henry C

2008-01-01

Shortcomings surrounding the care of patients with diabetes have been attributed largely to a fragmented, disorganized, and duplicative health care system that focuses more on acute conditions and complications than on managing chronic disease. To address these shortcomings, we developed a diabetes registry population management application to change the way our staff manages patients with diabetes. Use of this new application has helped us coordinate the responsibilities for intervening and monitoring patients in the registry among different users. Our experiences using this combined workflow-informatics intervention system suggest that integrating a chronic disease registry into clinical workflow for the treatment of chronic conditions creates a useful and efficient tool for managing disease.

Nexus: A modular workflow management system for quantum simulation codes

NASA Astrophysics Data System (ADS)

Krogel, Jaron T.

2016-01-01

The management of simulation workflows represents a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum simulation codes to be supported within the same framework. Current support includes quantum Monte Carlo calculations with QMCPACK, density functional theory calculations with Quantum Espresso or VASP, and quantum chemical calculations with GAMESS. Users can compose workflows through a transparent, text-based interface, resembling the input file of a typical simulation code. A usage example is provided to illustrate the process.

Biowep: a workflow enactment portal for bioinformatics applications.

PubMed

Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

2007-03-08

The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics - LITBIO.

Biowep: a workflow enactment portal for bioinformatics applications

PubMed Central

Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

2007-01-01

Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. Results We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. Conclusion We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO. PMID:17430563

How to Take HRMS Process Management to the Next Level with Workflow Business Event System

NASA Technical Reports Server (NTRS)

Rajeshuni, Sarala; Yagubian, Aram; Kunamaneni, Krishna

2006-01-01

Oracle Workflow with the Business Event System offers a complete process management solution for enterprises to manage business processes cost-effectively. Using Workflow event messaging, event subscriptions, AQ Servlet and advanced queuing technologies, this presentation will demonstrate the step-by-step design and implementation of system solutions in order to integrate two dissimilar systems and establish communication remotely. As a case study, the presentation walks you through the process of propagating organization name changes in other applications that originated from the HRMS module without changing applications code. The solution can be applied to your particular business cases for streamlining or modifying business processes across Oracle and non-Oracle applications.

Nexus: a modular workflow management system for quantum simulation codes

DOE PAGES

Krogel, Jaron T.

2015-08-24

The management of simulation workflows is a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum simulation codes to be supported within the same framework. Current support includes quantum Monte Carlo calculations with QMCPACK, density functional theory calculations with Quantum Espresso or VASP, and quantummore » chemical calculations with GAMESS. Users can compose workflows through a transparent, text-based interface, resembling the input file of a typical simulation code. A usage example is provided to illustrate the process.« less

Content and Workflow Management for Library Websites: Case Studies

ERIC Educational Resources Information Center

Yu, Holly, Ed.

2005-01-01

Using database-driven web pages or web content management (WCM) systems to manage increasingly diverse web content and to streamline workflows is a commonly practiced solution recognized in libraries today. However, limited library web content management models and funding constraints prevent many libraries from purchasing commercially available…

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

PubMed

Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

PubMed Central

Brown, David K.; Penkler, David L.; Musyoka, Thommas M.; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS. PMID:26280450

Design and implementation of workflow engine for service-oriented architecture

NASA Astrophysics Data System (ADS)

Peng, Shuqing; Duan, Huining; Chen, Deyun

2009-04-01

As computer network is developed rapidly and in the situation of the appearance of distribution specialty in enterprise application, traditional workflow engine have some deficiencies, such as complex structure, bad stability, poor portability, little reusability and difficult maintenance. In this paper, in order to improve the stability, scalability and flexibility of workflow management system, a four-layer architecture structure of workflow engine based on SOA is put forward according to the XPDL standard of Workflow Management Coalition, the route control mechanism in control model is accomplished and the scheduling strategy of cyclic routing and acyclic routing is designed, and the workflow engine which adopts the technology such as XML, JSP, EJB and so on is implemented.

Workflow as a Service in the Cloud: Architecture and Scheduling Algorithms.

PubMed

Wang, Jianwu; Korambath, Prakashan; Altintas, Ilkay; Davis, Jim; Crawl, Daniel

2014-01-01

With more and more workflow systems adopting cloud as their execution environment, it becomes increasingly challenging on how to efficiently manage various workflows, virtual machines (VMs) and workflow execution on VM instances. To make the system scalable and easy-to-extend, we design a Workflow as a Service (WFaaS) architecture with independent services. A core part of the architecture is how to efficiently respond continuous workflow requests from users and schedule their executions in the cloud. Based on different targets, we propose four heuristic workflow scheduling algorithms for the WFaaS architecture, and analyze the differences and best usages of the algorithms in terms of performance, cost and the price/performance ratio via experimental studies.

Workflow computing. Improving management and efficiency of pathology diagnostic services.

PubMed

Buffone, G J; Moreau, D; Beck, J R

1996-04-01

Traditionally, information technology in health care has helped practitioners to collect, store, and present information and also to add a degree of automation to simple tasks (instrument interfaces supporting result entry, for example). Thus commercially available information systems do little to support the need to model, execute, monitor, coordinate, and revise the various complex clinical processes required to support health-care delivery. Workflow computing, which is already implemented and improving the efficiency of operations in several nonmedical industries, can address the need to manage complex clinical processes. Workflow computing not only provides a means to define and manage the events, roles, and information integral to health-care delivery but also supports the explicit implementation of policy or rules appropriate to the process. This article explains how workflow computing may be applied to health-care and the inherent advantages of the technology, and it defines workflow system requirements for use in health-care delivery with special reference to diagnostic pathology.

Inferring Clinical Workflow Efficiency via Electronic Medical Record Utilization

PubMed Central

Chen, You; Xie, Wei; Gunter, Carl A; Liebovitz, David; Mehrotra, Sanjay; Zhang, He; Malin, Bradley

2015-01-01

Complexity in clinical workflows can lead to inefficiency in making diagnoses, ineffectiveness of treatment plans and uninformed management of healthcare organizations (HCOs). Traditional strategies to manage workflow complexity are based on measuring the gaps between workflows defined by HCO administrators and the actual processes followed by staff in the clinic. However, existing methods tend to neglect the influences of EMR systems on the utilization of workflows, which could be leveraged to optimize workflows facilitated through the EMR. In this paper, we introduce a framework to infer clinical workflows through the utilization of an EMR and show how such workflows roughly partition into four types according to their efficiency. Our framework infers workflows at several levels of granularity through data mining technologies. We study four months of EMR event logs from a large medical center, including 16,569 inpatient stays, and illustrate that over approximately 95% of workflows are efficient and that 80% of patients are on such workflows. At the same time, we show that the remaining 5% of workflows may be inefficient due to a variety of factors, such as complex patients. PMID:26958173

Contextual cloud-based service oriented architecture for clinical workflow.

PubMed

Moreno-Conde, Jesús; Moreno-Conde, Alberto; Núñez-Benjumea, Francisco J; Parra-Calderón, Carlos

2015-01-01

Given that acceptance of systems within the healthcare domain multiple papers highlighted the importance of integrating tools with the clinical workflow. This paper analyse how clinical context management could be deployed in order to promote the adoption of cloud advanced services and within the clinical workflow. This deployment will be able to be integrated with the eHealth European Interoperability Framework promoted specifications. Throughout this paper, it is proposed a cloud-based service-oriented architecture. This architecture will implement a context management system aligned with the HL7 standard known as CCOW.

Confidentiality Protection of User Data and Adaptive Resource Allocation for Managing Multiple Workflow Performance in Service-Based Systems

ERIC Educational Resources Information Center

An, Ho

2012-01-01

In this dissertation, two interrelated problems of service-based systems (SBS) are addressed: protecting users' data confidentiality from service providers, and managing performance of multiple workflows in SBS. Current SBSs pose serious limitations to protecting users' data confidentiality. Since users' sensitive data is sent in…

Changes in the cardiac rehabilitation workflow process needed for the implementation of a self-management system.

PubMed

Wiggers, Anne-Marieke; Vosbergen, Sandra; Kraaijenhagen, Roderik; Jaspers, Monique; Peek, Niels

2013-01-01

E-health interventions are of a growing importance for self-management of chronic conditions. This study aimed to describe the process adaptions that are needed in cardiac rehabilitation (CR) to implement a self-management system, called MyCARDSS. We created a generic workflow model based on interviews and observations at three CR clinics. Subsequently, a workflow model of the ideal situation after implementation of MyCARDSS was created. We found that the implementation will increase the complexity of existing working procedures because 1) not all patients will use MyCARDSS, 2) there is a transfer of tasks and responsibilities from professionals to patients, and 3) information in MyCARDSS needs to be synchronized with the EPR system for professionals.

Workflow-enabled distributed component-based information architecture for digital medical imaging enterprises.

PubMed

Wong, Stephen T C; Tjandra, Donny; Wang, Huili; Shen, Weimin

2003-09-01

Few information systems today offer a flexible means to define and manage the automated part of radiology processes, which provide clinical imaging services for the entire healthcare organization. Even fewer of them provide a coherent architecture that can easily cope with heterogeneity and inevitable local adaptation of applications and can integrate clinical and administrative information to aid better clinical, operational, and business decisions. We describe an innovative enterprise architecture of image information management systems to fill the needs. Such a system is based on the interplay of production workflow management, distributed object computing, Java and Web techniques, and in-depth domain knowledge in radiology operations. Our design adapts the approach of "4+1" architectural view. In this new architecture, PACS and RIS become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, the workflow-enabled digital radiology system would provide powerful query and statistical functions for managing resources and improving productivity. This paper will potentially lead to a new direction of image information management. We illustrate the innovative design with examples taken from an implemented system.

Schedule-Aware Workflow Management Systems

NASA Astrophysics Data System (ADS)

Mans, Ronny S.; Russell, Nick C.; van der Aalst, Wil M. P.; Moleman, Arnold J.; Bakker, Piet J. M.

Contemporary workflow management systems offer work-items to users through specific work-lists. Users select the work-items they will perform without having a specific schedule in mind. However, in many environments work needs to be scheduled and performed at particular times. For example, in hospitals many work-items are linked to appointments, e.g., a doctor cannot perform surgery without reserving an operating theater and making sure that the patient is present. One of the problems when applying workflow technology in such domains is the lack of calendar-based scheduling support. In this paper, we present an approach that supports the seamless integration of unscheduled (flow) and scheduled (schedule) tasks. Using CPN Tools we have developed a specification and simulation model for schedule-aware workflow management systems. Based on this a system has been realized that uses YAWL, Microsoft Exchange Server 2007, Outlook, and a dedicated scheduling service. The approach is illustrated using a real-life case study at the AMC hospital in the Netherlands. In addition, we elaborate on the experiences obtained when developing and implementing a system of this scale using formal techniques.

From chart tracking to workflow management.

PubMed Central

Srinivasan, P.; Vignes, G.; Venable, C.; Hazelwood, A.; Cade, T.

1994-01-01

The current interest in system-wide integration appears to be based on the assumption that an organization, by digitizing information and accepting a common standard for the exchange of such information, will improve the accessibility of this information and automatically experience benefits resulting from its more productive use. We do not dispute this reasoning, but assert that an organization's capacity for effective change is proportional to the understanding of the current structure among its personnel. Our workflow manager is based on the use of a Parameterized Petri Net (PPN) model which can be configured to represent an arbitrarily detailed picture of an organization. The PPN model can be animated to observe the model organization in action, and the results of the animation analyzed. This simulation is a dynamic ongoing process which changes with the system and allows members of the organization to pose "what if" questions as a means of exploring opportunities for change. We present, the "workflow management system" as the natural successor to the tracking program, incorporating modeling, scheduling, reactive planning, performance evaluation, and simulation. This workflow management system is more than adequate for meeting the needs of a paper chart tracking system, and, as the patient record is computerized, will serve as a planning and evaluation tool in converting the paper-based health information system into a computer-based system. PMID:7950051

Workflow as a Service in the Cloud: Architecture and Scheduling Algorithms

PubMed Central

Wang, Jianwu; Korambath, Prakashan; Altintas, Ilkay; Davis, Jim; Crawl, Daniel

2017-01-01

With more and more workflow systems adopting cloud as their execution environment, it becomes increasingly challenging on how to efficiently manage various workflows, virtual machines (VMs) and workflow execution on VM instances. To make the system scalable and easy-to-extend, we design a Workflow as a Service (WFaaS) architecture with independent services. A core part of the architecture is how to efficiently respond continuous workflow requests from users and schedule their executions in the cloud. Based on different targets, we propose four heuristic workflow scheduling algorithms for the WFaaS architecture, and analyze the differences and best usages of the algorithms in terms of performance, cost and the price/performance ratio via experimental studies. PMID:29399237

Medication Management: The Macrocognitive Workflow of Older Adults With Heart Failure.

PubMed

Mickelson, Robin S; Unertl, Kim M; Holden, Richard J

2016-10-12

Older adults with chronic disease struggle to manage complex medication regimens. Health information technology has the potential to improve medication management, but only if it is based on a thorough understanding of the complexity of medication management workflow as it occurs in natural settings. Prior research reveals that patient work related to medication management is complex, cognitive, and collaborative. Macrocognitive processes are theorized as how people individually and collaboratively think in complex, adaptive, and messy nonlaboratory settings supported by artifacts. The objective of this research was to describe and analyze the work of medication management by older adults with heart failure, using a macrocognitive workflow framework. We interviewed and observed 61 older patients along with 30 informal caregivers about self-care practices including medication management. Descriptive qualitative content analysis methods were used to develop categories, subcategories, and themes about macrocognitive processes used in medication management workflow. We identified 5 high-level macrocognitive processes affecting medication management-sensemaking, planning, coordination, monitoring, and decision making-and 15 subprocesses. Data revealed workflow as occurring in a highly collaborative, fragile system of interacting people, artifacts, time, and space. Process breakdowns were common and patients had little support for macrocognitive workflow from current tools. Macrocognitive processes affected medication management performance. Describing and analyzing this performance produced recommendations for technology supporting collaboration and sensemaking, decision making and problem detection, and planning and implementation.

Real-Time System for Water Modeling and Management

NASA Astrophysics Data System (ADS)

Lee, J.; Zhao, T.; David, C. H.; Minsker, B.

2012-12-01

Working closely with the Texas Commission on Environmental Quality (TCEQ) and the University of Texas at Austin (UT-Austin), we are developing a real-time system for water modeling and management using advanced cyberinfrastructure, data integration and geospatial visualization, and numerical modeling. The state of Texas suffered a severe drought in 2011 that cost the state $7.62 billion in agricultural losses (crops and livestock). Devastating situations such as this could potentially be avoided with better water modeling and management strategies that incorporate state of the art simulation and digital data integration. The goal of the project is to prototype a near-real-time decision support system for river modeling and management in Texas that can serve as a national and international model to promote more sustainable and resilient water systems. The system uses National Weather Service current and predicted precipitation data as input to the Noah-MP Land Surface model, which forecasts runoff, soil moisture, evapotranspiration, and water table levels given land surface features. These results are then used by a river model called RAPID, along with an error model currently under development at UT-Austin, to forecast stream flows in the rivers. Model forecasts are visualized as a Web application for TCEQ decision makers, who issue water diversion (withdrawal) permits and any needed drought restrictions; permit holders; and reservoir operation managers. Users will be able to adjust model parameters to predict the impacts of alternative curtailment scenarios or weather forecasts. A real-time optimization system under development will help TCEQ to identify optimal curtailment strategies to minimize impacts on permit holders and protect health and safety. To develop the system we have implemented RAPID as a remotely-executed modeling service using the Cyberintegrator workflow system with input data downloaded from the North American Land Data Assimilation System. The Cyberintegrator workflow system provides RESTful web services for users to provide inputs, execute workflows, and retrieve outputs. Along with REST endpoints, PAW (Publishable Active Workflows) provides the web user interface toolkit for us to develop web applications with scientific workflows. The prototype web application is built on top of workflows with PAW, so that users will have a user-friendly web environment to provide input parameters, execute the model, and visualize/retrieve the results using geospatial mapping tools. In future work the optimization model will be developed and integrated into the workflow.; Real-Time System for Water Modeling and Management

The Archive Solution for Distributed Workflow Management Agents of the CMS Experiment at LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuznetsov, Valentin; Fischer, Nils Leif; Guo, Yuyi

The CMS experiment at the CERN LHC developed the Workflow Management Archive system to persistently store unstructured framework job report documents produced by distributed workflow management agents. In this paper we present its architecture, implementation, deployment, and integration with the CMS and CERN computing infrastructures, such as central HDFS and Hadoop Spark cluster. The system leverages modern technologies such as a document oriented database and the Hadoop eco-system to provide the necessary flexibility to reliably process, store, and aggregatemore » $$\\mathcal{O}$$(1M) documents on a daily basis. We describe the data transformation, the short and long term storage layers, the query language, along with the aggregation pipeline developed to visualize various performance metrics to assist CMS data operators in assessing the performance of the CMS computing system.« less

The Archive Solution for Distributed Workflow Management Agents of the CMS Experiment at LHC

DOE PAGES

Kuznetsov, Valentin; Fischer, Nils Leif; Guo, Yuyi

2018-03-19

The CMS experiment at the CERN LHC developed the Workflow Management Archive system to persistently store unstructured framework job report documents produced by distributed workflow management agents. In this paper we present its architecture, implementation, deployment, and integration with the CMS and CERN computing infrastructures, such as central HDFS and Hadoop Spark cluster. The system leverages modern technologies such as a document oriented database and the Hadoop eco-system to provide the necessary flexibility to reliably process, store, and aggregatemore » $$\\mathcal{O}$$(1M) documents on a daily basis. We describe the data transformation, the short and long term storage layers, the query language, along with the aggregation pipeline developed to visualize various performance metrics to assist CMS data operators in assessing the performance of the CMS computing system.« less

Medication Management: The Macrocognitive Workflow of Older Adults With Heart Failure

PubMed Central

2016-01-01

Background Older adults with chronic disease struggle to manage complex medication regimens. Health information technology has the potential to improve medication management, but only if it is based on a thorough understanding of the complexity of medication management workflow as it occurs in natural settings. Prior research reveals that patient work related to medication management is complex, cognitive, and collaborative. Macrocognitive processes are theorized as how people individually and collaboratively think in complex, adaptive, and messy nonlaboratory settings supported by artifacts. Objective The objective of this research was to describe and analyze the work of medication management by older adults with heart failure, using a macrocognitive workflow framework. Methods We interviewed and observed 61 older patients along with 30 informal caregivers about self-care practices including medication management. Descriptive qualitative content analysis methods were used to develop categories, subcategories, and themes about macrocognitive processes used in medication management workflow. Results We identified 5 high-level macrocognitive processes affecting medication management—sensemaking, planning, coordination, monitoring, and decision making—and 15 subprocesses. Data revealed workflow as occurring in a highly collaborative, fragile system of interacting people, artifacts, time, and space. Process breakdowns were common and patients had little support for macrocognitive workflow from current tools. Conclusions Macrocognitive processes affected medication management performance. Describing and analyzing this performance produced recommendations for technology supporting collaboration and sensemaking, decision making and problem detection, and planning and implementation. PMID:27733331

A Two-Stage Probabilistic Approach to Manage Personal Worklist in Workflow Management Systems

NASA Astrophysics Data System (ADS)

Han, Rui; Liu, Yingbo; Wen, Lijie; Wang, Jianmin

The application of workflow scheduling in managing individual actor's personal worklist is one area that can bring great improvement to business process. However, current deterministic work cannot adapt to the dynamics and uncertainties in the management of personal worklist. For such an issue, this paper proposes a two-stage probabilistic approach which aims at assisting actors to flexibly manage their personal worklists. To be specific, the approach analyzes every activity instance's continuous probability of satisfying deadline at the first stage. Based on this stochastic analysis result, at the second stage, an innovative scheduling strategy is proposed to minimize the overall deadline violation cost for an actor's personal worklist. Simultaneously, the strategy recommends the actor a feasible worklist of activity instances which meet the required bottom line of successful execution. The effectiveness of our approach is evaluated in a real-world workflow management system and with large scale simulation experiments.

Web-Accessible Scientific Workflow System for Performance Monitoring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roelof Versteeg; Roelof Versteeg; Trevor Rowe

2006-03-01

We describe the design and implementation of a web accessible scientific workflow system for environmental monitoring. This workflow environment integrates distributed, automated data acquisition with server side data management and information visualization through flexible browser based data access tools. Component technologies include a rich browser-based client (using dynamic Javascript and HTML/CSS) for data selection, a back-end server which uses PHP for data processing, user management, and result delivery, and third party applications which are invoked by the back-end using webservices. This environment allows for reproducible, transparent result generation by a diverse user base. It has been implemented for several monitoringmore » systems with different degrees of complexity.« less

Defining Usability Heuristics for Adoption and Efficiency of an Electronic Workflow Document Management System

ERIC Educational Resources Information Center

Fuentes, Steven

2017-01-01

Usability heuristics have been established for different uses and applications as general guidelines for user interfaces. These can affect the implementation of industry solutions and play a significant role regarding cost reduction and process efficiency. The area of electronic workflow document management (EWDM) solutions, also known as…

Improving diabetes population management efficiency with an informatics solution.

PubMed

Zai, Adrian; Grant, Richard; Andrews, Carl; Yee, Ronnie; Chueh, Henry

2007-10-11

Despite intensive resource use for diabetes management in the U.S., our care continues to fall short of evidence-based goals, partly due to system inefficiencies. Diabetes registries are increasingly being utilized as a critical tool for population level disease management by providing real-time data. Since the successful adoption of a diabetes registry depends on how well it integrates with disease management workflows, we optimized our current diabetes management workflow and designed our registry application around it.

Opportunistic Computing with Lobster: Lessons Learned from Scaling up to 25k Non-Dedicated Cores

NASA Astrophysics Data System (ADS)

Wolf, Matthias; Woodard, Anna; Li, Wenzhao; Hurtado Anampa, Kenyi; Yannakopoulos, Anna; Tovar, Benjamin; Donnelly, Patrick; Brenner, Paul; Lannon, Kevin; Hildreth, Mike; Thain, Douglas

2017-10-01

We previously described Lobster, a workflow management tool for exploiting volatile opportunistic computing resources for computation in HEP. We will discuss the various challenges that have been encountered while scaling up the simultaneous CPU core utilization and the software improvements required to overcome these challenges. Categories: Workflows can now be divided into categories based on their required system resources. This allows the batch queueing system to optimize assignment of tasks to nodes with the appropriate capabilities. Within each category, limits can be specified for the number of running jobs to regulate the utilization of communication bandwidth. System resource specifications for a task category can now be modified while a project is running, avoiding the need to restart the project if resource requirements differ from the initial estimates. Lobster now implements time limits on each task category to voluntarily terminate tasks. This allows partially completed work to be recovered. Workflow dependency specification: One workflow often requires data from other workflows as input. Rather than waiting for earlier workflows to be completed before beginning later ones, Lobster now allows dependent tasks to begin as soon as sufficient input data has accumulated. Resource monitoring: Lobster utilizes a new capability in Work Queue to monitor the system resources each task requires in order to identify bottlenecks and optimally assign tasks. The capability of the Lobster opportunistic workflow management system for HEP computation has been significantly increased. We have demonstrated efficient utilization of 25 000 non-dedicated cores and achieved a data input rate of 30 Gb/s and an output rate of 500GB/h. This has required new capabilities in task categorization, workflow dependency specification, and resource monitoring.

SU-F-T-251: The Quality Assurance for the Heavy Patient Load Department in the Developing Country: The Primary Experience of An Entire Workflow QA Process Management in Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, J; Wang, J; Peng, J

Purpose: To implement an entire workflow quality assurance (QA) process in the radiotherapy department and to reduce the error rates of radiotherapy based on the entire workflow management in the developing country. Methods: The entire workflow QA process management starts from patient registration to the end of last treatment including all steps through the entire radiotherapy process. Error rate of chartcheck is used to evaluate the the entire workflow QA process. Two to three qualified senior medical physicists checked the documents before the first treatment fraction of every patient. Random check of the treatment history during treatment was also performed.more » A total of around 6000 patients treatment data before and after implementing the entire workflow QA process were compared from May, 2014 to December, 2015. Results: A systemic checklist was established. It mainly includes patient’s registration, treatment plan QA, information exporting to OIS(Oncology Information System), documents of treatment QAand QA of the treatment history. The error rate derived from the chart check decreases from 1.7% to 0.9% after our the entire workflow QA process. All checked errors before the first treatment fraction were corrected as soon as oncologist re-confirmed them and reinforce staff training was accordingly followed to prevent those errors. Conclusion: The entire workflow QA process improved the safety, quality of radiotherapy in our department and we consider that our QA experience can be applicable for the heavily-loaded radiotherapy departments in developing country.« less

Asterism: an integrated, complete, and open-source approach for running seismologist continuous data-intensive analysis on heterogeneous systems

NASA Astrophysics Data System (ADS)

Ferreira da Silva, R.; Filgueira, R.; Deelman, E.; Atkinson, M.

2016-12-01

We present Asterism, an open source data-intensive framework, which combines the Pegasus and dispel4py workflow systems. Asterism aims to simplify the effort required to develop data-intensive applications that run across multiple heterogeneous resources, without users having to: re-formulate their methods according to different enactment systems; manage the data distribution across systems; parallelize their methods; co-place and schedule their methods with computing resources; and store and transfer large/small volumes of data. Asterism's key element is to leverage the strengths of each workflow system: dispel4py allows developing scientific applications locally and then automatically parallelize and scale them on a wide range of HPC infrastructures with no changes to the application's code; Pegasus orchestrates the distributed execution of applications while providing portability, automated data management, recovery, debugging, and monitoring, without users needing to worry about the particulars of the target execution systems. Asterism leverages the level of abstractions provided by each workflow system to describe hybrid workflows where no information about the underlying infrastructure is required beforehand. The feasibility of Asterism has been evaluated using the seismic ambient noise cross-correlation application, a common data-intensive analysis pattern used by many seismologists. The application preprocesses (Phase1) and cross-correlates (Phase2) traces from several seismic stations. The Asterism workflow is implemented as a Pegasus workflow composed of two tasks (Phase1 and Phase2), where each phase represents a dispel4py workflow. Pegasus tasks describe the in/output data at a logical level, the data dependency between tasks, and the e-Infrastructures and the execution engine to run each dispel4py workflow. We have instantiated the workflow using data from 1000 stations from the IRIS services, and run it across two heterogeneous resources described as Docker containers: MPI (Container2) and Storm (Container3) clusters (Figure 1). Each dispel4py workflow is mapped to a particular execution engine, and data transfers between resources are automatically handled by Pegasus. Asterism is freely available online at http://github.com/dispel4py/pegasus_dispel4py.

Lessons from Implementing a Combined Workflow–Informatics System for Diabetes Management

PubMed Central

Zai, Adrian H.; Grant, Richard W.; Estey, Greg; Lester, William T.; Andrews, Carl T.; Yee, Ronnie; Mort, Elizabeth; Chueh, Henry C.

2008-01-01

Shortcomings surrounding the care of patients with diabetes have been attributed largely to a fragmented, disorganized, and duplicative health care system that focuses more on acute conditions and complications than on managing chronic disease. To address these shortcomings, we developed a diabetes registry population management application to change the way our staff manages patients with diabetes. Use of this new application has helped us coordinate the responsibilities for intervening and monitoring patients in the registry among different users. Our experiences using this combined workflow-informatics intervention system suggest that integrating a chronic disease registry into clinical workflow for the treatment of chronic conditions creates a useful and efficient tool for managing disease. PMID:18436907

SHIWA Services for Workflow Creation and Sharing in Hydrometeorolog

NASA Astrophysics Data System (ADS)

Terstyanszky, Gabor; Kiss, Tamas; Kacsuk, Peter; Sipos, Gergely

2014-05-01

Researchers want to run scientific experiments on Distributed Computing Infrastructures (DCI) to access large pools of resources and services. To run these experiments requires specific expertise that they may not have. Workflows can hide resources and services as a virtualisation layer providing a user interface that researchers can use. There are many scientific workflow systems but they are not interoperable. To learn a workflow system and create workflows may require significant efforts. Considering these efforts it is not reasonable to expect that researchers will learn new workflow systems if they want to run workflows developed in other workflow systems. To overcome it requires creating workflow interoperability solutions to allow workflow sharing. The FP7 'Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs' (SHIWA) project developed the Coarse-Grained Interoperability concept (CGI). It enables recycling and sharing workflows of different workflow systems and executing them on different DCIs. SHIWA developed the SHIWA Simulation Platform (SSP) to implement the CGI concept integrating three major components: the SHIWA Science Gateway, the workflow engines supported by the CGI concept and DCI resources where workflows are executed. The science gateway contains a portal, a submission service, a workflow repository and a proxy server to support the whole workflow life-cycle. The SHIWA Portal allows workflow creation, configuration, execution and monitoring through a Graphical User Interface using the WS-PGRADE workflow system as the host workflow system. The SHIWA Repository stores the formal description of workflows and workflow engines plus executables and data needed to execute them. It offers a wide-range of browse and search operations. To support non-native workflow execution the SHIWA Submission Service imports the workflow and workflow engine from the SHIWA Repository. This service either invokes locally or remotely pre-deployed workflow engines or submits workflow engines with the workflow to local or remote resources to execute workflows. The SHIWA Proxy Server manages certificates needed to execute the workflows on different DCIs. Currently SSP supports sharing of ASKALON, Galaxy, GWES, Kepler, LONI Pipeline, MOTEUR, Pegasus, P-GRADE, ProActive, Triana, Taverna and WS-PGRADE workflows. Further workflow systems can be added to the simulation platform as required by research communities. The FP7 'Building a European Research Community through Interoperable Workflows and Data' (ER-flow) project disseminates the achievements of the SHIWA project to build workflow user communities across Europe. ER-flow provides application supports to research communities within (Astrophysics, Computational Chemistry, Heliophysics and Life Sciences) and beyond (Hydrometeorology and Seismology) to develop, share and run workflows through the simulation platform. The simulation platform supports four usage scenarios: creating and publishing workflows in the repository, searching and selecting workflows in the repository, executing non-native workflows and creating and running meta-workflows. The presentation will outline the CGI concept, the SHIWA Simulation Platform, the ER-flow usage scenarios and how the Hydrometeorology research community runs simulations on SSP.

Experimental evaluation of a flexible I/O architecture for accelerating workflow engines in ultrascale environments

DOE PAGES

Duro, Francisco Rodrigo; Blas, Javier Garcia; Isaila, Florin; ...

2016-10-06

The increasing volume of scientific data and the limited scalability and performance of storage systems are currently presenting a significant limitation for the productivity of the scientific workflows running on both high-performance computing (HPC) and cloud platforms. Clearly needed is better integration of storage systems and workflow engines to address this problem. This paper presents and evaluates a novel solution that leverages codesign principles for integrating Hercules—an in-memory data store—with a workflow management system. We consider four main aspects: workflow representation, task scheduling, task placement, and task termination. As a result, the experimental evaluation on both cloud and HPC systemsmore » demonstrates significant performance and scalability improvements over existing state-of-the-art approaches.« less

Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments

NASA Astrophysics Data System (ADS)

Kintsakis, Athanassios M.; Psomopoulos, Fotis E.; Symeonidis, Andreas L.; Mitkas, Pericles A.

Hermes introduces a new "describe once, run anywhere" paradigm for the execution of bioinformatics workflows in hybrid cloud environments. It combines the traditional features of parallelization-enabled workflow management systems and of distributed computing platforms in a container-based approach. It offers seamless deployment, overcoming the burden of setting up and configuring the software and network requirements. Most importantly, Hermes fosters the reproducibility of scientific workflows by supporting standardization of the software execution environment, thus leading to consistent scientific workflow results and accelerating scientific output.

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience

PubMed Central

Stockton, David B.; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project. PMID:26528175

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience.

PubMed

Stockton, David B; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project.

qPortal: A platform for data-driven biomedical research.

PubMed

Mohr, Christopher; Friedrich, Andreas; Wojnar, David; Kenar, Erhan; Polatkan, Aydin Can; Codrea, Marius Cosmin; Czemmel, Stefan; Kohlbacher, Oliver; Nahnsen, Sven

2018-01-01

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software's strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on high-performance computing systems via coupling of workflow management systems. Integration of project and data management as well as workflow resources in one place present clear advantages over existing solutions.

Detecting distant homologies on protozoans metabolic pathways using scientific workflows.

PubMed

da Cruz, Sérgio Manuel Serra; Batista, Vanessa; Silva, Edno; Tosta, Frederico; Vilela, Clarissa; Cuadrat, Rafael; Tschoeke, Diogo; Dávila, Alberto M R; Campos, Maria Luiza Machado; Mattoso, Marta

2010-01-01

Bioinformatics experiments are typically composed of programs in pipelines manipulating an enormous quantity of data. An interesting approach for managing those experiments is through workflow management systems (WfMS). In this work we discuss WfMS features to support genome homology workflows and present some relevant issues for typical genomic experiments. Our evaluation used Kepler WfMS to manage a real genomic pipeline, named OrthoSearch, originally defined as a Perl script. We show a case study detecting distant homologies on trypanomatids metabolic pathways. Our results reinforce the benefits of WfMS over script languages and point out challenges to WfMS in distributed environments.

Managing and Communicating Operational Workflow: Designing and Implementing an Electronic Outpatient Whiteboard.

PubMed

Steitz, Bryan D; Weinberg, Stuart T; Danciu, Ioana; Unertl, Kim M

2016-01-01

Healthcare team members in emergency department contexts have used electronic whiteboard solutions to help manage operational workflow for many years. Ambulatory clinic settings have highly complex operational workflow, but are still limited in electronic assistance to communicate and coordinate work activities. To describe and discuss the design, implementation, use, and ongoing evolution of a coordination and collaboration tool supporting ambulatory clinic operational workflow at Vanderbilt University Medical Center (VUMC). The outpatient whiteboard tool was initially designed to support healthcare work related to an electronic chemotherapy order-entry application. After a highly successful initial implementation in an oncology context, a high demand emerged across the organization for the outpatient whiteboard implementation. Over the past 10 years, developers have followed an iterative user-centered design process to evolve the tool. The electronic outpatient whiteboard system supports 194 separate whiteboards and is accessed by over 2800 distinct users on a typical day. Clinics can configure their whiteboards to support unique workflow elements. Since initial release, features such as immunization clinical decision support have been integrated into the system, based on requests from end users. The success of the electronic outpatient whiteboard demonstrates the usefulness of an operational workflow tool within the ambulatory clinic setting. Operational workflow tools can play a significant role in supporting coordination, collaboration, and teamwork in ambulatory healthcare settings.

Towards an intelligent hospital environment: OR of the future.

PubMed

Sutherland, Jeffrey V; van den Heuvel, Willem-Jan; Ganous, Tim; Burton, Matthew M; Kumar, Animesh

2005-01-01

Patients, providers, payers, and government demand more effective and efficient healthcare services, and the healthcare industry needs innovative ways to re-invent core processes. Business process reengineering (BPR) showed adopting new hospital information systems can leverage this transformation and workflow management technologies can automate process management. Our research indicates workflow technologies in healthcare require real time patient monitoring, detection of adverse events, and adaptive responses to breakdown in normal processes. Adaptive workflow systems are rarely implemented making current workflow implementations inappropriate for healthcare. The advent of evidence based medicine, guideline based practice, and better understanding of cognitive workflow combined with novel technologies including Radio Frequency Identification (RFID), mobile/wireless technologies, internet workflow, intelligent agents, and Service Oriented Architectures (SOA) opens up new and exciting ways of automating business processes. Total situational awareness of events, timing, and location of healthcare activities can generate self-organizing change in behaviors of humans and machines. A test bed of a novel approach towards continuous process management was designed for the new Weinburg Surgery Building at the University of Maryland Medical. Early results based on clinical process mapping and analysis of patient flow bottlenecks demonstrated 100% improvement in delivery of supplies and instruments at surgery start time. This work has been directly applied to the design of the DARPA Trauma Pod research program where robotic surgery will be performed on wounded soldiers on the battlefield.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duro, Francisco Rodrigo; Blas, Javier Garcia; Isaila, Florin

The increasing volume of scientific data and the limited scalability and performance of storage systems are currently presenting a significant limitation for the productivity of the scientific workflows running on both high-performance computing (HPC) and cloud platforms. Clearly needed is better integration of storage systems and workflow engines to address this problem. This paper presents and evaluates a novel solution that leverages codesign principles for integrating Hercules—an in-memory data store—with a workflow management system. We consider four main aspects: workflow representation, task scheduling, task placement, and task termination. As a result, the experimental evaluation on both cloud and HPC systemsmore » demonstrates significant performance and scalability improvements over existing state-of-the-art approaches.« less

The future of scientific workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deelman, Ewa; Peterka, Tom; Altintas, Ilkay

Today’s computational, experimental, and observational sciences rely on computations that involve many related tasks. The success of a scientific mission often hinges on the computer automation of these workflows. In April 2015, the US Department of Energy (DOE) invited a diverse group of domain and computer scientists from national laboratories supported by the Office of Science, the National Nuclear Security Administration, from industry, and from academia to review the workflow requirements of DOE’s science and national security missions, to assess the current state of the art in science workflows, to understand the impact of emerging extreme-scale computing systems on thosemore » workflows, and to develop requirements for automated workflow management in future and existing environments. This article is a summary of the opinions of over 50 leading researchers attending this workshop. We highlight use cases, computing systems, workflow needs and conclude by summarizing the remaining challenges this community sees that inhibit large-scale scientific workflows from becoming a mainstream tool for extreme-scale science.« less

A Workflow-based Intelligent Network Data Movement Advisor with End-to-end Performance Optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Michelle M.; Wu, Chase Q.

2013-11-07

Next-generation eScience applications often generate large amounts of simulation, experimental, or observational data that must be shared and managed by collaborative organizations. Advanced networking technologies and services have been rapidly developed and deployed to facilitate such massive data transfer. However, these technologies and services have not been fully utilized mainly because their use typically requires significant domain knowledge and in many cases application users are even not aware of their existence. By leveraging the functionalities of an existing Network-Aware Data Movement Advisor (NADMA) utility, we propose a new Workflow-based Intelligent Network Data Movement Advisor (WINDMA) with end-to-end performance optimization formore » this DOE funded project. This WINDMA system integrates three major components: resource discovery, data movement, and status monitoring, and supports the sharing of common data movement workflows through account and database management. This system provides a web interface and interacts with existing data/space management and discovery services such as Storage Resource Management, transport methods such as GridFTP and GlobusOnline, and network resource provisioning brokers such as ION and OSCARS. We demonstrate the efficacy of the proposed transport-support workflow system in several use cases based on its implementation and deployment in DOE wide-area networks.« less

Optimizing CyberShake Seismic Hazard Workflows for Large HPC Resources

NASA Astrophysics Data System (ADS)

Callaghan, S.; Maechling, P. J.; Juve, G.; Vahi, K.; Deelman, E.; Jordan, T. H.

2014-12-01

The CyberShake computational platform is a well-integrated collection of scientific software and middleware that calculates 3D simulation-based probabilistic seismic hazard curves and hazard maps for the Los Angeles region. Currently each CyberShake model comprises about 235 million synthetic seismograms from about 415,000 rupture variations computed at 286 sites. CyberShake integrates large-scale parallel and high-throughput serial seismological research codes into a processing framework in which early stages produce files used as inputs by later stages. Scientific workflow tools are used to manage the jobs, data, and metadata. The Southern California Earthquake Center (SCEC) developed the CyberShake platform using USC High Performance Computing and Communications systems and open-science NSF resources.CyberShake calculations were migrated to the NSF Track 1 system NCSA Blue Waters when it became operational in 2013, via an interdisciplinary team approach including domain scientists, computer scientists, and middleware developers. Due to the excellent performance of Blue Waters and CyberShake software optimizations, we reduced the makespan (a measure of wallclock time-to-solution) of a CyberShake study from 1467 to 342 hours. We will describe the technical enhancements behind this improvement, including judicious introduction of new GPU software, improved scientific software components, increased workflow-based automation, and Blue Waters-specific workflow optimizations.Our CyberShake performance improvements highlight the benefits of scientific workflow tools. The CyberShake workflow software stack includes the Pegasus Workflow Management System (Pegasus-WMS, which includes Condor DAGMan), HTCondor, and Globus GRAM, with Pegasus-mpi-cluster managing the high-throughput tasks on the HPC resources. The workflow tools handle data management, automatically transferring about 13 TB back to SCEC storage.We will present performance metrics from the most recent CyberShake study, executed on Blue Waters. We will compare the performance of CPU and GPU versions of our large-scale parallel wave propagation code, AWP-ODC-SGT. Finally, we will discuss how these enhancements have enabled SCEC to move forward with plans to increase the CyberShake simulation frequency to 1.0 Hz.

Workflow Management for Complex HEP Analyses

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, R.; Rieger, M.; von Cube, R. F.

2017-10-01

We present the novel Analysis Workflow Management (AWM) that provides users with the tools and competences of professional large scale workflow systems, e.g. Apache’s Airavata[1]. The approach presents a paradigm shift from executing parts of the analysis to defining the analysis. Within AWM an analysis consists of steps. For example, a step defines to run a certain executable for multiple files of an input data collection. Each call to the executable for one of those input files can be submitted to the desired run location, which could be the local computer or a remote batch system. An integrated software manager enables automated user installation of dependencies in the working directory at the run location. Each execution of a step item creates one report for bookkeeping purposes containing error codes and output data or file references. Required files, e.g. created by previous steps, are retrieved automatically. Since data storage and run locations are exchangeable from the steps perspective, computing resources can be used opportunistically. A visualization of the workflow as a graph of the steps in the web browser provides a high-level view on the analysis. The workflow system is developed and tested alongside of a ttbb cross section measurement where, for instance, the event selection is represented by one step and a Bayesian statistical inference is performed by another. The clear interface and dependencies between steps enables a make-like execution of the whole analysis.

A patient workflow management system built on guidelines.

PubMed Central

Dazzi, L.; Fassino, C.; Saracco, R.; Quaglini, S.; Stefanelli, M.

1997-01-01

To provide high quality, shared, and distributed medical care, clinical and organizational issues need to be integrated. This work describes a methodology for developing a Patient Workflow Management System, based on a detailed model of both the medical work process and the organizational structure. We assume that the medical work process is represented through clinical practice guidelines, and that an ontological description of the organization is available. Thus, we developed tools 1) for acquiring the medical knowledge contained into a guideline, 2) to translate the derived formalized guideline into a computational formalism, precisely a Petri Net, 3) to maintain different representation levels. The high level representation guarantees that the Patient Workflow follows the guideline prescriptions, while the low level takes into account the specific organization characteristics and allow allocating resources for managing a specific patient in daily practice. PMID:9357606

Task Management in the New ATLAS Production System

NASA Astrophysics Data System (ADS)

De, K.; Golubkov, D.; Klimentov, A.; Potekhin, M.; Vaniachine, A.; Atlas Collaboration

2014-06-01

This document describes the design of the new Production System of the ATLAS experiment at the LHC [1]. The Production System is the top level workflow manager which translates physicists' needs for production level processing and analysis into actual workflows executed across over a hundred Grid sites used globally by ATLAS. As the production workload increased in volume and complexity in recent years (the ATLAS production tasks count is above one million, with each task containing hundreds or thousands of jobs) there is a need to upgrade the Production System to meet the challenging requirements of the next LHC run while minimizing the operating costs. In the new design, the main subsystems are the Database Engine for Tasks (DEFT) and the Job Execution and Definition Interface (JEDI). Based on users' requests, DEFT manages inter-dependent groups of tasks (Meta-Tasks) and generates corresponding data processing workflows. The JEDI component then dynamically translates the task definitions from DEFT into actual workload jobs executed in the PanDA Workload Management System [2]. We present the requirements, design parameters, basics of the object model and concrete solutions utilized in building the new Production System and its components.

[Application of information management system about medical equipment].

PubMed

Hang, Jianjin; Zhang, Chaoqun; Wu, Xiang-Yang

2011-05-01

Based on the practice of workflow, information management system about medical equipment was developed and its functions such as gathering, browsing, inquiring and counting were introduced. With dynamic and complete case management of medical equipment, the system improved the management of medical equipment.

Optimization of tomographic reconstruction workflows on geographically distributed resources

DOE PAGES

Bicer, Tekin; Gursoy, Doga; Kettimuthu, Rajkumar; ...

2016-01-01

New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modelingmore » of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13× speedup (on experimented resources). Furthermore, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks.« less

Optimization of tomographic reconstruction workflows on geographically distributed resources

PubMed Central

Bicer, Tekin; Gürsoy, Doǧa; Kettimuthu, Rajkumar; De Carlo, Francesco; Foster, Ian T.

2016-01-01

New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13× speedup (on experimented resources). Moreover, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks. PMID:27359149

Optimization of tomographic reconstruction workflows on geographically distributed resources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bicer, Tekin; Gursoy, Doga; Kettimuthu, Rajkumar

New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modelingmore » of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13× speedup (on experimented resources). Furthermore, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks.« less

SynTrack: DNA Assembly Workflow Management (SynTrack) v2.0.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

MENG, XIANWEI; SIMIRENKO, LISA

2016-12-01

SynTrack is a dynamic, workflow-driven data management system that tracks the DNA build process: Management of the hierarchical relationships of the DNA fragments; Monitoring of process tasks for the assembly of multiple DNA fragments into final constructs; Creations of vendor order forms with selectable building blocks. Organizing plate layouts barcodes for vendor/pcr/fusion/chewback/bioassay/glycerol/master plate maps (default/condensed); Creating or updating Pre-Assembly/Assembly process workflows with selected building blocks; Generating Echo pooling instructions based on plate maps; Tracking of building block orders, received and final assembled for delivering; Bulk updating of colony or PCR amplification information, fusion PCR and chewback results; Updating with QA/QCmore » outcome with .csv & .xlsx template files; Re-work assembly workflow enabled before and after sequencing validation; and Tracking of plate/well data changes and status updates and reporting of master plate status with QC outcomes.« less

Flexible Workflow Software enables the Management of an Increased Volume and Heterogeneity of Sensors, and evolves with the Expansion of Complex Ocean Observatory Infrastructures.

NASA Astrophysics Data System (ADS)

Tomlin, M. C.; Jenkyns, R.

2015-12-01

Ocean Networks Canada (ONC) collects data from observatories in the northeast Pacific, Salish Sea, Arctic Ocean, Atlantic Ocean, and land-based sites in British Columbia. Data are streamed, collected autonomously, or transmitted via satellite from a variety of instruments. The Software Engineering group at ONC develops and maintains Oceans 2.0, an in-house software system that acquires and archives data from sensors, and makes data available to scientists, the public, government and non-government agencies. The Oceans 2.0 workflow tool was developed by ONC to manage a large volume of tasks and processes required for instrument installation, recovery and maintenance activities. Since 2013, the workflow tool has supported 70 expeditions and grown to include 30 different workflow processes for the increasing complexity of infrastructures at ONC. The workflow tool strives to keep pace with an increasing heterogeneity of sensors, connections and environments by supporting versioning of existing workflows, and allowing the creation of new processes and tasks. Despite challenges in training and gaining mutual support from multidisciplinary teams, the workflow tool has become invaluable in project management in an innovative setting. It provides a collective place to contribute to ONC's diverse projects and expeditions and encourages more repeatable processes, while promoting interactions between the multidisciplinary teams who manage various aspects of instrument development and the data they produce. The workflow tool inspires documentation of terminologies and procedures, and effectively links to other tools at ONC such as JIRA, Alfresco and Wiki. Motivated by growing sensor schemes, modes of collecting data, archiving, and data distribution at ONC, the workflow tool ensures that infrastructure is managed completely from instrument purchase to data distribution. It integrates all areas of expertise and helps fulfill ONC's mandate to offer quality data to users.

A framework for service enterprise workflow simulation with multi-agents cooperation

NASA Astrophysics Data System (ADS)

Tan, Wenan; Xu, Wei; Yang, Fujun; Xu, Lida; Jiang, Chuanqun

2013-11-01

Process dynamic modelling for service business is the key technique for Service-Oriented information systems and service business management, and the workflow model of business processes is the core part of service systems. Service business workflow simulation is the prevalent approach to be used for analysis of service business process dynamically. Generic method for service business workflow simulation is based on the discrete event queuing theory, which is lack of flexibility and scalability. In this paper, we propose a service workflow-oriented framework for the process simulation of service businesses using multi-agent cooperation to address the above issues. Social rationality of agent is introduced into the proposed framework. Adopting rationality as one social factor for decision-making strategies, a flexible scheduling for activity instances has been implemented. A system prototype has been developed to validate the proposed simulation framework through a business case study.

RESTFul based heterogeneous Geoprocessing workflow interoperation for Sensor Web Service

NASA Astrophysics Data System (ADS)

Yang, Chao; Chen, Nengcheng; Di, Liping

2012-10-01

Advanced sensors on board satellites offer detailed Earth observations. A workflow is one approach for designing, implementing and constructing a flexible and live link between these sensors' resources and users. It can coordinate, organize and aggregate the distributed sensor Web services to meet the requirement of a complex Earth observation scenario. A RESTFul based workflow interoperation method is proposed to integrate heterogeneous workflows into an interoperable unit. The Atom protocols are applied to describe and manage workflow resources. The XML Process Definition Language (XPDL) and Business Process Execution Language (BPEL) workflow standards are applied to structure a workflow that accesses sensor information and one that processes it separately. Then, a scenario for nitrogen dioxide (NO2) from a volcanic eruption is used to investigate the feasibility of the proposed method. The RESTFul based workflows interoperation system can describe, publish, discover, access and coordinate heterogeneous Geoprocessing workflows.

Managing and Communicating Operational Workflow

PubMed Central

Weinberg, Stuart T.; Danciu, Ioana; Unertl, Kim M.

2016-01-01

Summary Background Healthcare team members in emergency department contexts have used electronic whiteboard solutions to help manage operational workflow for many years. Ambulatory clinic settings have highly complex operational workflow, but are still limited in electronic assistance to communicate and coordinate work activities. Objective To describe and discuss the design, implementation, use, and ongoing evolution of a coordination and collaboration tool supporting ambulatory clinic operational workflow at Vanderbilt University Medical Center (VUMC). Methods The outpatient whiteboard tool was initially designed to support healthcare work related to an electronic chemotherapy order-entry application. After a highly successful initial implementation in an oncology context, a high demand emerged across the organization for the outpatient whiteboard implementation. Over the past 10 years, developers have followed an iterative user-centered design process to evolve the tool. Results The electronic outpatient whiteboard system supports 194 separate whiteboards and is accessed by over 2800 distinct users on a typical day. Clinics can configure their whiteboards to support unique workflow elements. Since initial release, features such as immunization clinical decision support have been integrated into the system, based on requests from end users. Conclusions The success of the electronic outpatient whiteboard demonstrates the usefulness of an operational workflow tool within the ambulatory clinic setting. Operational workflow tools can play a significant role in supporting coordination, collaboration, and teamwork in ambulatory healthcare settings. PMID:27081407

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

PubMed Central

Morris, Chris; Pajon, Anne; Griffiths, Susanne L.; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M.; Wilter da Silva, Alan; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S.; Stuart, David I.; Henrick, Kim; Esnouf, Robert M.

2011-01-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service. PMID:21460443

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

PubMed

Morris, Chris; Pajon, Anne; Griffiths, Susanne L; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M; da Silva, Alan Wilter; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S; Stuart, David I; Henrick, Kim; Esnouf, Robert M

2011-04-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

Development of an Excel-based laboratory information management system for improving workflow efficiencies in early ADME screening.

PubMed

Lu, Xinyan

2016-01-01

There is a clear requirement for enhancing laboratory information management during early absorption, distribution, metabolism and excretion (ADME) screening. The application of a commercial laboratory information management system (LIMS) is limited by complexity, insufficient flexibility, high costs and extended timelines. An improved custom in-house LIMS for ADME screening was developed using Excel. All Excel templates were generated through macros and formulae, and information flow was streamlined as much as possible. This system has been successfully applied in task generation, process control and data management, with a reduction in both labor time and human error rates. An Excel-based LIMS can provide a simple, flexible and cost/time-saving solution for improving workflow efficiencies in early ADME screening.

Applying Content Management to Automated Provenance Capture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schuchardt, Karen L.; Gibson, Tara D.; Stephan, Eric G.

2008-04-10

Workflows and data pipelines are becoming increasingly valuable in both computational and experimen-tal sciences. These automated systems are capable of generating significantly more data within the same amount of time than their manual counterparts. Automatically capturing and recording data prove-nance and annotation as part of these workflows is critical for data management, verification, and dis-semination. Our goal in addressing the provenance challenge was to develop and end-to-end system that demonstrates real-time capture, persistent content management, and ad-hoc searches of both provenance and metadata using open source software and standard protocols. We describe our prototype, which extends the Kepler workflow toolsmore » for the execution environment, the Scientific Annotation Middleware (SAM) content management software for data services, and an existing HTTP-based query protocol. Our implementation offers several unique capabilities, and through the use of standards, is able to pro-vide access to the provenance record to a variety of commonly available client tools.« less

Producing an Infrared Multiwavelength Galactic Plane Atlas Using Montage, Pegasus, and Amazon Web Services

NASA Astrophysics Data System (ADS)

Rynge, M.; Juve, G.; Kinney, J.; Good, J.; Berriman, B.; Merrihew, A.; Deelman, E.

2014-05-01

In this paper, we describe how to leverage cloud resources to generate large-scale mosaics of the galactic plane in multiple wavelengths. Our goal is to generate a 16-wavelength infrared Atlas of the Galactic Plane at a common spatial sampling of 1 arcsec, processed so that they appear to have been measured with a single instrument. This will be achieved by using the Montage image mosaic engine process observations from the 2MASS, GLIMPSE, MIPSGAL, MSX and WISE datasets, over a wavelength range of 1 μm to 24 μm, and by using the Pegasus Workflow Management System for managing the workload. When complete, the Atlas will be made available to the community as a data product. We are generating images that cover ±180° in Galactic longitude and ±20° in Galactic latitude, to the extent permitted by the spatial coverage of each dataset. Each image will be 5°x5° in size (including an overlap of 1° with neighboring tiles), resulting in an atlas of 1,001 images. The final size will be about 50 TBs. This paper will focus on the computational challenges, solutions, and lessons learned in producing the Atlas. To manage the computation we are using the Pegasus Workflow Management System, a mature, highly fault-tolerant system now in release 4.2.2 that has found wide applicability across many science disciplines. A scientific workflow describes the dependencies between the tasks and in most cases the workflow is described as a directed acyclic graph, where the nodes are tasks and the edges denote the task dependencies. A defining property for a scientific workflow is that it manages data flow between tasks. Applied to the galactic plane project, each 5 by 5 mosaic is a Pegasus workflow. Pegasus is used to fetch the source images, execute the image mosaicking steps of Montage, and store the final outputs in a storage system. As these workflows are very I/O intensive, care has to be taken when choosing what infrastructure to execute the workflow on. In our setup, we choose to use dynamically provisioned compute clusters running on the Amazon Elastic Compute Cloud (EC2). All our instances are using the same base image, which is configured to come up as a master node by default. The master node is a central instance from where the workflow can be managed. Additional worker instances are provisioned and configured to accept work assignments from the master node. The system allows for adding/removing workers in an ad hoc fashion, and could be run in large configurations. To-date we have performed 245,000 CPU hours of computing and generated 7,029 images and totaling 30 TB. With the current set up our runtime would be 340,000 CPU hours for the whole project. Using spot m2.4xlarge instances, the cost would be approximately $5,950. Using faster AWS instances, such as cc2.8xlarge could potentially decrease the total CPU hours and further reduce the compute costs. The paper will explore these tradeoffs.

A pattern-based analysis of clinical computer-interpretable guideline modeling languages.

PubMed

Mulyar, Nataliya; van der Aalst, Wil M P; Peleg, Mor

2007-01-01

Languages used to specify computer-interpretable guidelines (CIGs) differ in their approaches to addressing particular modeling challenges. The main goals of this article are: (1) to examine the expressive power of CIG modeling languages, and (2) to define the differences, from the control-flow perspective, between process languages in workflow management systems and modeling languages used to design clinical guidelines. The pattern-based analysis was applied to guideline modeling languages Asbru, EON, GLIF, and PROforma. We focused on control-flow and left other perspectives out of consideration. We evaluated the selected CIG modeling languages and identified their degree of support of 43 control-flow patterns. We used a set of explicitly defined evaluation criteria to determine whether each pattern is supported directly, indirectly, or not at all. PROforma offers direct support for 22 of 43 patterns, Asbru 20, GLIF 17, and EON 11. All four directly support basic control-flow patterns, cancellation patterns, and some advance branching and synchronization patterns. None support multiple instances patterns. They offer varying levels of support for synchronizing merge patterns and state-based patterns. Some support a few scenarios not covered by the 43 control-flow patterns. CIG modeling languages are remarkably close to traditional workflow languages from the control-flow perspective, but cover many fewer workflow patterns. CIG languages offer some flexibility that supports modeling of complex decisions and provide ways for modeling some decisions not covered by workflow management systems. Workflow management systems may be suitable for clinical guideline applications.

Development of the workflow kine systems for support on KAIZEN.

PubMed

Mizuno, Yuki; Ito, Toshihiko; Yoshikawa, Toru; Yomogida, Satoshi; Morio, Koji; Sakai, Kazuhiro

2012-01-01

In this paper, we introduce the new workflow line system consisted of the location and image recording, which led to the acquisition of workflow information and the analysis display. From the results of workflow line investigation, we considered the anticipated effects and the problems on KAIZEN. Workflow line information included the location information and action contents information. These technologies suggest the viewpoints to help improvement, for example, exclusion of useless movement, the redesign of layout and the review of work procedure. Manufacturing factory, it was clear that there was much movement from the standard operation place and accumulation residence time. The following was shown as a result of this investigation, to be concrete, the efficient layout was suggested by this system. In the case of the hospital, similarly, it is pointed out that the workflow has the problem of layout and setup operations based on the effective movement pattern of the experts. This system could adapt to routine work, including as well as non-routine work. By the development of this system which can fit and adapt to industrial diversification, more effective "visual management" (visualization of work) is expected in the future.

Creating a comprehensive customer service program to help convey critical and acute results of radiology studies.

PubMed

Towbin, Alexander J; Hall, Seth; Moskovitz, Jay; Johnson, Neil D; Donnelly, Lane F

2011-01-01

Communication of acute or critical results between the radiology department and referring clinicians has been a deficiency of many radiology departments. The failure to perform or document these communications can lead to poor patient care, patient safety issues, medical-legal issues, and complaints from referring clinicians. To mitigate these factors, a communication and documentation tool was created and incorporated into our departmental customer service program. This article will describe the implementation of a comprehensive customer service program in a hospital-based radiology department. A comprehensive customer service program was created in the radiology department. Customer service representatives were hired to answer the telephone calls to the radiology reading rooms and to help convey radiology results. The radiologists, referring clinicians, and customer service representatives were then linked via a novel workflow management system. This workflow management system provided tools to help facilitate the communication needs of each group. The number of studies with results conveyed was recorded from the implementation of the workflow management system. Between the implementation of the workflow management system on August 1, 2005, and June 1, 2009, 116,844 radiology results were conveyed to the referring clinicians and documented in the system. This accounts for more than 14% of the 828,516 radiology cases performed in this time frame. We have been successful in creating a comprehensive customer service program to convey and document communication of radiology results. This program has been widely used by the ordering clinicians as well as radiologists since its inception.

78 FR 20087 - Privacy Act of 1974; Proposed New System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-03

... is comprised of two components--Enterprise Content Management (ECM) and the Account Management System (AMS). The heart of the system is the ECM component, which manages the workflows that were developed..., digital media, and/or CD-ROM. PAS is a customized module within USDA's Enterprise Content Management (ECM...

Workflow management in large distributed systems

NASA Astrophysics Data System (ADS)

Legrand, I.; Newman, H.; Voicu, R.; Dobre, C.; Grigoras, C.

2011-12-01

The MonALISA (Monitoring Agents using a Large Integrated Services Architecture) framework provides a distributed service system capable of controlling and optimizing large-scale, data-intensive applications. An essential part of managing large-scale, distributed data-processing facilities is a monitoring system for computing facilities, storage, networks, and the very large number of applications running on these systems in near realtime. All this monitoring information gathered for all the subsystems is essential for developing the required higher-level services—the components that provide decision support and some degree of automated decisions—and for maintaining and optimizing workflow in large-scale distributed systems. These management and global optimization functions are performed by higher-level agent-based services. We present several applications of MonALISA's higher-level services including optimized dynamic routing, control, data-transfer scheduling, distributed job scheduling, dynamic allocation of storage resource to running jobs and automated management of remote services among a large set of grid facilities.

Task Delegation Based Access Control Models for Workflow Systems

NASA Astrophysics Data System (ADS)

Gaaloul, Khaled; Charoy, François

e-Government organisations are facilitated and conducted using workflow management systems. Role-based access control (RBAC) is recognised as an efficient access control model for large organisations. The application of RBAC in workflow systems cannot, however, grant permissions to users dynamically while business processes are being executed. We currently observe a move away from predefined strict workflow modelling towards approaches supporting flexibility on the organisational level. One specific approach is that of task delegation. Task delegation is a mechanism that supports organisational flexibility, and ensures delegation of authority in access control systems. In this paper, we propose a Task-oriented Access Control (TAC) model based on RBAC to address these requirements. We aim to reason about task from organisational perspectives and resources perspectives to analyse and specify authorisation constraints. Moreover, we present a fine grained access control protocol to support delegation based on the TAC model.

A case study on the impacts of computerized provider order entry (CPOE) system on hospital clinical workflow.

PubMed

Mominah, Maher; Yunus, Faisel; Househ, Mowafa S

2013-01-01

Computerized provider order entry (CPOE) is a health informatics system that helps health care providers create and manage orders for medications and other health care services. Through the automation of the ordering process, CPOE has improved the overall efficiency of hospital processes and workflow. In Saudi Arabia, CPOE has been used for years, with only a few studies evaluating the impacts of CPOE on clinical workflow. In this paper, we discuss the experience of a local hospital with the use of CPOE and its impacts on clinical workflow. Results show that there are many issues related to the implementation and use of CPOE within Saudi Arabia that must be addressed, including design, training, medication errors, alert fatigue, and system dep Recommendations for improving CPOE use within Saudi Arabia are also discussed.

An ontological knowledge framework for adaptive medical workflow.

PubMed

Dang, Jiangbo; Hedayati, Amir; Hampel, Ken; Toklu, Candemir

2008-10-01

As emerging technologies, semantic Web and SOA (Service-Oriented Architecture) allow BPMS (Business Process Management System) to automate business processes that can be described as services, which in turn can be used to wrap existing enterprise applications. BPMS provides tools and methodologies to compose Web services that can be executed as business processes and monitored by BPM (Business Process Management) consoles. Ontologies are a formal declarative knowledge representation model. It provides a foundation upon which machine understandable knowledge can be obtained, and as a result, it makes machine intelligence possible. Healthcare systems can adopt these technologies to make them ubiquitous, adaptive, and intelligent, and then serve patients better. This paper presents an ontological knowledge framework that covers healthcare domains that a hospital encompasses-from the medical or administrative tasks, to hospital assets, medical insurances, patient records, drugs, and regulations. Therefore, our ontology makes our vision of personalized healthcare possible by capturing all necessary knowledge for a complex personalized healthcare scenario involving patient care, insurance policies, and drug prescriptions, and compliances. For example, our ontology facilitates a workflow management system to allow users, from physicians to administrative assistants, to manage, even create context-aware new medical workflows and execute them on-the-fly.

Implementing standards for the interoperability among healthcare providers in the public regionalized Healthcare Information System of the Lombardy Region.

PubMed

Barbarito, Fulvio; Pinciroli, Francesco; Mason, John; Marceglia, Sara; Mazzola, Luca; Bonacina, Stefano

2012-08-01

Information technologies (ITs) have now entered the everyday workflow in a variety of healthcare providers with a certain degree of independence. This independence may be the cause of difficulty in interoperability between information systems and it can be overcome through the implementation and adoption of standards. Here we present the case of the Lombardy Region, in Italy, that has been able, in the last 10 years, to set up the Regional Social and Healthcare Information System, connecting all the healthcare providers within the region, and providing full access to clinical and health-related documents independently from the healthcare organization that generated the document itself. This goal, in a region with almost 10 millions citizens, was achieved through a twofold approach: first, the political and operative push towards the adoption of the Health Level 7 (HL7) standard within single hospitals and, second, providing a technological infrastructure for data sharing based on interoperability specifications recognized at the regional level for messages transmitted from healthcare providers to the central domain. The adoption of such regional interoperability specifications enabled the communication among heterogeneous systems placed in different hospitals in Lombardy. Integrating the Healthcare Enterprise (IHE) integration profiles which refer to HL7 standards are adopted within hospitals for message exchange and for the definition of integration scenarios. The IHE patient administration management (PAM) profile with its different workflows is adopted for patient management, whereas the Scheduled Workflow (SWF), the Laboratory Testing Workflow (LTW), and the Ambulatory Testing Workflow (ATW) are adopted for order management. At present, the system manages 4,700,000 pharmacological e-prescriptions, and 1,700,000 e-prescriptions for laboratory exams per month. It produces, monthly, 490,000 laboratory medical reports, 180,000 radiology medical reports, 180,000 first aid medical reports, and 58,000 discharge summaries. Hence, despite there being still work in progress, the Lombardy Region healthcare system is a fully interoperable social healthcare system connecting patients, healthcare providers, healthcare organizations, and healthcare professionals in a large and heterogeneous territory through the implementation of international health standards. Copyright © 2012 Elsevier Inc. All rights reserved.

Implementing CORAL: An Electronic Resource Management System

ERIC Educational Resources Information Center

Whitfield, Sharon

2011-01-01

A 2010 electronic resource management survey conducted by Maria Collins of North Carolina State University and Jill E. Grogg of University of Alabama Libraries found that the top six electronic resources management priorities included workflow management, communications management, license management, statistics management, administrative…

Use of contextual inquiry to understand anatomic pathology workflow: Implications for digital pathology adoption

PubMed Central

Ho, Jonhan; Aridor, Orly; Parwani, Anil V.

2012-01-01

Background: For decades anatomic pathology (AP) workflow have been a highly manual process based on the use of an optical microscope and glass slides. Recent innovations in scanning and digitizing of entire glass slides are accelerating a move toward widespread adoption and implementation of a workflow based on digital slides and their supporting information management software. To support the design of digital pathology systems and ensure their adoption into pathology practice, the needs of the main users within the AP workflow, the pathologists, should be identified. Contextual inquiry is a qualitative, user-centered, social method designed to identify and understand users’ needs and is utilized for collecting, interpreting, and aggregating in-detail aspects of work. Objective: Contextual inquiry was utilized to document current AP workflow, identify processes that may benefit from the introduction of digital pathology systems, and establish design requirements for digital pathology systems that will meet pathologists’ needs. Materials and Methods: Pathologists were observed and interviewed at a large academic medical center according to contextual inquiry guidelines established by Holtzblatt et al. 1998. Notes representing user-provided data were documented during observation sessions. An affinity diagram, a hierarchal organization of the notes based on common themes in the data, was created. Five graphical models were developed to help visualize the data including sequence, flow, artifact, physical, and cultural models. Results: A total of six pathologists were observed by a team of two researchers. A total of 254 affinity notes were documented and organized using a system based on topical hierarchy, including 75 third-level, 24 second-level, and five main-level categories, including technology, communication, synthesis/preparation, organization, and workflow. Current AP workflow was labor intensive and lacked scalability. A large number of processes that may possibly improve following the introduction of digital pathology systems were identified. These work processes included case management, case examination and review, and final case reporting. Furthermore, a digital slide system should integrate with the anatomic pathologic laboratory information system. Conclusions: To our knowledge, this is the first study that utilized the contextual inquiry method to document AP workflow. Findings were used to establish key requirements for the design of digital pathology systems. PMID:23243553

Managing the life cycle of electronic clinical documents.

PubMed

Payne, Thomas H; Graham, Gail

2006-01-01

To develop a model of the life cycle of clinical documents from inception to use in a person's medical record, including workflow requirements from clinical practice, local policy, and regulation. We propose a model for the life cycle of clinical documents as a framework for research on documentation within electronic medical record (EMR) systems. Our proposed model includes three axes: the stages of the document, the roles of those involved with the document, and the actions those involved may take on the document at each stage. The model includes the rules to describe who (in what role) can perform what actions on the document, and at what stages they can perform them. Rules are derived from needs of clinicians, and requirements of hospital bylaws and regulators. Our model encompasses current practices for paper medical records and workflow in some EMR systems. Commercial EMR systems include methods for implementing document workflow rules. Workflow rules that are part of this model mirror functionality in the Department of Veterans Affairs (VA) EMR system where the Authorization/ Subscription Utility permits document life cycle rules to be written in English-like fashion. Creating a model of the life cycle of clinical documents serves as a framework for discussion of document workflow, how rules governing workflow can be implemented in EMR systems, and future research of electronic documentation.

CERES AuTomAted job Loading SYSTem (CATALYST): An automated workflow manager for satellite data production

NASA Astrophysics Data System (ADS)

Gleason, J. L.; Hillyer, T. N.; Wilkins, J.

2012-12-01

The CERES Science Team integrates data from 5 CERES instruments onboard the Terra, Aqua and NPP missions. The processing chain fuses CERES observations with data from 19 other unique sources. The addition of CERES Flight Model 5 (FM5) onboard NPP, coupled with ground processing system upgrades further emphasizes the need for an automated job-submission utility to manage multiple processing streams concurrently. The operator-driven, legacy-processing approach relied on manually staging data from magnetic tape to limited spinning disk attached to a shared memory architecture system. The migration of CERES production code to a distributed, cluster computing environment with approximately one petabyte of spinning disk containing all precursor input data products facilitates the development of a CERES-specific, automated workflow manager. In the cluster environment, I/O is the primary system resource in contention across jobs. Therefore, system load can be maximized with a throttling workload manager. This poster discusses a Java and Perl implementation of an automated job management tool tailored for CERES processing.

Development and Appraisal of Multiple Accounting Record System (Mars).

PubMed

Yu, H C; Chen, M C

2016-01-01

The aim of the system is to achieve simplification of workflow, reduction of recording time, and increase the income for the study hospital. The project team decided to develop a multiple accounting record system that generates the account records based on the nursing records automatically, reduces the time and effort for nurses to review the procedure and provide another note of material consumption. Three configuration files were identified to demonstrate the relationship of treatments and reimbursement items. The workflow was simplified. The nurses averagely reduced 10 minutes of daily recording time, and the reimbursement points have been increased by 7.49%. The project streamlined the workflow and provides the institute a better way in finical management.

An access control model with high security for distributed workflow and real-time application

NASA Astrophysics Data System (ADS)

Han, Ruo-Fei; Wang, Hou-Xiang

2007-11-01

The traditional mandatory access control policy (MAC) is regarded as a policy with strict regulation and poor flexibility. The security policy of MAC is so compelling that few information systems would adopt it at the cost of facility, except some particular cases with high security requirement as military or government application. However, with the increasing requirement for flexibility, even some access control systems in military application have switched to role-based access control (RBAC) which is well known as flexible. Though RBAC can meet the demands for flexibility but it is weak in dynamic authorization and consequently can not fit well in the workflow management systems. The task-role-based access control (T-RBAC) is then introduced to solve the problem. It combines both the advantages of RBAC and task-based access control (TBAC) which uses task to manage permissions dynamically. To satisfy the requirement of system which is distributed, well defined with workflow process and critically for time accuracy, this paper will analyze the spirit of MAC, introduce it into the improved T&RBAC model which is based on T-RBAC. At last, a conceptual task-role-based access control model with high security for distributed workflow and real-time application (A_T&RBAC) is built, and its performance is simply analyzed.

[Applications of the hospital statistics management system].

PubMed

Zhai, Hong; Ren, Yong; Liu, Jing; Li, You-Zhang; Ma, Xiao-Long; Jiao, Tao-Tao

2008-01-01

The Hospital Statistics Management System is built on an Office Automation Platform of Shandong provincial hospital system. Its workflow, role and popedom technologies are used to standardize and optimize the management program of statistics in the total quality control of hospital statistics. The system's applications have combined the office automation platform with the statistics management in a hospital and this provides a practical example of a modern hospital statistics management model.

Jflow: a workflow management system for web applications.

PubMed

Mariette, Jérôme; Escudié, Frédéric; Bardou, Philippe; Nabihoudine, Ibouniyamine; Noirot, Céline; Trotard, Marie-Stéphane; Gaspin, Christine; Klopp, Christophe

2016-02-01

Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows. Jflow is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/jflow. The package is coming with full documentation, quick start and a running test portal. Jerome.Mariette@toulouse.inra.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

IceProd 2 Usage Experience

NASA Astrophysics Data System (ADS)

Delventhal, D.; Schultz, D.; Diaz Velez, J. C.

2017-10-01

IceProd is a data processing and management framework developed by the IceCube Neutrino Observatory for processing of Monte Carlo simulations, detector data, and data driven analysis. It runs as a separate layer on top of grid and batch systems. This is accomplished by a set of daemons which process job workflow, maintaining configuration and status information on the job before, during, and after processing. IceProd can also manage complex workflow DAGs across distributed computing grids in order to optimize usage of resources. IceProd has recently been rewritten to increase its scaling capabilities, handle user analysis workflows together with simulation production, and facilitate the integration with 3rd party scheduling tools. IceProd 2, the second generation of IceProd, has been running in production for several months now. We share our experience setting up the system and things we’ve learned along the way.

Using Semantic Components to Represent Dynamics of an Interdisciplinary Healthcare Team in a Multi-Agent Decision Support System.

PubMed

Wilk, Szymon; Kezadri-Hamiaz, Mounira; Rosu, Daniela; Kuziemsky, Craig; Michalowski, Wojtek; Amyot, Daniel; Carrier, Marc

2016-02-01

In healthcare organizations, clinical workflows are executed by interdisciplinary healthcare teams (IHTs) that operate in ways that are difficult to manage. Responding to a need to support such teams, we designed and developed the MET4 multi-agent system that allows IHTs to manage patients according to presentation-specific clinical workflows. In this paper, we describe a significant extension of the MET4 system that allows for supporting rich team dynamics (understood as team formation, management and task-practitioner allocation), including selection and maintenance of the most responsible physician and more complex rules of selecting practitioners for the workflow tasks. In order to develop this extension, we introduced three semantic components: (1) a revised ontology describing concepts and relations pertinent to IHTs, workflows, and managed patients, (2) a set of behavioral rules describing the team dynamics, and (3) an instance base that stores facts corresponding to instances of concepts from the ontology and to relations between these instances. The semantic components are represented in first-order logic and they can be automatically processed using theorem proving and model finding techniques. We employ these techniques to find models that correspond to specific decisions controlling the dynamics of IHT. In the paper, we present the design of extended MET4 with a special focus on the new semantic components. We then describe its proof-of-concept implementation using the WADE multi-agent platform and the Z3 solver (theorem prover/model finder). We illustrate the main ideas discussed in the paper with a clinical scenario of an IHT managing a patient with chronic kidney disease.

PIMS-Universal Payload Information Management

NASA Technical Reports Server (NTRS)

Elmore, Ralph; McNair, Ann R. (Technical Monitor)

2002-01-01

As the overall manager and integrator of International Space Station (ISS) science payloads and experiments, the Payload Operations Integration Center (POIC) at Marshall Space Flight Center had a critical need to provide an information management system for exchange and management of ISS payload files as well as to coordinate ISS payload related operational changes. The POIC's information management system has a fundamental requirement to provide secure operational access not only to users physically located at the POIC, but also to provide collaborative access to remote experimenters and International Partners. The Payload Information Management System (PIMS) is a ground based electronic document configuration management and workflow system that was built to service that need. Functionally, PIMS provides the following document management related capabilities: 1. File access control, storage and retrieval from a central repository vault. 2. Collect supplemental data about files in the vault. 3. File exchange with a PMS GUI client, or any FTP connection. 4. Files placement into an FTP accessible dropbox for pickup by interfacing facilities, included files transmitted for spacecraft uplink. 5. Transmission of email messages to users notifying them of new version availability. 6. Polling of intermediate facility dropboxes for files that will automatically be processed by PIMS. 7. Provide an API that allows other POIC applications to access PIMS information. Functionally, PIMS provides the following Change Request processing capabilities: 1. Ability to create, view, manipulate, and query information about Operations Change Requests (OCRs). 2. Provides an adaptable workflow approval of OCRs with routing through developers, facility leads, POIC leads, reviewers, and implementers. Email messages can be sent to users either involving them in the workflow process or simply notifying them of OCR approval progress. All PIMS document management and OCR workflow controls are coordinated through and routed to individual user's "to do" list tasks. A user is given a task when it is their turn to perform some action relating to the approval of the Document or OCR. The user's available actions are restricted to only functions available for the assigned task. Certain actions, such as review or action implementation by non-PIMS users, can also be coordinated through automated emails.

Integration of Earth System Models and Workflow Management under iRODS for the Northeast Regional Earth System Modeling Project

NASA Astrophysics Data System (ADS)

Lengyel, F.; Yang, P.; Rosenzweig, B.; Vorosmarty, C. J.

2012-12-01

The Northeast Regional Earth System Model (NE-RESM, NSF Award #1049181) integrates weather research and forecasting models, terrestrial and aquatic ecosystem models, a water balance/transport model, and mesoscale and energy systems input-out economic models developed by interdisciplinary research team from academia and government with expertise in physics, biogeochemistry, engineering, energy, economics, and policy. NE-RESM is intended to forecast the implications of planning decisions on the region's environment, ecosystem services, energy systems and economy through the 21st century. Integration of model components and the development of cyberinfrastructure for interacting with the system is facilitated with the integrated Rule Oriented Data System (iRODS), a distributed data grid that provides archival storage with metadata facilities and a rule-based workflow engine for automating and auditing scientific workflows.

DIaaS: Data-Intensive workflows as a service - Enabling easy composition and deployment of data-intensive workflows on Virtual Research Environments

NASA Astrophysics Data System (ADS)

Filgueira, R.; Ferreira da Silva, R.; Deelman, E.; Atkinson, M.

2016-12-01

We present the Data-Intensive workflows as a Service (DIaaS) model for enabling easy data-intensive workflow composition and deployment on clouds using containers. DIaaS model backbone is Asterism, an integrated solution for running data-intensive stream-based applications on heterogeneous systems, which combines the benefits of dispel4py with Pegasus workflow systems. The stream-based executions of an Asterism workflow are managed by dispel4py, while the data movement between different e-Infrastructures, and the coordination of the application execution are automatically managed by Pegasus. DIaaS combines Asterism framework with Docker containers to provide an integrated, complete, easy-to-use, portable approach to run data-intensive workflows on distributed platforms. Three containers integrate the DIaaS model: a Pegasus node, and an MPI and an Apache Storm clusters. Container images are described as Dockerfiles (available online at http://github.com/dispel4py/pegasus_dispel4py), linked to Docker Hub for providing continuous integration (automated image builds), and image storing and sharing. In this model, all required software (workflow systems and execution engines) for running scientific applications are packed into the containers, which significantly reduces the effort (and possible human errors) required by scientists or VRE administrators to build such systems. The most common use of DIaaS will be to act as a backend of VREs or Scientific Gateways to run data-intensive applications, deploying cloud resources upon request. We have demonstrated the feasibility of DIaaS using the data-intensive seismic ambient noise cross-correlation application (Figure 1). The application preprocesses (Phase1) and cross-correlates (Phase2) traces from several seismic stations. The application is submitted via Pegasus (Container1), and Phase1 and Phase2 are executed in the MPI (Container2) and Storm (Container3) clusters respectively. Although both phases could be executed within the same environment, this setup demonstrates the flexibility of DIaaS to run applications across e-Infrastructures. In summary, DIaaS delivers specialized software to execute data-intensive applications in a scalable, efficient, and robust manner reducing the engineering time and computational cost.

Multi-core processing and scheduling performance in CMS

NASA Astrophysics Data System (ADS)

Hernández, J. M.; Evans, D.; Foulkes, S.

2012-12-01

Commodity hardware is going many-core. We might soon not be able to satisfy the job memory needs per core in the current single-core processing model in High Energy Physics. In addition, an ever increasing number of independent and incoherent jobs running on the same physical hardware not sharing resources might significantly affect processing performance. It will be essential to effectively utilize the multi-core architecture. CMS has incorporated support for multi-core processing in the event processing framework and the workload management system. Multi-core processing jobs share common data in memory, such us the code libraries, detector geometry and conditions data, resulting in a much lower memory usage than standard single-core independent jobs. Exploiting this new processing model requires a new model in computing resource allocation, departing from the standard single-core allocation for a job. The experiment job management system needs to have control over a larger quantum of resource since multi-core aware jobs require the scheduling of multiples cores simultaneously. CMS is exploring the approach of using whole nodes as unit in the workload management system where all cores of a node are allocated to a multi-core job. Whole-node scheduling allows for optimization of the data/workflow management (e.g. I/O caching, local merging) but efficient utilization of all scheduled cores is challenging. Dedicated whole-node queues have been setup at all Tier-1 centers for exploring multi-core processing workflows in CMS. We present the evaluation of the performance scheduling and executing multi-core workflows in whole-node queues compared to the standard single-core processing workflows.

A knowledge-based decision support system in bioinformatics: an application to protein complex extraction

PubMed Central

2013-01-01

Background We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for the current experiment and furthermore it offers support in the configuration and running of every processing component of that workflow. This last feature makes our system a crossover between classical DSS and Workflow Management Systems. Results We briefly present the KDSS' architecture and basic concepts used in the design of the knowledge base and the reasoning component. The system is then tested using a subset of Saccharomyces cerevisiae Protein-Protein interaction dataset. We used this subset because it has been well studied in literature by several research groups in the field of complex extraction: in this way we could easily compare the results obtained through our KDSS with theirs. Our system suggests both a preprocessing and a clustering strategy, and for each of them it proposes and eventually runs suited algorithms. Our system's final results are then composed of a workflow of tasks, that can be reused for other experiments, and the specific numerical results for that particular trial. Conclusions The proposed approach, using the KDSS' knowledge base, provides a novel workflow that gives the best results with regard to the other workflows produced by the system. This workflow and its numeric results have been compared with other approaches about PPI network analysis found in literature, offering similar results. PMID:23368995

Potential of Laboratory Execution Systems (LESs) to Simplify the Application of Business Process Management Systems (BPMSs) in Laboratory Automation.

PubMed

Neubert, Sebastian; Göde, Bernd; Gu, Xiangyu; Stoll, Norbert; Thurow, Kerstin

2017-04-01

Modern business process management (BPM) is increasingly interesting for laboratory automation. End-to-end workflow automation and improved top-level systems integration for information technology (IT) and automation systems are especially prominent objectives. With the ISO Standard Business Process Model and Notation (BPMN) 2.X, a system-independent and interdisciplinary accepted graphical process control notation is provided, allowing process analysis, while also being executable. The transfer of BPM solutions to structured laboratory automation places novel demands, for example, concerning the real-time-critical process and systems integration. The article discusses the potential of laboratory execution systems (LESs) for an easier implementation of the business process management system (BPMS) in hierarchical laboratory automation. In particular, complex application scenarios, including long process chains based on, for example, several distributed automation islands and mobile laboratory robots for a material transport, are difficult to handle in BPMSs. The presented approach deals with the displacement of workflow control tasks into life science specialized LESs, the reduction of numerous different interfaces between BPMSs and subsystems, and the simplification of complex process modelings. Thus, the integration effort for complex laboratory workflows can be significantly reduced for strictly structured automation solutions. An example application, consisting of a mixture of manual and automated subprocesses, is demonstrated by the presented BPMS-LES approach.

Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach.

PubMed

Haston, Elspeth; Cubey, Robert; Pullan, Martin; Atkins, Hannah; Harris, David J

2012-01-01

Digitisation programmes in many institutes frequently involve disparate and irregular funding, diverse selection criteria and scope, with different members of staff managing and operating the processes. These factors have influenced the decision at the Royal Botanic Garden Edinburgh to develop an integrated workflow for the digitisation of herbarium specimens which is modular and scalable to enable a single overall workflow to be used for all digitisation projects. This integrated workflow is comprised of three principal elements: a specimen workflow, a data workflow and an image workflow.The specimen workflow is strongly linked to curatorial processes which will impact on the prioritisation, selection and preparation of the specimens. The importance of including a conservation element within the digitisation workflow is highlighted. The data workflow includes the concept of three main categories of collection data: label data, curatorial data and supplementary data. It is shown that each category of data has its own properties which influence the timing of data capture within the workflow. Development of software has been carried out for the rapid capture of curatorial data, and optical character recognition (OCR) software is being used to increase the efficiency of capturing label data and supplementary data. The large number and size of the images has necessitated the inclusion of automated systems within the image workflow.

Incorporating Brokers within Collaboration Environments

NASA Astrophysics Data System (ADS)

Rajasekar, A.; Moore, R.; de Torcy, A.

2013-12-01

A collaboration environment, such as the integrated Rule Oriented Data System (iRODS - http://irods.diceresearch.org), provides interoperability mechanisms for accessing storage systems, authentication systems, messaging systems, information catalogs, networks, and policy engines from a wide variety of clients. The interoperability mechanisms function as brokers, translating actions requested by clients to the protocol required by a specific technology. The iRODS data grid is used to enable collaborative research within hydrology, seismology, earth science, climate, oceanography, plant biology, astronomy, physics, and genomics disciplines. Although each domain has unique resources, data formats, semantics, and protocols, the iRODS system provides a generic framework that is capable of managing collaborative research initiatives that span multiple disciplines. Each interoperability mechanism (broker) is linked to a name space that enables unified access across the heterogeneous systems. The collaboration environment provides not only support for brokers, but also support for virtualization of name spaces for users, files, collections, storage systems, metadata, and policies. The broker enables access to data or information in a remote system using the appropriate protocol, while the collaboration environment provides a uniform naming convention for accessing and manipulating each object. Within the NSF DataNet Federation Consortium project (http://www.datafed.org), three basic types of interoperability mechanisms have been identified and applied: 1) drivers for managing manipulation at the remote resource (such as data subsetting), 2) micro-services that execute the protocol required by the remote resource, and 3) policies for controlling the execution. For example, drivers have been written for manipulating NetCDF and HDF formatted files within THREDDS servers. Micro-services have been written that manage interactions with the CUAHSI data repository, the DataONE information catalog, and the GeoBrain broker. Policies have been written that manage transfer of messages between an iRODS message queue and the Advanced Message Queuing Protocol. Examples of these brokering mechanisms will be presented. The DFC collaboration environment serves as the intermediary between community resources and compute grids, enabling reproducible data-driven research. It is possible to create an analysis workflow that retrieves data subsets from a remote server, assemble the required input files, automate the execution of the workflow, automatically track the provenance of the workflow, and share the input files, workflow, and output files. A collaborator can re-execute a shared workflow, compare results, change input files, and re-execute an analysis.

Implementation of a single sign-on system between practice, research and learning systems.

PubMed

Purkayastha, Saptarshi; Gichoya, Judy W; Addepally, Siva Abhishek

2017-03-29

Multiple specialized electronic medical systems are utilized in the health enterprise. Each of these systems has their own user management, authentication and authorization process, which makes it a complex web for navigation and use without a coherent process workflow. Users often have to remember multiple passwords, login/logout between systems that disrupt their clinical workflow. Challenges exist in managing permissions for various cadres of health care providers. This case report describes our experience of implementing a single sign-on system, used between an electronic medical records system and a learning management system at a large academic institution with an informatics department responsible for student education and a medical school affiliated with a hospital system caring for patients and conducting research. At our institution, we use OpenMRS for research registry tracking of interventional radiology patients as well as to provide access to medical records to students studying health informatics. To provide authentication across different users of the system with different permissions, we developed a Central Authentication Service (CAS) module for OpenMRS, released under the Mozilla Public License and deployed it for single sign-on across the academic enterprise. The module has been in implementation since August 2015 to present, and we assessed usability of the registry and education system before and after implementation of the CAS module. 54 students and 3 researchers were interviewed. The module authenticates users with appropriate privileges in the medical records system, providing secure access with minimal disruption to their workflow. No passwords requests were sent and users reported ease of use, with streamlined workflow. The project demonstrates that enterprise-wide single sign-on systems should be used in healthcare to reduce complexity like "password hell", improve usability and user navigation. We plan to extend this to work with other systems used in the health care enterprise.

Towards a Scalable and Adaptive Application Support Platform for Large-Scale Distributed E-Sciences in High-Performance Network Environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Chase Qishi; Zhu, Michelle Mengxia

The advent of large-scale collaborative scientific applications has demonstrated the potential for broad scientific communities to pool globally distributed resources to produce unprecedented data acquisition, movement, and analysis. System resources including supercomputers, data repositories, computing facilities, network infrastructures, storage systems, and display devices have been increasingly deployed at national laboratories and academic institutes. These resources are typically shared by large communities of users over Internet or dedicated networks and hence exhibit an inherent dynamic nature in their availability, accessibility, capacity, and stability. Scientific applications using either experimental facilities or computation-based simulations with various physical, chemical, climatic, and biological models featuremore » diverse scientific workflows as simple as linear pipelines or as complex as a directed acyclic graphs, which must be executed and supported over wide-area networks with massively distributed resources. Application users oftentimes need to manually configure their computing tasks over networks in an ad hoc manner, hence significantly limiting the productivity of scientists and constraining the utilization of resources. The success of these large-scale distributed applications requires a highly adaptive and massively scalable workflow platform that provides automated and optimized computing and networking services. This project is to design and develop a generic Scientific Workflow Automation and Management Platform (SWAMP), which contains a web-based user interface specially tailored for a target application, a set of user libraries, and several easy-to-use computing and networking toolkits for application scientists to conveniently assemble, execute, monitor, and control complex computing workflows in heterogeneous high-performance network environments. SWAMP will enable the automation and management of the entire process of scientific workflows with the convenience of a few mouse clicks while hiding the implementation and technical details from end users. Particularly, we will consider two types of applications with distinct performance requirements: data-centric and service-centric applications. For data-centric applications, the main workflow task involves large-volume data generation, catalog, storage, and movement typically from supercomputers or experimental facilities to a team of geographically distributed users; while for service-centric applications, the main focus of workflow is on data archiving, preprocessing, filtering, synthesis, visualization, and other application-specific analysis. We will conduct a comprehensive comparison of existing workflow systems and choose the best suited one with open-source code, a flexible system structure, and a large user base as the starting point for our development. Based on the chosen system, we will develop and integrate new components including a black box design of computing modules, performance monitoring and prediction, and workflow optimization and reconfiguration, which are missing from existing workflow systems. A modular design for separating specification, execution, and monitoring aspects will be adopted to establish a common generic infrastructure suited for a wide spectrum of science applications. We will further design and develop efficient workflow mapping and scheduling algorithms to optimize the workflow performance in terms of minimum end-to-end delay, maximum frame rate, and highest reliability. We will develop and demonstrate the SWAMP system in a local environment, the grid network, and the 100Gpbs Advanced Network Initiative (ANI) testbed. The demonstration will target scientific applications in climate modeling and high energy physics and the functions to be demonstrated include workflow deployment, execution, steering, and reconfiguration. Throughout the project period, we will work closely with the science communities in the fields of climate modeling and high energy physics including Spallation Neutron Source (SNS) and Large Hadron Collider (LHC) projects to mature the system for production use.« less

Meta-manager: a requirements analysis.

PubMed

Cook, J F; Rozenblit, J W; Chacko, A K; Martinez, R; Timboe, H L

1999-05-01

The digital imaging network-picture-archiving and communications system (DIN-PACS) will be implemented in ten sites within the Great Plains Regional Medical Command (GPRMC). This network of PACS and teleradiology technology over a shared T1 network has opened the door for round the clock radiology coverage of all sites. However, the concept of a virtual radiology environment poses new issues for military medicine. A new workflow management system must be developed. This workflow management system will allow us to efficiently resolve these issues including quality of care, availability, severe capitation, and quality of the workforce. The design process of this management system must employ existing technology, operate over various telecommunication networks and protocols, be independent of platform operating systems, be flexible and scaleable, and involve the end user at the outset in the design process for which it is developed. Using the unified modeling language (UML), the specifications for this new business management system were created in concert between the University of Arizona and the GPRMC. These specifications detail a management system operating through a common object request brokered architecture (CORBA) environment. In this presentation, we characterize the Meta-Manager management system including aspects of intelligence, interfacility routing, fail-safe operations, and expected improvements in patient care and efficiency.

DietPal: A Web-Based Dietary Menu-Generating and Management System

PubMed Central

Abdullah, Siti Norulhuda; Shahar, Suzana; Abdul-Hamid, Helmi; Khairudin, Nurkahirizan; Yusoff, Mohamed; Ghazali, Rafidah; Mohd-Yusoff, Nooraini; Shafii, Nik Shanita; Abdul-Manaf, Zaharah

2004-01-01

Background Attempts in current health care practice to make health care more accessible, effective, and efficient through the use of information technology could include implementation of computer-based dietary menu generation. While several of such systems already exist, their focus is mainly to assist healthy individuals calculate their calorie intake and to help monitor the selection of menus based upon a prespecified calorie value. Although these prove to be helpful in some ways, they are not suitable for monitoring, planning, and managing patients' dietary needs and requirements. This paper presents a Web-based application that simulates the process of menu suggestions according to a standard practice employed by dietitians. Objective To model the workflow of dietitians and to develop, based on this workflow, a Web-based system for dietary menu generation and management. The system is aimed to be used by dietitians or by medical professionals of health centers in rural areas where there are no designated qualified dietitians. Methods First, a user-needs study was conducted among dietitians in Malaysia. The first survey of 93 dietitians (with 52 responding) was an assessment of information needed for dietary management and evaluation of compliance towards a dietary regime. The second study consisted of ethnographic observation and semi-structured interviews with 14 dietitians in order to identify the workflow of a menu-suggestion process. We subsequently designed and developed a Web-based dietary menu generation and management system called DietPal. DietPal has the capability of automatically calculating the nutrient and calorie intake of each patient based on the dietary recall as well as generating suitable diet and menu plans according to the calorie and nutrient requirement of the patient, calculated from anthropometric measurements. The system also allows reusing stored or predefined menus for other patients with similar health and nutrient requirements. Results We modeled the workflow of menu-suggestion activity currently adhered to by dietitians in Malaysia. Based on this workflow, a Web-based system was developed. Initial post evaluation among 10 dietitians indicates that they are comfortable with the organization of the modules and information. Conclusions The system has the potential of enhancing the quality of services with the provision of standard and healthy menu plans and at the same time increasing outreach, particularly to rural areas. With its potential capability of optimizing the time spent by dietitians to plan suitable menus, more quality time could be spent delivering nutrition education to the patients. PMID:15111270

DietPal: a Web-based dietary menu-generating and management system.

PubMed

Noah, Shahrul A; Abdullah, Siti Norulhuda; Shahar, Suzana; Abdul-Hamid, Helmi; Khairudin, Nurkahirizan; Yusoff, Mohamed; Ghazali, Rafidah; Mohd-Yusoff, Nooraini; Shafii, Nik Shanita; Abdul-Manaf, Zaharah

2004-01-30

Attempts in current health care practice to make health care more accessible, effective, and efficient through the use of information technology could include implementation of computer-based dietary menu generation. While several of such systems already exist, their focus is mainly to assist healthy individuals calculate their calorie intake and to help monitor the selection of menus based upon a prespecified calorie value. Although these prove to be helpful in some ways, they are not suitable for monitoring, planning, and managing patients' dietary needs and requirements. This paper presents a Web-based application that simulates the process of menu suggestions according to a standard practice employed by dietitians. To model the workflow of dietitians and to develop, based on this workflow, a Web-based system for dietary menu generation and management. The system is aimed to be used by dietitians or by medical professionals of health centers in rural areas where there are no designated qualified dietitians. First, a user-needs study was conducted among dietitians in Malaysia. The first survey of 93 dietitians (with 52 responding) was an assessment of information needed for dietary management and evaluation of compliance towards a dietary regime. The second study consisted of ethnographic observation and semi-structured interviews with 14 dietitians in order to identify the workflow of a menu-suggestion process. We subsequently designed and developed a Web-based dietary menu generation and management system called DietPal. DietPal has the capability of automatically calculating the nutrient and calorie intake of each patient based on the dietary recall as well as generating suitable diet and menu plans according to the calorie and nutrient requirement of the patient, calculated from anthropometric measurements. The system also allows reusing stored or predefined menus for other patients with similar health and nutrient requirements. We modeled the workflow of menu-suggestion activity currently adhered to by dietitians in Malaysia. Based on this workflow, a Web-based system was developed. Initial post evaluation among 10 dietitians indicates that they are comfortable with the organization of the modules and information. The system has the potential of enhancing the quality of services with the provision of standard and healthy menu plans and at the same time increasing outreach, particularly to rural areas. With its potential capability of optimizing the time spent by dietitians to plan suitable menus, more quality time could be spent delivering nutrition education to the patients.

Electronic Resource Management 2.0: Using Web 2.0 Technologies as Cost-Effective Alternatives to an Electronic Resource Management System

ERIC Educational Resources Information Center

Murray, Adam

2008-01-01

Designed to assist with the management of e-resources, electronic resource management (ERM) systems are time- and fund-consuming to purchase and maintain. Questions of system compatibility, data population, and workflow design/redesign can be difficult to answer; sometimes those answers are not what we'd prefer to hear. The two primary functions…

Interplay between Clinical Guidelines and Organizational Workflow Systems. Experience from the MobiGuide Project.

PubMed

Shabo, Amnon; Peleg, Mor; Parimbelli, Enea; Quaglini, Silvana; Napolitano, Carlo

2016-12-07

Implementing a decision-support system within a healthcare organization requires integration of clinical domain knowledge with resource constraints. Computer-interpretable guidelines (CIG) are excellent instruments for addressing clinical aspects while business process management (BPM) languages and Workflow (Wf) engines manage the logistic organizational constraints. Our objective is the orchestration of all the relevant factors needed for a successful execution of patient's care pathways, especially when spanning the continuum of care, from acute to community or home care. We considered three strategies for integrating CIGs with organizational workflows: extending the CIG or BPM languages and their engines, or creating an interplay between them. We used the interplay approach to implement a set of use cases arising from a CIG implementation in the domain of Atrial Fibrillation. To provide a more scalable and standards-based solution, we explored the use of Cross-Enterprise Document Workflow Integration Profile. We describe our proof-of-concept implementation of five use cases. We utilized the Personal Health Record of the MobiGuide project to implement a loosely-coupled approach between the Activiti BPM engine and the Picard CIG engine. Changes in the PHR were detected by polling. IHE profiles were used to develop workflow documents that orchestrate cross-enterprise execution of cardioversion. Interplay between CIG and BPM engines can support orchestration of care flows within organizational settings.

The impact of missing sensor information on surgical workflow management.

PubMed

Liebmann, Philipp; Meixensberger, Jürgen; Wiedemann, Peter; Neumuth, Thomas

2013-09-01

Sensor systems in the operating room may encounter intermittent data losses that reduce the performance of surgical workflow management systems (SWFMS). Sensor data loss could impact SWFMS-based decision support, device parameterization, and information presentation. The purpose of this study was to understand the robustness of surgical process models when sensor information is partially missing. SWFMS changes caused by wrong or no data from the sensor system which tracks the progress of a surgical intervention were tested. The individual surgical process models (iSPMs) from 100 different cataract procedures of 3 ophthalmologic surgeons were used to select a randomized subset and create a generalized surgical process model (gSPM). A disjoint subset was selected from the iSPMs and used to simulate the surgical process against the gSPM. The loss of sensor data was simulated by removing some information from one task in the iSPM. The effect of missing sensor data was measured using several metrics: (a) successful relocation of the path in the gSPM, (b) the number of steps to find the converging point, and (c) the perspective with the highest occurrence of unsuccessful path findings. A gSPM built using 30% of the iSPMs successfully found the correct path in 90% of the cases. The most critical sensor data were the information regarding the instrument used by the surgeon. We found that use of a gSPM to provide input data for a SWFMS is robust and can be accurate despite missing sensor data. A surgical workflow management system can provide the surgeon with workflow guidance in the OR for most cases. Sensor systems for surgical process tracking can be evaluated based on the stability and accuracy of functional and spatial operative results.

Managing the CMS Data and Monte Carlo Processing during LHC Run 2

NASA Astrophysics Data System (ADS)

Wissing, C.; CMS Collaboration

2017-10-01

In order to cope with the challenges expected during the LHC Run 2 CMS put in a number of enhancements into the main software packages and the tools used for centrally managed processing. In the presentation we will highlight these improvements that allow CMS to deal with the increased trigger output rate, the increased pileup and the evolution in computing technology. The overall system aims at high flexibility, improved operational flexibility and largely automated procedures. The tight coupling of workflow classes to types of sites has been drastically relaxed. Reliable and high-performing networking between most of the computing sites and the successful deployment of a data-federation allow the execution of workflows using remote data access. That required the development of a largely automatized system to assign workflows and to handle necessary pre-staging of data. Another step towards flexibility has been the introduction of one large global HTCondor Pool for all types of processing workflows and analysis jobs. Besides classical Grid resources also some opportunistic resources as well as Cloud resources have been integrated into that Pool, which gives reach to more than 200k CPU cores.

FluxCTTX: A LIMS-based tool for management and analysis of cytotoxicity assays data

PubMed Central

2015-01-01

Background Cytotoxicity assays have been used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds or screen "hits" from initial high-throughput drug screens for unwanted cytotoxic effects before investing in their development as a pharmaceutical. These assays may be used as an alternative to animal experimentation and are becoming increasingly important in modern laboratories. However, the execution of these assays in large scale and different laboratories requires, among other things, the management of protocols, reagents, cell lines used as well as the data produced, which can be a challenge. The management of all this information is greatly improved by the utilization of computational tools to save time and guarantee quality. However, a tool that performs this task designed specifically for cytotoxicity assays is not yet available. Results In this work, we have used a workflow based LIMS -- the Flux system -- and the Together Workflow Editor as a framework to develop FluxCTTX, a tool for management of data from cytotoxicity assays performed at different laboratories. The main work is the development of a workflow, which represents all stages of the assay and has been developed and uploaded in Flux. This workflow models the activities of cytotoxicity assays performed as described in the OECD 129 Guidance Document. Conclusions FluxCTTX presents a solution for the management of the data produced by cytotoxicity assays performed at Interlaboratory comparisons. Its adoption will contribute to guarantee the quality of activities in the process of cytotoxicity tests and enforce the use of Good Laboratory Practices (GLP). Furthermore, the workflow developed is complete and can be adapted to other contexts and different tests for management of other types of data. PMID:26696462

Wireless remote control clinical image workflow: utilizing a PDA for offsite distribution

NASA Astrophysics Data System (ADS)

Liu, Brent J.; Documet, Luis; Documet, Jorge; Huang, H. K.; Muldoon, Jean

2004-04-01

Last year we presented in RSNA an application to perform wireless remote control of PACS image distribution utilizing a handheld device such as a Personal Digital Assistant (PDA). This paper describes the clinical experiences including workflow scenarios of implementing the PDA application to route exams from the clinical PACS archive server to various locations for offsite distribution of clinical PACS exams. By utilizing this remote control application, radiologists can manage image workflow distribution with a single wireless handheld device without impacting their clinical workflow on diagnostic PACS workstations. A PDA application was designed and developed to perform DICOM Query and C-Move requests by a physician from a clinical PACS Archive to a CD-burning device for automatic burning of PACS data for the distribution to offsite. In addition, it was also used for convenient routing of historical PACS exams to the local web server, local workstations, and teleradiology systems. The application was evaluated by radiologists as well as other clinical staff who need to distribute PACS exams to offsite referring physician"s offices and offsite radiologists. An application for image workflow management utilizing wireless technology was implemented in a clinical environment and evaluated. A PDA application was successfully utilized to perform DICOM Query and C-Move requests from the clinical PACS archive to various offsite exam distribution devices. Clinical staff can utilize the PDA to manage image workflow and PACS exam distribution conveniently for offsite consultations by referring physicians and radiologists. This solution allows the radiologist to expand their effectiveness in health care delivery both within the radiology department as well as offisite by improving their clinical workflow.

Automation in an addiction treatment research clinic: computerised contingency management, ecological momentary assessment and a protocol workflow system.

PubMed

Vahabzadeh, Massoud; Lin, Jia-Ling; Mezghanni, Mustapha; Epstein, David H; Preston, Kenzie L

2009-01-01

A challenge in treatment research is the necessity of adhering to protocol and regulatory strictures while maintaining flexibility to meet patients' treatment needs and to accommodate variations among protocols. Another challenge is the acquisition of large amounts of data in an occasionally hectic environment, along with the provision of seamless methods for exporting, mining and querying the data. We have automated several major functions of our outpatient treatment research clinic for studies in drug abuse and dependence. Here we describe three such specialised applications: the Automated Contingency Management (ACM) system for the delivery of behavioural interventions, the transactional electronic diary (TED) system for the management of behavioural assessments and the Protocol Workflow System (PWS) for computerised workflow automation and guidance of each participant's daily clinic activities. These modules are integrated into our larger information system to enable data sharing in real time among authorised staff. ACM and the TED have each permitted us to conduct research that was not previously possible. In addition, the time to data analysis at the end of each study is substantially shorter. With the implementation of the PWS, we have been able to manage a research clinic with an 80 patient capacity, having an annual average of 18,000 patient visits and 7300 urine collections with a research staff of five. Finally, automated data management has considerably enhanced our ability to monitor and summarise participant safety data for research oversight. When developed in consultation with end users, automation in treatment research clinics can enable more efficient operations, better communication among staff and expansions in research methods.

A virtual data language and system for scientific workflow management in data grid environments

NASA Astrophysics Data System (ADS)

Zhao, Yong

With advances in scientific instrumentation and simulation, scientific data is growing fast in both size and analysis complexity. So-called Data Grids aim to provide high performance, distributed data analysis infrastructure for data- intensive sciences, where scientists distributed worldwide need to extract information from large collections of data, and to share both data products and the resources needed to produce and store them. However, the description, composition, and execution of even logically simple scientific workflows are often complicated by the need to deal with "messy" issues like heterogeneous storage formats and ad-hoc file system structures. We show how these difficulties can be overcome via a typed workflow notation called virtual data language, within which issues of physical representation are cleanly separated from logical typing, and by the implementation of this notation within the context of a powerful virtual data system that supports distributed execution. The resulting language and system are capable of expressing complex workflows in a simple compact form, enacting those workflows in distributed environments, monitoring and recording the execution processes, and tracing the derivation history of data products. We describe the motivation, design, implementation, and evaluation of the virtual data language and system, and the application of the virtual data paradigm in various science disciplines, including astronomy, cognitive neuroscience.

Scheduling Multilevel Deadline-Constrained Scientific Workflows on Clouds Based on Cost Optimization

DOE PAGES

Malawski, Maciej; Figiela, Kamil; Bubak, Marian; ...

2015-01-01

This paper presents a cost optimization model for scheduling scientific workflows on IaaS clouds such as Amazon EC2 or RackSpace. We assume multiple IaaS clouds with heterogeneous virtual machine instances, with limited number of instances per cloud and hourly billing. Input and output data are stored on a cloud object store such as Amazon S3. Applications are scientific workflows modeled as DAGs as in the Pegasus Workflow Management System. We assume that tasks in the workflows are grouped into levels of identical tasks. Our model is specified using mathematical programming languages (AMPL and CMPL) and allows us to minimize themore » cost of workflow execution under deadline constraints. We present results obtained using our model and the benchmark workflows representing real scientific applications in a variety of domains. The data used for evaluation come from the synthetic workflows and from general purpose cloud benchmarks, as well as from the data measured in our own experiments with Montage, an astronomical application, executed on Amazon EC2 cloud. We indicate how this model can be used for scenarios that require resource planning for scientific workflows and their ensembles.« less

Multi-core processing and scheduling performance in CMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez, J. M.; Evans, D.; Foulkes, S.

2012-01-01

Commodity hardware is going many-core. We might soon not be able to satisfy the job memory needs per core in the current single-core processing model in High Energy Physics. In addition, an ever increasing number of independent and incoherent jobs running on the same physical hardware not sharing resources might significantly affect processing performance. It will be essential to effectively utilize the multi-core architecture. CMS has incorporated support for multi-core processing in the event processing framework and the workload management system. Multi-core processing jobs share common data in memory, such us the code libraries, detector geometry and conditions data, resultingmore » in a much lower memory usage than standard single-core independent jobs. Exploiting this new processing model requires a new model in computing resource allocation, departing from the standard single-core allocation for a job. The experiment job management system needs to have control over a larger quantum of resource since multi-core aware jobs require the scheduling of multiples cores simultaneously. CMS is exploring the approach of using whole nodes as unit in the workload management system where all cores of a node are allocated to a multi-core job. Whole-node scheduling allows for optimization of the data/workflow management (e.g. I/O caching, local merging) but efficient utilization of all scheduled cores is challenging. Dedicated whole-node queues have been setup at all Tier-1 centers for exploring multi-core processing workflows in CMS. We present the evaluation of the performance scheduling and executing multi-core workflows in whole-node queues compared to the standard single-core processing workflows.« less

COSMOS: Python library for massively parallel workflows

PubMed Central

Gafni, Erik; Luquette, Lovelace J.; Lancaster, Alex K.; Hawkins, Jared B.; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P.; Tonellato, Peter J.

2014-01-01

Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Availability and implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. Contact: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24982428

COSMOS: Python library for massively parallel workflows.

PubMed

Gafni, Erik; Luquette, Lovelace J; Lancaster, Alex K; Hawkins, Jared B; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P; Tonellato, Peter J

2014-10-15

Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach

PubMed Central

Haston, Elspeth; Cubey, Robert; Pullan, Martin; Atkins, Hannah; Harris, David J

2012-01-01

Abstract Digitisation programmes in many institutes frequently involve disparate and irregular funding, diverse selection criteria and scope, with different members of staff managing and operating the processes. These factors have influenced the decision at the Royal Botanic Garden Edinburgh to develop an integrated workflow for the digitisation of herbarium specimens which is modular and scalable to enable a single overall workflow to be used for all digitisation projects. This integrated workflow is comprised of three principal elements: a specimen workflow, a data workflow and an image workflow. The specimen workflow is strongly linked to curatorial processes which will impact on the prioritisation, selection and preparation of the specimens. The importance of including a conservation element within the digitisation workflow is highlighted. The data workflow includes the concept of three main categories of collection data: label data, curatorial data and supplementary data. It is shown that each category of data has its own properties which influence the timing of data capture within the workflow. Development of software has been carried out for the rapid capture of curatorial data, and optical character recognition (OCR) software is being used to increase the efficiency of capturing label data and supplementary data. The large number and size of the images has necessitated the inclusion of automated systems within the image workflow. PMID:22859881

[Development of a medical equipment support information system based on PDF portable document].

PubMed

Cheng, Jiangbo; Wang, Weidong

2010-07-01

According to the organizational structure and management system of the hospital medical engineering support, integrate medical engineering support workflow to ensure the medical engineering data effectively, accurately and comprehensively collected and kept in electronic archives. Analyse workflow of the medical, equipment support work and record all work processes by the portable electronic document. Using XML middleware technology and SQL Server database, complete process management, data calculation, submission, storage and other functions. The practical application shows that the medical equipment support information system optimizes the existing work process, standardized and digital, automatic and efficient orderly and controllable. The medical equipment support information system based on portable electronic document can effectively optimize and improve hospital medical engineering support work, improve performance, reduce costs, and provide full and accurate digital data

The Boston Marathon Bombings Mass Casualty Incident: One Emergency Department's Information Systems Challenges and Opportunities.

PubMed

Landman, Adam; Teich, Jonathan M; Pruitt, Peter; Moore, Samantha E; Theriault, Jennifer; Dorisca, Elizabeth; Harris, Sheila; Crim, Heidi; Lurie, Nicole; Goralnick, Eric

2015-07-01

Emergency department (ED) information systems are designed to support efficient and safe emergency care. These same systems often play a critical role in disasters to facilitate real-time situation awareness, information management, and communication. In this article, we describe one ED's experiences with ED information systems during the April 2013 Boston Marathon bombings. During postevent debriefings, staff shared that our ED information systems and workflow did not optimally support this incident; we found challenges with our unidentified patient naming convention, real-time situational awareness of patient location, and documentation of assessments, orders, and procedures. As a result, before our next mass gathering event, we changed our unidentified patient naming convention to more clearly distinguish multiple, simultaneous, unidentified patients. We also made changes to the disaster registration workflow and enhanced roles and responsibilities for updating electronic systems. Health systems should conduct disaster drills using their ED information systems to identify inefficiencies before an actual incident. ED information systems may require enhancements to better support disasters. Newer technologies, such as radiofrequency identification, could further improve disaster information management and communication but require careful evaluation and implementation into daily ED workflow. Copyright © 2014 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

Workflow in clinical trial sites & its association with near miss events for data quality: ethnographic, workflow & systems simulation.

PubMed

de Carvalho, Elias Cesar Araujo; Batilana, Adelia Portero; Claudino, Wederson; Reis, Luiz Fernando Lima; Schmerling, Rafael A; Shah, Jatin; Pietrobon, Ricardo

2012-01-01

With the exponential expansion of clinical trials conducted in (Brazil, Russia, India, and China) and VISTA (Vietnam, Indonesia, South Africa, Turkey, and Argentina) countries, corresponding gains in cost and enrolment efficiency quickly outpace the consonant metrics in traditional countries in North America and European Union. However, questions still remain regarding the quality of data being collected in these countries. We used ethnographic, mapping and computer simulation studies to identify/address areas of threat to near miss events for data quality in two cancer trial sites in Brazil. Two sites in Sao Paolo and Rio Janeiro were evaluated using ethnographic observations of workflow during subject enrolment and data collection. Emerging themes related to threats to near miss events for data quality were derived from observations. They were then transformed into workflows using UML-AD and modeled using System Dynamics. 139 tasks were observed and mapped through the ethnographic study. The UML-AD detected four major activities in the workflow evaluation of potential research subjects prior to signature of informed consent, visit to obtain subject́s informed consent, regular data collection sessions following study protocol and closure of study protocol for a given project. Field observations pointed to three major emerging themes: (a) lack of standardized process for data registration at source document, (b) multiplicity of data repositories and (c) scarcity of decision support systems at the point of research intervention. Simulation with policy model demonstrates a reduction of the rework problem. Patterns of threats to data quality at the two sites were similar to the threats reported in the literature for American sites. The clinical trial site managers need to reorganize staff workflow by using information technology more efficiently, establish new standard procedures and manage professionals to reduce near miss events and save time/cost. Clinical trial sponsors should improve relevant support systems.

Workflow in Clinical Trial Sites & Its Association with Near Miss Events for Data Quality: Ethnographic, Workflow & Systems Simulation

PubMed Central

Araujo de Carvalho, Elias Cesar; Batilana, Adelia Portero; Claudino, Wederson; Lima Reis, Luiz Fernando; Schmerling, Rafael A.; Shah, Jatin; Pietrobon, Ricardo

2012-01-01

Background With the exponential expansion of clinical trials conducted in (Brazil, Russia, India, and China) and VISTA (Vietnam, Indonesia, South Africa, Turkey, and Argentina) countries, corresponding gains in cost and enrolment efficiency quickly outpace the consonant metrics in traditional countries in North America and European Union. However, questions still remain regarding the quality of data being collected in these countries. We used ethnographic, mapping and computer simulation studies to identify/address areas of threat to near miss events for data quality in two cancer trial sites in Brazil. Methodology/Principal Findings Two sites in Sao Paolo and Rio Janeiro were evaluated using ethnographic observations of workflow during subject enrolment and data collection. Emerging themes related to threats to near miss events for data quality were derived from observations. They were then transformed into workflows using UML-AD and modeled using System Dynamics. 139 tasks were observed and mapped through the ethnographic study. The UML-AD detected four major activities in the workflow evaluation of potential research subjects prior to signature of informed consent, visit to obtain subject́s informed consent, regular data collection sessions following study protocol and closure of study protocol for a given project. Field observations pointed to three major emerging themes: (a) lack of standardized process for data registration at source document, (b) multiplicity of data repositories and (c) scarcity of decision support systems at the point of research intervention. Simulation with policy model demonstrates a reduction of the rework problem. Conclusions/Significance Patterns of threats to data quality at the two sites were similar to the threats reported in the literature for American sites. The clinical trial site managers need to reorganize staff workflow by using information technology more efficiently, establish new standard procedures and manage professionals to reduce near miss events and save time/cost. Clinical trial sponsors should improve relevant support systems. PMID:22768105

Experiences and lessons learned from creating a generalized workflow for data publication of field campaign datasets

NASA Astrophysics Data System (ADS)

Santhana Vannan, S. K.; Ramachandran, R.; Deb, D.; Beaty, T.; Wright, D.

2017-12-01

This paper summarizes the workflow challenges of curating and publishing data produced from disparate data sources and provides a generalized workflow solution to efficiently archive data generated by researchers. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemical dynamics and the Global Hydrology Resource Center (GHRC) DAAC have been collaborating on the development of a generalized workflow solution to efficiently manage the data publication process. The generalized workflow presented here are built on lessons learned from implementations of the workflow system. Data publication consists of the following steps: Accepting the data package from the data providers, ensuring the full integrity of the data files. Identifying and addressing data quality issues Assembling standardized, detailed metadata and documentation, including file level details, processing methodology, and characteristics of data files Setting up data access mechanisms Setup of the data in data tools and services for improved data dissemination and user experience Registering the dataset in online search and discovery catalogues Preserving the data location through Digital Object Identifiers (DOI) We will describe the steps taken to automate, and realize efficiencies to the above process. The goals of the workflow system are to reduce the time taken to publish a dataset, to increase the quality of documentation and metadata, and to track individual datasets through the data curation process. Utilities developed to achieve these goal will be described. We will also share metrics driven value of the workflow system and discuss the future steps towards creation of a common software framework.

Model medication management process in Australian nursing homes using business process modeling.

PubMed

Qian, Siyu; Yu, Ping

2013-01-01

One of the reasons for end user avoidance or rejection to use health information systems is poor alignment of the system with healthcare workflow, likely causing by system designers' lack of thorough understanding about healthcare process. Therefore, understanding the healthcare workflow is the essential first step for the design of optimal technologies that will enable care staff to complete the intended tasks faster and better. The often use of multiple or "high risk" medicines by older people in nursing homes has the potential to increase medication error rate. To facilitate the design of information systems with most potential to improve patient safety, this study aims to understand medication management process in nursing homes using business process modeling method. The paper presents study design and preliminary findings from interviewing two registered nurses, who were team leaders in two nursing homes. Although there were subtle differences in medication management between the two homes, major medication management activities were similar. Further field observation will be conducted. Based on the data collected from observations, an as-is process model for medication management will be developed.

Context-aware workflow management of mobile health applications.

PubMed

Salden, Alfons; Poortinga, Remco

2006-01-01

We propose a medical application management architecture that allows medical (IT) experts readily designing, developing and deploying context-aware mobile health (m-health) applications or services. In particular, we elaborate on how our application workflow management architecture enables chaining, coordinating, composing, and adapting context-sensitive medical application components such that critical Quality of Service (QoS) and Quality of Context (QoC) requirements typical for m-health applications or services can be met. This functional architectural support requires learning modules for distilling application-critical selection of attention and anticipation models. These models will help medical experts constructing and adjusting on-the-fly m-health application workflows and workflow strategies. We illustrate our context-aware workflow management paradigm for a m-health data delivery problem, in which optimal communication network configurations have to be determined.

Understanding the dispensary workflow at the Birmingham Free Clinic: a proposed framework for an informatics intervention.

PubMed

Fisher, Arielle M; Herbert, Mary I; Douglas, Gerald P

2016-02-19

The Birmingham Free Clinic (BFC) in Pittsburgh, Pennsylvania, USA is a free, walk-in clinic that serves medically uninsured populations through the use of volunteer health care providers and an on-site medication dispensary. The introduction of an electronic medical record (EMR) has improved several aspects of clinic workflow. However, pharmacists' tasks involving medication management and dispensing have become more challenging since EMR implementation due to its inability to support workflows between the medical and pharmaceutical services. To inform the design of a systematic intervention, we conducted a needs assessment study to identify workflow challenges and process inefficiencies in the dispensary. We used contextual inquiry to document the dispensary workflow and facilitate identification of critical aspects of intervention design specific to the user. Pharmacists were observed according to contextual inquiry guidelines. Graphical models were produced to aid data and process visualization. We created a list of themes describing workflow challenges and asked the pharmacists to rank them in order of significance to narrow the scope of intervention design. Three pharmacists were observed at the BFC. Observer notes were documented and analyzed to produce 13 themes outlining the primary challenges pharmacists encounter during dispensation at the BFC. The dispensary workflow is labor intensive, redundant, and inefficient when integrated with the clinical service. Observations identified inefficiencies that may benefit from the introduction of informatics interventions including: medication labeling, insufficient process notification, triple documentation, and inventory control. We propose a system for Prescription Management and General Inventory Control (RxMAGIC). RxMAGIC is a framework designed to mitigate workflow challenges and improve the processes of medication management and inventory control. While RxMAGIC is described in the context of the BFC dispensary, we believe it will be generalizable to pharmacies in other low-resource settings, both domestically and internationally.

Cyberinfrastructure for End-to-End Environmental Explorations

NASA Astrophysics Data System (ADS)

Merwade, V.; Kumar, S.; Song, C.; Zhao, L.; Govindaraju, R.; Niyogi, D.

2007-12-01

The design and implementation of a cyberinfrastructure for End-to-End Environmental Exploration (C4E4) is presented. The C4E4 framework addresses the need for an integrated data/computation platform for studying broad environmental impacts by combining heterogeneous data resources with state-of-the-art modeling and visualization tools. With Purdue being a TeraGrid Resource Provider, C4E4 builds on top of the Purdue TeraGrid data management system and Grid resources, and integrates them through a service-oriented workflow system. It allows researchers to construct environmental workflows for data discovery, access, transformation, modeling, and visualization. Using the C4E4 framework, we have implemented an end-to-end SWAT simulation and analysis workflow that connects our TeraGrid data and computation resources. It enables researchers to conduct comprehensive studies on the impact of land management practices in the St. Joseph watershed using data from various sources in hydrologic, atmospheric, agricultural, and other related disciplines.

Case Report: Activity Diagrams for Integrating Electronic Prescribing Tools into Clinical Workflow

PubMed Central

Johnson, Kevin B.; FitzHenry, Fern

2006-01-01

To facilitate the future implementation of an electronic prescribing system, this case study modeled prescription management processes in various primary care settings. The Vanderbilt e-prescribing design team conducted initial interviews with clinic managers, physicians and nurses, and then represented the sequences of steps carried out to complete prescriptions in activity diagrams. The diagrams covered outpatient prescribing for patients during a clinic visit and between clinic visits. Practice size, practice setting, and practice specialty type influenced the prescribing processes used. The model developed may be useful to others engaged in building or tailoring an e-prescribing system to meet the specific workflows of various clinic settings. PMID:16622168

MouseNet database: digital management of a large-scale mutagenesis project.

PubMed

Pargent, W; Heffner, S; Schäble, K F; Soewarto, D; Fuchs, H; Hrabé de Angelis, M

2000-07-01

The Munich ENU Mouse Mutagenesis Screen is a large-scale mutant production, phenotyping, and mapping project. It encompasses two animal breeding facilities and a number of screening groups located in the general area of Munich. A central database is required to manage and process the immense amount of data generated by the mutagenesis project. This database, which we named MouseNet(c), runs on a Sybase platform and will finally store and process all data from the entire project. In addition, the system comprises a portfolio of functions needed to support the workflow management of the core facility and the screening groups. MouseNet(c) will make all of the data available to the participating screening groups, and later to the international scientific community. MouseNet(c) will consist of three major software components:* Animal Management System (AMS)* Sample Tracking System (STS)* Result Documentation System (RDS)MouseNet(c) provides the following major advantages:* being accessible from different client platforms via the Internet* being a full-featured multi-user system (including access restriction and data locking mechanisms)* relying on a professional RDBMS (relational database management system) which runs on a UNIX server platform* supplying workflow functions and a variety of plausibility checks.

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

PubMed

Liu, Yang; Khan, Saad M; Wang, Juexin; Rynge, Mats; Zhang, Yuanxun; Zeng, Shuai; Chen, Shiyuan; Maldonado Dos Santos, Joao V; Valliyodan, Babu; Calyam, Prasad P; Merchant, Nirav; Nguyen, Henry T; Xu, Dong; Joshi, Trupti

2016-10-06

With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way. We have developed both a Linux version in GitHub ( https://github.com/pegasus-isi/PGen-GenomicVariations-Workflow ) and a web-based implementation of the PGen workflow integrated within the Soybean Knowledge Base (SoyKB), ( http://soykb.org/Pegasus/index.php ). Using PGen, we identified 10,218,140 single-nucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 15X coverage. 297,245 non-synonymous SNPs and 3330 copy number variation (CNV) regions were identified from this analysis. SNPs identified using PGen from additional soybean resequencing projects adding to 500+ soybean germplasm lines in total have been integrated. These SNPs are being utilized for trait improvement using genotype to phenotype prediction approaches developed in-house. In order to browse and access NGS data easily, we have also developed an NGS resequencing data browser ( http://soykb.org/NGS_Resequence/NGS_index.php ) within SoyKB to provide easy access to SNP and downstream analysis results for soybean researchers. PGen workflow has been optimized for the most efficient analysis of soybean data using thorough testing and validation. This research serves as an example of best practices for development of genomics data analysis workflows by integrating remote HPC resources and efficient data management with ease of use for biological users. PGen workflow can also be easily customized for analysis of data in other species.

Purdue ionomics information management system. An integrated functional genomics platform.

PubMed

Baxter, Ivan; Ouzzani, Mourad; Orcun, Seza; Kennedy, Brad; Jandhyala, Shrinivas S; Salt, David E

2007-02-01

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.

A big data approach for climate change indicators processing in the CLIP-C project

NASA Astrophysics Data System (ADS)

D'Anca, Alessandro; Conte, Laura; Palazzo, Cosimo; Fiore, Sandro; Aloisio, Giovanni

2016-04-01

Defining and implementing processing chains with multiple (e.g. tens or hundreds of) data analytics operators can be a real challenge in many practical scientific use cases such as climate change indicators. This is usually done via scripts (e.g. bash) on the client side and requires climate scientists to take care of, implement and replicate workflow-like control logic aspects (which may be error-prone too) in their scripts, along with the expected application-level part. Moreover, the big amount of data and the strong I/O demand pose additional challenges related to the performance. In this regard, production-level tools for climate data analysis are mostly sequential and there is a lack of big data analytics solutions implementing fine-grain data parallelism or adopting stronger parallel I/O strategies, data locality, workflow optimization, etc. High-level solutions leveraging on workflow-enabled big data analytics frameworks for eScience could help scientists in defining and implementing the workflows related to their experiments by exploiting a more declarative, efficient and powerful approach. This talk will start introducing the main needs and challenges regarding big data analytics workflow management for eScience and will then provide some insights about the implementation of some real use cases related to some climate change indicators on large datasets produced in the context of the CLIP-C project - a EU FP7 project aiming at providing access to climate information of direct relevance to a wide variety of users, from scientists to policy makers and private sector decision makers. All the proposed use cases have been implemented exploiting the Ophidia big data analytics framework. The software stack includes an internal workflow management system, which coordinates, orchestrates, and optimises the execution of multiple scientific data analytics and visualization tasks. Real-time workflow monitoring execution is also supported through a graphical user interface. In order to address the challenges of the use cases, the implemented data analytics workflows include parallel data analysis, metadata management, virtual file system tasks, maps generation, rolling of datasets, and import/export of datasets in NetCDF format. The use cases have been implemented on a HPC cluster of 8-nodes (16-cores/node) of the Athena Cluster available at the CMCC Supercomputing Centre. Benchmark results will be also presented during the talk.

Akuna: An Open Source User Environment for Managing Subsurface Simulation Workflows

NASA Astrophysics Data System (ADS)

Freedman, V. L.; Agarwal, D.; Bensema, K.; Finsterle, S.; Gable, C. W.; Keating, E. H.; Krishnan, H.; Lansing, C.; Moeglein, W.; Pau, G. S. H.; Porter, E.; Scheibe, T. D.

2014-12-01

The U.S. Department of Energy (DOE) is investing in development of a numerical modeling toolset called ASCEM (Advanced Simulation Capability for Environmental Management) to support modeling analyses at legacy waste sites. ASCEM is an open source and modular computing framework that incorporates new advances and tools for predicting contaminant fate and transport in natural and engineered systems. The ASCEM toolset includes both a Platform with Integrated Toolsets (called Akuna) and a High-Performance Computing multi-process simulator (called Amanzi). The focus of this presentation is on Akuna, an open-source user environment that manages subsurface simulation workflows and associated data and metadata. In this presentation, key elements of Akuna are demonstrated, which includes toolsets for model setup, database management, sensitivity analysis, parameter estimation, uncertainty quantification, and visualization of both model setup and simulation results. A key component of the workflow is in the automated job launching and monitoring capabilities, which allow a user to submit and monitor simulation runs on high-performance, parallel computers. Visualization of large outputs can also be performed without moving data back to local resources. These capabilities make high-performance computing accessible to the users who might not be familiar with batch queue systems and usage protocols on different supercomputers and clusters.

How I do it: a practical database management system to assist clinical research teams with data collection, organization, and reporting.

PubMed

Lee, Howard; Chapiro, Julius; Schernthaner, Rüdiger; Duran, Rafael; Wang, Zhijun; Gorodetski, Boris; Geschwind, Jean-François; Lin, MingDe

2015-04-01

The objective of this study was to demonstrate that an intra-arterial liver therapy clinical research database system is a more workflow efficient and robust tool for clinical research than a spreadsheet storage system. The database system could be used to generate clinical research study populations easily with custom search and retrieval criteria. A questionnaire was designed and distributed to 21 board-certified radiologists to assess current data storage problems and clinician reception to a database management system. Based on the questionnaire findings, a customized database and user interface system were created to perform automatic calculations of clinical scores including staging systems such as the Child-Pugh and Barcelona Clinic Liver Cancer, and facilitates data input and output. Questionnaire participants were favorable to a database system. The interface retrieved study-relevant data accurately and effectively. The database effectively produced easy-to-read study-specific patient populations with custom-defined inclusion/exclusion criteria. The database management system is workflow efficient and robust in retrieving, storing, and analyzing data. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Dynamic Voltage Frequency Scaling Simulator for Real Workflows Energy-Aware Management in Green Cloud Computing

PubMed Central

Cotes-Ruiz, Iván Tomás; Prado, Rocío P.; García-Galán, Sebastián; Muñoz-Expósito, José Enrique; Ruiz-Reyes, Nicolás

2017-01-01

Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS). The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique. PMID:28085932

Dynamic Voltage Frequency Scaling Simulator for Real Workflows Energy-Aware Management in Green Cloud Computing.

PubMed

Cotes-Ruiz, Iván Tomás; Prado, Rocío P; García-Galán, Sebastián; Muñoz-Expósito, José Enrique; Ruiz-Reyes, Nicolás

2017-01-01

Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS). The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique.

A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows.

PubMed

Blattner, Timothy; Keyrouz, Walid; Bhattacharyya, Shuvra S; Halem, Milton; Brady, Mary

2017-12-01

Designing applications for scalability is key to improving their performance in hybrid and cluster computing. Scheduling code to utilize parallelism is difficult, particularly when dealing with data dependencies, memory management, data motion, and processor occupancy. The Hybrid Task Graph Scheduler (HTGS) improves programmer productivity when implementing hybrid workflows for multi-core and multi-GPU systems. The Hybrid Task Graph Scheduler (HTGS) is an abstract execution model, framework, and API that increases programmer productivity when implementing hybrid workflows for such systems. HTGS manages dependencies between tasks, represents CPU and GPU memories independently, overlaps computations with disk I/O and memory transfers, keeps multiple GPUs occupied, and uses all available compute resources. Through these abstractions, data motion and memory are explicit; this makes data locality decisions more accessible. To demonstrate the HTGS application program interface (API), we present implementations of two example algorithms: (1) a matrix multiplication that shows how easily task graphs can be used; and (2) a hybrid implementation of microscopy image stitching that reduces code size by ≈ 43% compared to a manually coded hybrid workflow implementation and showcases the minimal overhead of task graphs in HTGS. Both of the HTGS-based implementations show good performance. In image stitching the HTGS implementation achieves similar performance to the hybrid workflow implementation. Matrix multiplication with HTGS achieves 1.3× and 1.8× speedup over the multi-threaded OpenBLAS library for 16k × 16k and 32k × 32k size matrices, respectively.

Support for Taverna workflows in the VPH-Share cloud platform.

PubMed

Kasztelnik, Marek; Coto, Ernesto; Bubak, Marian; Malawski, Maciej; Nowakowski, Piotr; Arenas, Juan; Saglimbeni, Alfredo; Testi, Debora; Frangi, Alejandro F

2017-07-01

To address the increasing need for collaborative endeavours within the Virtual Physiological Human (VPH) community, the VPH-Share collaborative cloud platform allows researchers to expose and share sequences of complex biomedical processing tasks in the form of computational workflows. The Taverna Workflow System is a very popular tool for orchestrating complex biomedical & bioinformatics processing tasks in the VPH community. This paper describes the VPH-Share components that support the building and execution of Taverna workflows, and explains how they interact with other VPH-Share components to improve the capabilities of the VPH-Share platform. Taverna workflow support is delivered by the Atmosphere cloud management platform and the VPH-Share Taverna plugin. These components are explained in detail, along with the two main procedures that were developed to enable this seamless integration: workflow composition and execution. 1) Seamless integration of VPH-Share with other components and systems. 2) Extended range of different tools for workflows. 3) Successful integration of scientific workflows from other VPH projects. 4) Execution speed improvement for medical applications. The presented workflow integration provides VPH-Share users with a wide range of different possibilities to compose and execute workflows, such as desktop or online composition, online batch execution, multithreading, remote execution, etc. The specific advantages of each supported tool are presented, as are the roles of Atmosphere and the VPH-Share plugin within the VPH-Share project. The combination of the VPH-Share plugin and Atmosphere engenders the VPH-Share infrastructure with far more flexible, powerful and usable capabilities for the VPH-Share community. As both components can continue to evolve and improve independently, we acknowledge that further improvements are still to be developed and will be described. Copyright © 2017 Elsevier B.V. All rights reserved.

Automation in an Addiction Treatment Research Clinic: Computerized Contingency Management, Ecological Momentary Assessment, and a Protocol Workflow System

PubMed Central

Vahabzadeh, Massoud; Lin, Jia-Ling; Mezghanni, Mustapha; Epstein, David H.; Preston, Kenzie L.

2009-01-01

Issues A challenge in treatment research is the necessity of adhering to protocol and regulatory strictures while maintaining flexibility to meet patients’ treatment needs and accommodate variations among protocols. Another challenge is the acquisition of large amounts of data in an occasionally hectic environment, along with provision of seamless methods for exporting, mining, and querying the data. Approach We have automated several major functions of our outpatient treatment research clinic for studies in drug abuse and dependence. Here we describe three such specialized applications: the Automated Contingency Management (ACM) system for delivery of behavioral interventions, the Transactional Electronic Diary (TED) system for management of behavioral assessments, and the Protocol Workflow System (PWS) for computerized workflow automation and guidance of each participant’s daily clinic activities. These modules are integrated into our larger information system to enable data sharing in real time among authorized staff. Key Findings ACM and TED have each permitted us to conduct research that was not previously possible. In addition, the time to data analysis at the end of each study is substantially shorter. With the implementation of the PWS, we have been able to manage a research clinic with an 80-patient capacity having an annual average of 18,000 patient-visits and 7,300 urine collections with a research staff of five. Finally, automated data management has considerably enhanced our ability to monitor and summarize participant-safety data for research oversight. Implications and conclusion When developed in consultation with end users, automation in treatment-research clinics can enable more efficient operations, better communication among staff, and expansions in research methods. PMID:19320669

Autonomic Management of Application Workflows on Hybrid Computing Infrastructure

DOE PAGES

Kim, Hyunjoo; el-Khamra, Yaakoub; Rodero, Ivan; ...

2011-01-01

In this paper, we present a programming and runtime framework that enables the autonomic management of complex application workflows on hybrid computing infrastructures. The framework is designed to address system and application heterogeneity and dynamics to ensure that application objectives and constraints are satisfied. The need for such autonomic system and application management is becoming critical as computing infrastructures become increasingly heterogeneous, integrating different classes of resources from high-end HPC systems to commodity clusters and clouds. For example, the framework presented in this paper can be used to provision the appropriate mix of resources based on application requirements and constraints.more » The framework also monitors the system/application state and adapts the application and/or resources to respond to changing requirements or environment. To demonstrate the operation of the framework and to evaluate its ability, we employ a workflow used to characterize an oil reservoir executing on a hybrid infrastructure composed of TeraGrid nodes and Amazon EC2 instances of various types. Specifically, we show how different applications objectives such as acceleration, conservation and resilience can be effectively achieved while satisfying deadline and budget constraints, using an appropriate mix of dynamically provisioned resources. Our evaluations also demonstrate that public clouds can be used to complement and reinforce the scheduling and usage of traditional high performance computing infrastructure.« less

Big Data Challenges in Global Seismic 'Adjoint Tomography' (Invited)

NASA Astrophysics Data System (ADS)

Tromp, J.; Bozdag, E.; Krischer, L.; Lefebvre, M.; Lei, W.; Smith, J.

2013-12-01

The challenge of imaging Earth's interior on a global scale is closely linked to the challenge of handling large data sets. The related iterative workflow involves five distinct phases, namely, 1) data gathering and culling, 2) synthetic seismogram calculations, 3) pre-processing (time-series analysis and time-window selection), 4) data assimilation and adjoint calculations, 5) post-processing (pre-conditioning, regularization, model update). In order to implement this workflow on modern high-performance computing systems, a new seismic data format is being developed. The Adaptable Seismic Data Format (ASDF) is designed to replace currently used data formats with a more flexible format that allows for fast parallel I/O. The metadata is divided into abstract categories, such as "source" and "receiver", along with provenance information for complete reproducibility. The structure of ASDF is designed keeping in mind three distinct applications: earthquake seismology, seismic interferometry, and exploration seismology. Existing time-series analysis tool kits, such as SAC and ObsPy, can be easily interfaced with ASDF so that seismologists can use robust, previously developed software packages. ASDF accommodates an automated, efficient workflow for global adjoint tomography. Manually managing the large number of simulations associated with the workflow can rapidly become a burden, especially with increasing numbers of earthquakes and stations. Therefore, it is of importance to investigate the possibility of automating the entire workflow. Scientific Workflow Management Software (SWfMS) allows users to execute workflows almost routinely. SWfMS provides additional advantages. In particular, it is possible to group independent simulations in a single job to fit the available computational resources. They also give a basic level of fault resilience as the workflow can be resumed at the correct state preceding a failure. Some of the best candidates for our particular workflow are Kepler and Swift, and the latter appears to be the most serious candidate for a large-scale workflow on a single supercomputer, remaining sufficiently simple to accommodate further modifications and improvements.

A Web application for the management of clinical workflow in image-guided and adaptive proton therapy for prostate cancer treatments.

PubMed

Yeung, Daniel; Boes, Peter; Ho, Meng Wei; Li, Zuofeng

2015-05-08

Image-guided radiotherapy (IGRT), based on radiopaque markers placed in the prostate gland, was used for proton therapy of prostate patients. Orthogonal X-rays and the IBA Digital Image Positioning System (DIPS) were used for setup correction prior to treatment and were repeated after treatment delivery. Following a rationale for margin estimates similar to that of van Herk,(1) the daily post-treatment DIPS data were analyzed to determine if an adaptive radiotherapy plan was necessary. A Web application using ASP.NET MVC5, Entity Framework, and an SQL database was designed to automate this process. The designed features included state-of-the-art Web technologies, a domain model closely matching the workflow, a database-supporting concurrency and data mining, access to the DIPS database, secured user access and roles management, and graphing and analysis tools. The Model-View-Controller (MVC) paradigm allowed clean domain logic, unit testing, and extensibility. Client-side technologies, such as jQuery, jQuery Plug-ins, and Ajax, were adopted to achieve a rich user environment and fast response. Data models included patients, staff, treatment fields and records, correction vectors, DIPS images, and association logics. Data entry, analysis, workflow logics, and notifications were implemented. The system effectively modeled the clinical workflow and IGRT process.

[Change in process management by implementing RIS, PACS and flat-panel detectors].

PubMed

Imhof, H; Dirisamer, A; Fischer, H; Grampp, S; Heiner, L; Kaderk, M; Krestan, C; Kainberger, F

2002-05-01

Implementation of radiological information systems (RIS) and picture archiving and communicating systems (PACS) results in significant changes of workflow in a radiological department. Additional connection with flat-panel detectors leads to a shortening of the work process. RIS and PACS implementation alone reduces the complete workflow by 21-80%. With flatpanel technology the image production process is further shortened by 25-30%. The workflow-steps are changed from original 17-12 with the implementation of RIS and PACS and to 5 with the integrated use of flatpanels. This clearly recognizable advantages in the workflow need an according financial investment. Several studies could show that the capitalisation-factor calculated over eight years is positive, with a gain range between 5-25%. Whether the additional implementation of flatpanel detectors results also in a positive capitalisation over the years, cannot be estimated exactly, at the moment, because the experiences are too short. Particularly critical are the interfaces, which needs a constant quality control. Our flatpanel detector-system is fixed, special images--as we have them in about 3-5% of all cases--need still conventional filmscreen or phosphorplate-systems. Full-spine and long-leg examinations cannot be performed with sufficient exactness. Without any questions implementation of integrated RIS, PACS and flatpanel detector-system needs excellent training of the employees, because of the changes in workflow etc. The main profits of such an integrated implementation are an increase in quality in image and report datas, easier handling--there are almost no more cassettes necessary--and excessive shortening of workflow.

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences.

PubMed

Inda, Márcia A; van Batenburg, Marinus F; Roos, Marco; Belloum, Adam S Z; Vasunin, Dmitry; Wibisono, Adianto; van Kampen, Antoine H C; Breit, Timo M

2008-08-08

Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To perform in silico experimentation conveniently with this genomics data, biologists need tools to process and compare datasets routinely and explore the obtained results interactively. The complexity of such experimentation requires these tools to be based on an e-Science approach, hence generic, modular, and reusable. A virtual laboratory environment with workflows, workflow management systems, and Grid computation are therefore essential. Here we apply an e-Science approach to develop SigWin-detector, a workflow-based tool that can detect significantly enriched windows of (genomic) features in a (DNA) sequence in a fast and reproducible way. For proof-of-principle, we utilize a biological use case to detect regions of increased and decreased gene expression (RIDGEs and anti-RIDGEs) in human transcriptome maps. We improved the original method for RIDGE detection by replacing the costly step of estimation by random sampling with a faster analytical formula for computing the distribution of the null hypothesis being tested and by developing a new algorithm for computing moving medians. SigWin-detector was developed using the WS-VLAM workflow management system and consists of several reusable modules that are linked together in a basic workflow. The configuration of this basic workflow can be adapted to satisfy the requirements of the specific in silico experiment. As we show with the results from analyses in the biological use case on RIDGEs, SigWin-detector is an efficient and reusable Grid-based tool for discovering windows enriched for features of a particular type in any sequence of values. Thus, SigWin-detector provides the proof-of-principle for the modular e-Science based concept of integrative bioinformatics experimentation.

Improving data collection, documentation, and workflow in a dementia screening study.

PubMed

Read, Kevin B; LaPolla, Fred Willie Zametkin; Tolea, Magdalena I; Galvin, James E; Surkis, Alisa

2017-04-01

A clinical study team performing three multicultural dementia screening studies identified the need to improve data management practices and facilitate data sharing. A collaboration was initiated with librarians as part of the National Library of Medicine (NLM) informationist supplement program. The librarians identified areas for improvement in the studies' data collection, entry, and processing workflows. The librarians' role in this project was to meet needs expressed by the study team around improving data collection and processing workflows to increase study efficiency and ensure data quality. The librarians addressed the data collection, entry, and processing weaknesses through standardizing and renaming variables, creating an electronic data capture system using REDCap, and developing well-documented, reproducible data processing workflows. NLM informationist supplements provide librarians with valuable experience in collaborating with study teams to address their data needs. For this project, the librarians gained skills in project management, REDCap, and understanding of the challenges and specifics of a clinical research study. However, the time and effort required to provide targeted and intensive support for one study team was not scalable to the library's broader user community.

Scalable and cost-effective NGS genotyping in the cloud.

PubMed

Souilmi, Yassine; Lancaster, Alex K; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J; Wall, Dennis P

2015-10-15

While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

Mobile task management tool that improves workflow of an acute general surgical service.

PubMed

Foo, Elizabeth; McDonald, Rod; Savage, Earle; Floyd, Richard; Butler, Anthony; Rumball-Smith, Alistair; Connor, Saxon

2015-10-01

Understanding and being able to measure constraints within a health system is crucial if outcomes are to be improved. Current systems lack the ability to capture decision making with regard to tasks performed within a patient journey. The aim of this study was to assess the impact of a mobile task management tool on clinical workflow within an acute general surgical service by analysing data capture and usability of the application tool. The Cortex iOS application was developed to digitize patient flow and provide real-time visibility over clinical decision making and task performance. Study outcomes measured were workflow data capture for patient and staff events. Usability was assessed using an electronic survey. There were 449 unique patient journeys tracked with a total of 3072 patient events recorded. The results repository was accessed 7792 times. The participants reported that the application sped up decision making, reduced redundancy of work and improved team communication. The mode of the estimated time the application saved participants was 5-9 min/h of work. Of the 14 respondents, nine discarded their analogue methods of tracking tasks by the end of the study period. The introduction of a mobile task management system improved the working efficiency of junior clinical staff. The application allowed capture of data not previously available to hospital systems. In the future, such data will contribute to the accurate mapping of patient journeys through the health system. © 2015 Royal Australasian College of Surgeons.

Talkoot Portals: Discover, Tag, Share, and Reuse Collaborative Science Workflows

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Ramachandran, R.; Lynnes, C.

2009-05-01

A small but growing number of scientists are beginning to harness Web 2.0 technologies, such as wikis, blogs, and social tagging, as a transformative way of doing science. These technologies provide researchers easy mechanisms to critique, suggest and share ideas, data and algorithms. At the same time, large suites of algorithms for science analysis are being made available as remotely-invokable Web Services, which can be chained together to create analysis workflows. This provides the research community an unprecedented opportunity to collaborate by sharing their workflows with one another, reproducing and analyzing research results, and leveraging colleagues' expertise to expedite the process of scientific discovery. However, wikis and similar technologies are limited to text, static images and hyperlinks, providing little support for collaborative data analysis. A team of information technology and Earth science researchers from multiple institutions have come together to improve community collaboration in science analysis by developing a customizable "software appliance" to build collaborative portals for Earth Science services and analysis workflows. The critical requirement is that researchers (not just information technologists) be able to build collaborative sites around service workflows within a few hours. We envision online communities coming together, much like Finnish "talkoot" (a barn raising), to build a shared research space. Talkoot extends a freely available, open source content management framework with a series of modules specific to Earth Science for registering, creating, managing, discovering, tagging and sharing Earth Science web services and workflows for science data processing, analysis and visualization. Users will be able to author a "science story" in shareable web notebooks, including plots or animations, backed up by an executable workflow that directly reproduces the science analysis. New services and workflows of interest will be discoverable using tag search, and advertised using "service casts" and "interest casts" (Atom feeds). Multiple science workflow systems will be plugged into the system, with initial support for UAH's Mining Workflow Composer and the open-source Active BPEL engine, and JPL's SciFlo engine and the VizFlow visual programming interface. With the ability to share and execute analysis workflows, Talkoot portals can be used to do collaborative science in addition to communicate ideas and results. It will be useful for different science domains, mission teams, research projects and organizations. Thus, it will help to solve the "sociological" problem of bringing together disparate groups of researchers, and the technical problem of advertising, discovering, developing, documenting, and maintaining inter-agency science workflows. The presentation will discuss the goals of and barriers to Science 2.0, the social web technologies employed in the Talkoot software appliance (e.g. CMS, social tagging, personal presence, advertising by feeds, etc.), illustrate the resulting collaborative capabilities, and show early prototypes of the web interfaces (e.g. embedded workflows).

Scientific Data Management (SDM) Center for Enabling Technologies. Final Report, 2007-2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ludascher, Bertram; Altintas, Ilkay

Our contributions to advancing the State of the Art in scientific workflows have focused on the following areas: Workflow development; Generic workflow components and templates; Provenance collection and analysis; and, Workflow reliability and fault tolerance.

The development and implementation of MOSAIQ Integration Platform (MIP) based on the radiotherapy workflow

NASA Astrophysics Data System (ADS)

Yang, Xin; He, Zhen-yu; Jiang, Xiao-bo; Lin, Mao-sheng; Zhong, Ning-shan; Hu, Jiang; Qi, Zhen-yu; Bao, Yong; Li, Qiao-qiao; Li, Bao-yue; Hu, Lian-ying; Lin, Cheng-guang; Gao, Yuan-hong; Liu, Hui; Huang, Xiao-yan; Deng, Xiao-wu; Xia, Yun-fei; Liu, Meng-zhong; Sun, Ying

2017-03-01

To meet the special demands in China and the particular needs for the radiotherapy department, a MOSAIQ Integration Platform CHN (MIP) based on the workflow of radiation therapy (RT) has been developed, as a supplement system to the Elekta MOSAIQ. The MIP adopts C/S (client-server) structure mode, and its database is based on the Treatment Planning System (TPS) and MOSAIQ SQL Server 2008, running on the hospital local network. Five network servers, as a core hardware, supply data storage and network service based on the cloud services. The core software, using C# programming language, is developed based on Microsoft Visual Studio Platform. The MIP server could offer network service, including entry, query, statistics and print information for about 200 workstations at the same time. The MIP was implemented in the past one and a half years, and some practical patient-oriented functions were developed. And now the MIP is almost covering the whole workflow of radiation therapy. There are 15 function modules, such as: Notice, Appointment, Billing, Document Management (application/execution), System Management, and so on. By June of 2016, recorded data in the MIP are as following: 13546 patients, 13533 plan application, 15475 RT records, 14656 RT summaries, 567048 billing records and 506612 workload records, etc. The MIP based on the RT workflow has been successfully developed and clinically implemented with real-time performance, data security, stable operation. And it is demonstrated to be user-friendly and is proven to significantly improve the efficiency of the department. It is a key to facilitate the information sharing and department management. More functions can be added or modified for further enhancement its potentials in research and clinical practice.

Common Workflow Service: Standards Based Solution for Managing Operational Processes

NASA Astrophysics Data System (ADS)

Tinio, A. W.; Hollins, G. A.

2017-06-01

The Common Workflow Service is a collaborative and standards-based solution for managing mission operations processes using techniques from the Business Process Management (BPM) discipline. This presentation describes the CWS and its benefits.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garzoglio, Gabriele

The Fermilab Grid and Cloud Computing Department and the KISTI Global Science experimental Data hub Center are working on a multi-year Collaborative Research and Development Agreement.With the knowledge developed in the first year on how to provision and manage a federation of virtual machines through Cloud management systems. In this second year, we expanded the work on provisioning and federation, increasing both scale and diversity of solutions, and we started to build on-demand services on the established fabric, introducing the paradigm of Platform as a Service to assist with the execution of scientific workflows. We have enabled scientific workflows ofmore » stakeholders to run on multiple cloud resources at the scale of 1,000 concurrent machines. The demonstrations have been in the areas of (a) Virtual Infrastructure Automation and Provisioning, (b) Interoperability and Federation of Cloud Resources, and (c) On-demand Services for ScientificWorkflows.« less

Purdue Ionomics Information Management System. An Integrated Functional Genomics Platform1[C][W][OA

PubMed Central

Baxter, Ivan; Ouzzani, Mourad; Orcun, Seza; Kennedy, Brad; Jandhyala, Shrinivas S.; Salt, David E.

2007-01-01

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics. PMID:17189337

iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

PubMed Central

2009-01-01

Background In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques. Results We have developed iLAP (Laboratory data management, Analysis, and Protocol development), a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH) protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from http://genome.tugraz.at/iLAP/. Conclusion iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community. PMID:19941647

[Measures to prevent patient identification errors in blood collection/physiological function testing utilizing a laboratory information system].

PubMed

Shimazu, Chisato; Hoshino, Satoshi; Furukawa, Taiji

2013-08-01

We constructed an integrated personal identification workflow chart using both bar code reading and an all in-one laboratory information system. The information system not only handles test data but also the information needed for patient guidance in the laboratory department. The reception terminals at the entrance, displays for patient guidance and patient identification tools at blood-sampling booths are all controlled by the information system. The number of patient identification errors was greatly reduced by the system. However, identification errors have not been abolished in the ultrasound department. After re-evaluation of the patient identification process in this department, we recognized that the major reason for the errors came from excessive identification workflow. Ordinarily, an ultrasound test requires patient identification 3 times, because 3 different systems are required during the entire test process, i.e. ultrasound modality system, laboratory information system and a system for producing reports. We are trying to connect the 3 different systems to develop a one-time identification workflow, but it is not a simple task and has not been completed yet. Utilization of the laboratory information system is effective, but is not yet perfect for patient identification. The most fundamental procedure for patient identification is to ask a person's name even today. Everyday checks in the ordinary workflow and everyone's participation in safety-management activity are important for the prevention of patient identification errors.

Knowledge Annotations in Scientific Workflows: An Implementation in Kepler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gandara, Aida G.; Chin, George; Pinheiro Da Silva, Paulo

2011-07-20

Abstract. Scientic research products are the result of long-term collaborations between teams. Scientic workfows are capable of helping scientists in many ways including the collection of information as to howresearch was conducted, e.g. scientic workfow tools often collect and manage information about datasets used and data transformations. However,knowledge about why data was collected is rarely documented in scientic workflows. In this paper we describe a prototype system built to support the collection of scientic expertise that infuences scientic analysis. Through evaluating a scientic research eort underway at Pacific Northwest National Laboratory, we identied features that would most benefit PNNL scientistsmore » in documenting how and why they conduct their research making this information available to the entire team. The prototype system was built by enhancing the Kepler Scientic Work-flow System to create knowledge-annotated scientic workfows and topublish them as semantic annotations.« less

Integrating pathology and radiology disciplines: an emerging opportunity?

PubMed Central

2012-01-01

Pathology and radiology form the core of cancer diagnosis, yet the workflows of both specialties remain ad hoc and occur in separate "silos," with no direct linkage between their case accessioning and/or reporting systems, even when both departments belong to the same host institution. Because both radiologists' and pathologists' data are essential to making correct diagnoses and appropriate patient management and treatment decisions, this isolation of radiology and pathology workflows can be detrimental to the quality and outcomes of patient care. These detrimental effects underscore the need for pathology and radiology workflow integration and for systems that facilitate the synthesis of all data produced by both specialties. With the enormous technological advances currently occurring in both fields, the opportunity has emerged to develop an integrated diagnostic reporting system that supports both specialties and, therefore, improves the overall quality of patient care. PMID:22950414

Using AI and Semantic Web Technologies to attack Process Complexity in Open Systems

NASA Astrophysics Data System (ADS)

Thompson, Simon; Giles, Nick; Li, Yang; Gharib, Hamid; Nguyen, Thuc Duong

Recently many vendors and groups have advocated using BPEL and WS-BPEL as a workflow language to encapsulate business logic. While encapsulating workflow and process logic in one place is a sensible architectural decision the implementation of complex workflows suffers from the same problems that made managing and maintaining hierarchical procedural programs difficult. BPEL lacks constructs for logical modularity such as the requirements construct from the STL [12] or the ability to adapt constructs like pure abstract classes for the same purpose. We describe a system that uses semantic web and agent concepts to implement an abstraction layer for BPEL based on the notion of Goals and service typing. AI planning was used to enable process engineers to create and validate systems that used services and goals as first class concepts and compiled processes at run time for execution.

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

PubMed

Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

2017-12-15

This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

Software Project Management and Measurement on the World-Wide-Web (WWW)

NASA Technical Reports Server (NTRS)

Callahan, John; Ramakrishnan, Sudhaka

1996-01-01

We briefly describe a system for forms-based, work-flow management that helps members of a software development team overcome geographical barriers to collaboration. Our system, called the Web Integrated Software Environment (WISE), is implemented as a World-Wide-Web service that allows for management and measurement of software development projects based on dynamic analysis of change activity in the workflow. WISE tracks issues in a software development process, provides informal communication between the users with different roles, supports to-do lists, and helps in software process improvement. WISE minimizes the time devoted to metrics collection and analysis by providing implicit delivery of messages between users based on the content of project documents. The use of a database in WISE is hidden from the users who view WISE as maintaining a personal 'to-do list' of tasks related to the many projects on which they may play different roles.

Using conceptual work products of health care to design health IT.

PubMed

Berry, Andrew B L; Butler, Keith A; Harrington, Craig; Braxton, Melissa O; Walker, Amy J; Pete, Nikki; Johnson, Trevor; Oberle, Mark W; Haselkorn, Jodie; Paul Nichol, W; Haselkorn, Mark

2016-02-01

This paper introduces a new, model-based design method for interactive health information technology (IT) systems. This method extends workflow models with models of conceptual work products. When the health care work being modeled is substantially cognitive, tacit, and complex in nature, graphical workflow models can become too complex to be useful to designers. Conceptual models complement and simplify workflows by providing an explicit specification for the information product they must produce. We illustrate how conceptual work products can be modeled using standard software modeling language, which allows them to provide fundamental requirements for what the workflow must accomplish and the information that a new system should provide. Developers can use these specifications to envision how health IT could enable an effective cognitive strategy as a workflow with precise information requirements. We illustrate the new method with a study conducted in an outpatient multiple sclerosis (MS) clinic. This study shows specifically how the different phases of the method can be carried out, how the method allows for iteration across phases, and how the method generated a health IT design for case management of MS that is efficient and easy to use. Copyright © 2015 Elsevier Inc. All rights reserved.

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management.

PubMed

Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

2005-12-01

Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

Errors detected in pediatric oral liquid medication doses prepared in an automated workflow management system.

PubMed

Bledsoe, Sarah; Van Buskirk, Alex; Falconer, R James; Hollon, Andrew; Hoebing, Wendy; Jokic, Sladan

2018-02-01

The effectiveness of barcode-assisted medication preparation (BCMP) technology on detecting oral liquid dose preparation errors. From June 1, 2013, through May 31, 2014, a total of 178,344 oral doses were processed at Children's Mercy, a 301-bed pediatric hospital, through an automated workflow management system. Doses containing errors detected by the system's barcode scanning system or classified as rejected by the pharmacist were further reviewed. Errors intercepted by the barcode-scanning system were classified as (1) expired product, (2) incorrect drug, (3) incorrect concentration, and (4) technological error. Pharmacist-rejected doses were categorized into 6 categories based on the root cause of the preparation error: (1) expired product, (2) incorrect concentration, (3) incorrect drug, (4) incorrect volume, (5) preparation error, and (6) other. Of the 178,344 doses examined, 3,812 (2.1%) errors were detected by either the barcode-assisted scanning system (1.8%, n = 3,291) or a pharmacist (0.3%, n = 521). The 3,291 errors prevented by the barcode-assisted system were classified most commonly as technological error and incorrect drug, followed by incorrect concentration and expired product. Errors detected by pharmacists were also analyzed. These 521 errors were most often classified as incorrect volume, preparation error, expired product, other, incorrect drug, and incorrect concentration. BCMP technology detected errors in 1.8% of pediatric oral liquid medication doses prepared in an automated workflow management system, with errors being most commonly attributed to technological problems or incorrect drugs. Pharmacists rejected an additional 0.3% of studied doses. Copyright © 2018 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

A Web application for the management of clinical workflow in image‐guided and adaptive proton therapy for prostate cancer treatments

PubMed Central

Boes, Peter; Ho, Meng Wei; Li, Zuofeng

2015-01-01

Image‐guided radiotherapy (IGRT), based on radiopaque markers placed in the prostate gland, was used for proton therapy of prostate patients. Orthogonal X‐rays and the IBA Digital Image Positioning System (DIPS) were used for setup correction prior to treatment and were repeated after treatment delivery. Following a rationale for margin estimates similar to that of van Herk,(1) the daily post‐treatment DIPS data were analyzed to determine if an adaptive radiotherapy plan was necessary. A Web application using ASP.NET MVC5, Entity Framework, and an SQL database was designed to automate this process. The designed features included state‐of‐the‐art Web technologies, a domain model closely matching the workflow, a database‐supporting concurrency and data mining, access to the DIPS database, secured user access and roles management, and graphing and analysis tools. The Model‐View‐Controller (MVC) paradigm allowed clean domain logic, unit testing, and extensibility. Client‐side technologies, such as jQuery, jQuery Plug‐ins, and Ajax, were adopted to achieve a rich user environment and fast response. Data models included patients, staff, treatment fields and records, correction vectors, DIPS images, and association logics. Data entry, analysis, workflow logics, and notifications were implemented. The system effectively modeled the clinical workflow and IGRT process. PACS number: 87 PMID:26103504

Coupling of a continuum ice sheet model and a discrete element calving model using a scientific workflow system

NASA Astrophysics Data System (ADS)

Memon, Shahbaz; Vallot, Dorothée; Zwinger, Thomas; Neukirchen, Helmut

2017-04-01

Scientific communities generate complex simulations through orchestration of semi-structured analysis pipelines which involves execution of large workflows on multiple, distributed and heterogeneous computing and data resources. Modeling ice dynamics of glaciers requires workflows consisting of many non-trivial, computationally expensive processing tasks which are coupled to each other. From this domain, we present an e-Science use case, a workflow, which requires the execution of a continuum ice flow model and a discrete element based calving model in an iterative manner. Apart from the execution, this workflow also contains data format conversion tasks that support the execution of ice flow and calving by means of transition through sequential, nested and iterative steps. Thus, the management and monitoring of all the processing tasks including data management and transfer of the workflow model becomes more complex. From the implementation perspective, this workflow model was initially developed on a set of scripts using static data input and output references. In the course of application usage when more scripts or modifications introduced as per user requirements, the debugging and validation of results were more cumbersome to achieve. To address these problems, we identified a need to have a high-level scientific workflow tool through which all the above mentioned processes can be achieved in an efficient and usable manner. We decided to make use of the e-Science middleware UNICORE (Uniform Interface to Computing Resources) that allows seamless and automated access to different heterogenous and distributed resources which is supported by a scientific workflow engine. Based on this, we developed a high-level scientific workflow model for coupling of massively parallel High-Performance Computing (HPC) jobs: a continuum ice sheet model (Elmer/Ice) and a discrete element calving and crevassing model (HiDEM). In our talk we present how the use of a high-level scientific workflow middleware enables reproducibility of results more convenient and also provides a reusable and portable workflow template that can be deployed across different computing infrastructures. Acknowledgements This work was kindly supported by NordForsk as part of the Nordic Center of Excellence (NCoE) eSTICC (eScience Tools for Investigating Climate Change at High Northern Latitudes) and the Top-level Research Initiative NCoE SVALI (Stability and Variation of Arctic Land Ice).

Scientific Workflow Management in Proteomics

PubMed Central

de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

2012-01-01

Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

Scientific Workflows + Provenance = Better (Meta-)Data Management

NASA Astrophysics Data System (ADS)

Ludaescher, B.; Cuevas-Vicenttín, V.; Missier, P.; Dey, S.; Kianmajd, P.; Wei, Y.; Koop, D.; Chirigati, F.; Altintas, I.; Belhajjame, K.; Bowers, S.

2013-12-01

The origin and processing history of an artifact is known as its provenance. Data provenance is an important form of metadata that explains how a particular data product came about, e.g., how and when it was derived in a computational process, which parameter settings and input data were used, etc. Provenance information provides transparency and helps to explain and interpret data products. Other common uses and applications of provenance include quality control, data curation, result debugging, and more generally, 'reproducible science'. Scientific workflow systems (e.g. Kepler, Taverna, VisTrails, and others) provide controlled environments for developing computational pipelines with built-in provenance support. Workflow results can then be explained in terms of workflow steps, parameter settings, input data, etc. using provenance that is automatically captured by the system. Scientific workflows themselves provide a user-friendly abstraction of the computational process and are thus a form of ('prospective') provenance in their own right. The full potential of provenance information is realized when combining workflow-level information (prospective provenance) with trace-level information (retrospective provenance). To this end, the DataONE Provenance Working Group (ProvWG) has developed an extension of the W3C PROV standard, called D-PROV. Whereas PROV provides a 'least common denominator' for exchanging and integrating provenance information, D-PROV adds new 'observables' that described workflow-level information (e.g., the functional steps in a pipeline), as well as workflow-specific trace-level information ( timestamps for each workflow step executed, the inputs and outputs used, etc.) Using examples, we will demonstrate how the combination of prospective and retrospective provenance provides added value in managing scientific data. The DataONE ProvWG is also developing tools based on D-PROV that allow scientists to get more mileage from provenance metadata. DataONE is a federation of member nodes that store data and metadata for discovery and access. By enriching metadata with provenance information, search and reuse of data is enhanced, and the 'social life' of data (being the product of many workflow runs, different people, etc.) is revealed. We are currently prototyping a provenance repository (PBase) to demonstrate what can be achieved with advanced provenance queries. The ProvExplorer and ProPub tools support advanced ad-hoc querying and visualization of provenance as well as customized provenance publications (e.g., to address privacy issues, or to focus provenance to relevant details). In a parallel line of work, we are exploring ways to add provenance support to widely-used scripting platforms (e.g. R and Python) and then expose that information via D-PROV.

The provider perspective: investigating the effect of the Electronic Patient-Reported Outcome (ePRO) mobile application and portal on primary care provider workflow.

PubMed

Hans, Parminder K; Gray, Carolyn Steele; Gill, Ashlinder; Tiessen, James

2018-03-01

Aim This qualitative study investigates how the Electronic Patient-Reported Outcome (ePRO) mobile application and portal system, designed to capture patient-reported measures to support self-management, affected primary care provider workflows. The Canadian health system is facing an ageing population that is living with chronic disease. Disruptive innovations like mobile health technologies can help to support health system transformation needed to better meet the multifaceted needs of the complex care patient. However, there are challenges with implementing these technologies in primary care settings, in particular the effect on primary care provider workflows. Over a six-week period interdisciplinary primary care providers (n=6) and their complex care patients (n=12), used the ePRO mobile application and portal to collaboratively goal-set, manage care plans, and support self-management using patient-reported measures. Secondary thematic analysis of focus groups, training sessions, and issue tracker reports captured user experiences at a Toronto area Family Health Team from October 2014 to January 2015. Findings Key issues raised by providers included: liability concerns associated with remote monitoring, increased documentation activities due to a lack of interoperability between the app and the electronic patient record, increased provider anxiety with regard to the potential for the app to disrupt and infringe upon appointment time, and increased demands for patient engagement. Primary care providers reported the app helped to focus care plans and to begin a collaborative conversation on goal-setting. However, throughout our investigation we found a high level of provider resistance evidenced by consistent attempts to shift the app towards fitting with existing workflows rather than adapting much of their behaviour. As health systems seek innovative and disruptive models to better serve this complex patient population, provider change resistance will need to be addressed. New models and technologies cannot be disruptive in an environment that is resisting change.

SWS: accessing SRS sites contents through Web Services.

PubMed

Romano, Paolo; Marra, Domenico

2008-03-26

Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis. New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services. We have developed 'SRS by WS' (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems. Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.

Talkoot Portals: Discover, Tag, Share, and Reuse Collaborative Science Workflows (Invited)

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Ramachandran, R.; Lynnes, C.

2009-12-01

A small but growing number of scientists are beginning to harness Web 2.0 technologies, such as wikis, blogs, and social tagging, as a transformative way of doing science. These technologies provide researchers easy mechanisms to critique, suggest and share ideas, data and algorithms. At the same time, large suites of algorithms for science analysis are being made available as remotely-invokable Web Services, which can be chained together to create analysis workflows. This provides the research community an unprecedented opportunity to collaborate by sharing their workflows with one another, reproducing and analyzing research results, and leveraging colleagues’ expertise to expedite the process of scientific discovery. However, wikis and similar technologies are limited to text, static images and hyperlinks, providing little support for collaborative data analysis. A team of information technology and Earth science researchers from multiple institutions have come together to improve community collaboration in science analysis by developing a customizable “software appliance” to build collaborative portals for Earth Science services and analysis workflows. The critical requirement is that researchers (not just information technologists) be able to build collaborative sites around service workflows within a few hours. We envision online communities coming together, much like Finnish “talkoot” (a barn raising), to build a shared research space. Talkoot extends a freely available, open source content management framework with a series of modules specific to Earth Science for registering, creating, managing, discovering, tagging and sharing Earth Science web services and workflows for science data processing, analysis and visualization. Users will be able to author a “science story” in shareable web notebooks, including plots or animations, backed up by an executable workflow that directly reproduces the science analysis. New services and workflows of interest will be discoverable using tag search, and advertised using “service casts” and “interest casts” (Atom feeds). Multiple science workflow systems will be plugged into the system, with initial support for UAH’s Mining Workflow Composer and the open-source Active BPEL engine, and JPL’s SciFlo engine and the VizFlow visual programming interface. With the ability to share and execute analysis workflows, Talkoot portals can be used to do collaborative science in addition to communicate ideas and results. It will be useful for different science domains, mission teams, research projects and organizations. Thus, it will help to solve the “sociological” problem of bringing together disparate groups of researchers, and the technical problem of advertising, discovering, developing, documenting, and maintaining inter-agency science workflows. The presentation will discuss the goals of and barriers to Science 2.0, the social web technologies employed in the Talkoot software appliance (e.g. CMS, social tagging, personal presence, advertising by feeds, etc.), illustrate the resulting collaborative capabilities, and show early prototypes of the web interfaces (e.g. embedded workflows).

Improving data collection, documentation, and workflow in a dementia screening study

PubMed Central

Read, Kevin B.; LaPolla, Fred Willie Zametkin; Tolea, Magdalena I.; Galvin, James E.; Surkis, Alisa

2017-01-01

Background A clinical study team performing three multicultural dementia screening studies identified the need to improve data management practices and facilitate data sharing. A collaboration was initiated with librarians as part of the National Library of Medicine (NLM) informationist supplement program. The librarians identified areas for improvement in the studies’ data collection, entry, and processing workflows. Case Presentation The librarians’ role in this project was to meet needs expressed by the study team around improving data collection and processing workflows to increase study efficiency and ensure data quality. The librarians addressed the data collection, entry, and processing weaknesses through standardizing and renaming variables, creating an electronic data capture system using REDCap, and developing well-documented, reproducible data processing workflows. Conclusions NLM informationist supplements provide librarians with valuable experience in collaborating with study teams to address their data needs. For this project, the librarians gained skills in project management, REDCap, and understanding of the challenges and specifics of a clinical research study. However, the time and effort required to provide targeted and intensive support for one study team was not scalable to the library’s broader user community. PMID:28377680

Pegasus Workflow Management System: Helping Applications From Earth and Space

NASA Astrophysics Data System (ADS)

Mehta, G.; Deelman, E.; Vahi, K.; Silva, F.

2010-12-01

Pegasus WMS is a Workflow Management System that can manage large-scale scientific workflows across Grid, local and Cloud resources simultaneously. Pegasus WMS provides a means for representing the workflow of an application in an abstract XML form, agnostic of the resources available to run it and the location of data and executables. It then compiles these workflows into concrete plans by querying catalogs and farming computations across local and distributed computing resources, as well as emerging commercial and community cloud environments in an easy and reliable manner. Pegasus WMS optimizes the execution as well as data movement by leveraging existing Grid and cloud technologies via a flexible pluggable interface and provides advanced features like reusing existing data, automatic cleanup of generated data, and recursive workflows with deferred planning. It also captures all the provenance of the workflow from the planning stage to the execution of the generated data, helping scientists to accurately measure performance metrics of their workflow as well as data reproducibility issues. Pegasus WMS was initially developed as part of the GriPhyN project to support large-scale high-energy physics and astrophysics experiments. Direct funding from the NSF enabled support for a wide variety of applications from diverse domains including earthquake simulation, bacterial RNA studies, helioseismology and ocean modeling. Earthquake Simulation: Pegasus WMS was recently used in a large scale production run in 2009 by the Southern California Earthquake Centre to run 192 million loosely coupled tasks and about 2000 tightly coupled MPI style tasks on National Cyber infrastructure for generating a probabilistic seismic hazard map of the Southern California region. SCEC ran 223 workflows over a period of eight weeks, using on average 4,420 cores, with a peak of 14,540 cores. A total of 192 million files were produced totaling about 165TB out of which 11TB of data was saved. Astrophysics: The Laser Interferometer Gravitational-Wave Observatory (LIGO) uses Pegasus WMS to search for binary inspiral gravitational waves. A month of LIGO data requires many thousands of jobs, running for days on hundreds of CPUs on the LIGO Data Grid (LDG) and Open Science Grid (OSG). Ocean Temperature Forecast: Researchers at the Jet Propulsion Laboratory are exploring Pegasus WMS to run ocean forecast ensembles of the California coastal region. These models produce a number of daily forecasts for water temperature, salinity, and other measures. Helioseismology: The Solar Dynamics Observatory (SDO) is NASA's most important solar physics mission of this coming decade. Pegasus WMS is being used to analyze the data from SDO, which will be predominantly used to learn about solar magnetic activity and to probe the internal structure and dynamics of the Sun with helioseismology. Bacterial RNA studies: SIPHT is an application in bacterial genomics, which predicts sRNA (small non-coding RNAs)-encoding genes in bacteria. This project currently provides a web-based interface using Pegasus WMS at the backend to facilitate large-scale execution of the workflows on varied resources and provide better notifications of task/workflow completion.

Barriers to effective, safe communication and workflow between nurses and non-consultant hospital doctors during out-of-hours.

PubMed

Brady, Anne-Marie; Byrne, Gobnait; Quirke, Mary Brigid; Lynch, Aine; Ennis, Shauna; Bhangu, Jaspreet; Prendergast, Meabh

2017-11-01

This study aimed to evaluate the nature and type of communication and workflow arrangements between nurses and doctors out-of-hours (OOH). Effective communication and workflow arrangements between nurses and doctors are essential to minimize risk in hospital settings, particularly in the out-of-hour's period. Timely patient flow is a priority for all healthcare organizations and the quality of communication and workflow arrangements influences patient safety. Qualitative descriptive design and data collection methods included focus groups and individual interviews. A 500 bed tertiary referral acute hospital in Ireland. Junior and senior Non-Consultant Hospital Doctors, staff nurses and nurse managers. Both nurses and doctors acknowledged the importance of good interdisciplinary communication and collaborative working, in sustaining effective workflow and enabling a supportive working environment and patient safety. Indeed, issues of safety and missed care OOH were found to be primarily due to difficulties of communication and workflow. Medical workflow OOH is often dependent on cues and communication to/from nursing. However, communication systems and, in particular the bleep system, considered central to the process of communication between doctors and nurses OOH, can contribute to workflow challenges and increased staff stress. It was reported as commonplace for routine work, that should be completed during normal hours, to fall into OOH when resources were most limited, further compounding risk to patient safety. Enhancement of communication strategies between nurses and doctors has the potential to remove barriers to effective decision-making and patient flow. © The Author 2017. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Implementation of Epic Beaker Anatomic Pathology at an Academic Medical Center.

PubMed

Blau, John Larry; Wilford, Joseph D; Dane, Susan K; Karandikar, Nitin J; Fuller, Emily S; Jacobsmeier, Debbie J; Jans, Melissa A; Horning, Elisabeth A; Krasowski, Matthew D; Ford, Bradley A; Becker, Kent R; Beranek, Jeanine M; Robinson, Robert A

2017-01-01

Beaker is a relatively new laboratory information system (LIS) offered by Epic Systems Corporation as part of its suite of health-care software and bundled with its electronic medical record, EpicCare. It is divided into two modules, Beaker anatomic pathology (Beaker AP) and Beaker Clinical Pathology. In this report, we describe our experience implementing Beaker AP version 2014 at an academic medical center with a go-live date of October 2015. This report covers preimplementation preparations and challenges beginning in September 2014, issues discovered soon after go-live in October 2015, and some post go-live optimizations using data from meetings, debriefings, and the project closure document. We share specific issues that we encountered during implementation, including difficulties with the proposed frozen section workflow, developing a shared specimen source dictionary, and implementation of the standard Beaker workflow in large institution with trainees. We share specific strategies that we used to overcome these issues for a successful Beaker AP implementation. Several areas of the laboratory-required adaptation of the default Beaker build parameters to meet the needs of the workflow in a busy academic medical center. In a few areas, our laboratory was unable to use the Beaker functionality to support our workflow, and we have continued to use paper or have altered our workflow. In spite of several difficulties that required creative solutions before go-live, the implementation has been successful based on satisfaction surveys completed by pathologists and others who use the software. However, optimization of Beaker workflows has continued to be an ongoing process after go-live to the present time. The Beaker AP LIS can be successfully implemented at an academic medical center but requires significant forethought, creative adaptation, and continued shared management of the ongoing product by institutional and departmental information technology staff as well as laboratory managers to meet the needs of the laboratory.

Commercial applications for optical data storage

NASA Astrophysics Data System (ADS)

Tas, Jeroen

1991-03-01

Optical data storage has spurred the market for document imaging systems. These systems are increasingly being used to electronically manage the processing, storage and retrieval of documents. Applications range from straightforward archives to sophisticated workflow management systems. The technology is developing rapidly and within a few years optical imaging facilities will be incorporated in most of the office information systems. This paper gives an overview of the status of the market, the applications and the trends of optical imaging systems.

Science Gateways, Scientific Workflows and Open Community Software

NASA Astrophysics Data System (ADS)

Pierce, M. E.; Marru, S.

2014-12-01

Science gateways and scientific workflows occupy different ends of the spectrum of user-focused cyberinfrastructure. Gateways, sometimes called science portals, provide a way for enabling large numbers of users to take advantage of advanced computing resources (supercomputers, advanced storage systems, science clouds) by providing Web and desktop interfaces and supporting services. Scientific workflows, at the other end of the spectrum, support advanced usage of cyberinfrastructure that enable "power users" to undertake computational experiments that are not easily done through the usual mechanisms (managing simulations across multiple sites, for example). Despite these different target communities, gateways and workflows share many similarities and can potentially be accommodated by the same software system. For example, pipelines to process InSAR imagery sets or to datamine GPS time series data are workflows. The results and the ability to make downstream products may be made available through a gateway, and power users may want to provide their own custom pipelines. In this abstract, we discuss our efforts to build an open source software system, Apache Airavata, that can accommodate both gateway and workflow use cases. Our approach is general, and we have applied the software to problems in a number of scientific domains. In this talk, we discuss our applications to usage scenarios specific to earth science, focusing on earthquake physics examples drawn from the QuakSim.org and GeoGateway.org efforts. We also examine the role of the Apache Software Foundation's open community model as a way to build up common commmunity codes that do not depend upon a single "owner" to sustain. Pushing beyond open source software, we also see the need to provide gateways and workflow systems as cloud services. These services centralize operations, provide well-defined programming interfaces, scale elastically, and have global-scale fault tolerance. We discuss our work providing Apache Airavata as a hosted service to provide these features.

Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support.

PubMed

Abouelhoda, Mohamed; Issa, Shadi Alaa; Ghanem, Moustafa

2012-05-04

Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis.The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.

A Tool Supporting Collaborative Data Analytics Workflow Design and Management

NASA Astrophysics Data System (ADS)

Zhang, J.; Bao, Q.; Lee, T. J.

2016-12-01

Collaborative experiment design could significantly enhance the sharing and adoption of the data analytics algorithms and models emerged in Earth science. Existing data-oriented workflow tools, however, are not suitable to support collaborative design of such a workflow, to name a few, to support real-time co-design; to track how a workflow evolves over time based on changing designs contributed by multiple Earth scientists; and to capture and retrieve collaboration knowledge on workflow design (discussions that lead to a design). To address the aforementioned challenges, we have designed and developed a technique supporting collaborative data-oriented workflow composition and management, as a key component toward supporting big data collaboration through the Internet. Reproducibility and scalability are two major targets demanding fundamental infrastructural support. One outcome of the project os a software tool, supporting an elastic number of groups of Earth scientists to collaboratively design and compose data analytics workflows through the Internet. Instead of recreating the wheel, we have extended an existing workflow tool VisTrails into an online collaborative environment as a proof of concept.

Metadata Management on the SCEC PetaSHA Project: Helping Users Describe, Discover, Understand, and Use Simulation Data in a Large-Scale Scientific Collaboration

NASA Astrophysics Data System (ADS)

Okaya, D.; Deelman, E.; Maechling, P.; Wong-Barnum, M.; Jordan, T. H.; Meyers, D.

2007-12-01

Large scientific collaborations, such as the SCEC Petascale Cyberfacility for Physics-based Seismic Hazard Analysis (PetaSHA) Project, involve interactions between many scientists who exchange ideas and research results. These groups must organize, manage, and make accessible their community materials of observational data, derivative (research) results, computational products, and community software. The integration of scientific workflows as a paradigm to solve complex computations provides advantages of efficiency, reliability, repeatability, choices, and ease of use. The underlying resource needed for a scientific workflow to function and create discoverable and exchangeable products is the construction, tracking, and preservation of metadata. In the scientific workflow environment there is a two-tier structure of metadata. Workflow-level metadata and provenance describe operational steps, identity of resources, execution status, and product locations and names. Domain-level metadata essentially define the scientific meaning of data, codes and products. To a large degree the metadata at these two levels are separate. However, between these two levels is a subset of metadata produced at one level but is needed by the other. This crossover metadata suggests that some commonality in metadata handling is needed. SCEC researchers are collaborating with computer scientists at SDSC, the USC Information Sciences Institute, and Carnegie Mellon Univ. in order to perform earthquake science using high-performance computational resources. A primary objective of the "PetaSHA" collaboration is to perform physics-based estimations of strong ground motion associated with real and hypothetical earthquakes located within Southern California. Construction of 3D earth models, earthquake representations, and numerical simulation of seismic waves are key components of these estimations. Scientific workflows are used to orchestrate the sequences of scientific tasks and to access distributed computational facilities such as the NSF TeraGrid. Different types of metadata are produced and captured within the scientific workflows. One workflow within PetaSHA ("Earthworks") performs a linear sequence of tasks with workflow and seismological metadata preserved. Downstream scientific codes ingest these metadata produced by upstream codes. The seismological metadata uses attribute-value pairing in plain text; an identified need is to use more advanced handling methods. Another workflow system within PetaSHA ("Cybershake") involves several complex workflows in order to perform statistical analysis of ground shaking due to thousands of hypothetical but plausible earthquakes. Metadata management has been challenging due to its construction around a number of legacy scientific codes. We describe difficulties arising in the scientific workflow due to the lack of this metadata and suggest corrective steps, which in some cases include the cultural shift of domain science programmers coding for metadata.

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

PubMed Central

Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

2014-01-01

Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. PMID:24462600

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.

PubMed

Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

2014-06-01

Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. Copyright © 2014 Elsevier Inc. All rights reserved.

[Quality management and strategic consequences of assessing documentation and coding under the German Diagnostic Related Groups system].

PubMed

Schnabel, M; Mann, D; Efe, T; Schrappe, M; V Garrel, T; Gotzen, L; Schaeg, M

2004-10-01

The introduction of the German Diagnostic Related Groups (D-DRG) system requires redesigning administrative patient management strategies. Wrong coding leads to inaccurate grouping and endangers the reimbursement of treatment costs. This situation emphasizes the roles of documentation and coding as factors of economical success. The aims of this study were to assess the quantity and quality of initial documentation and coding (ICD-10 and OPS-301) and find operative strategies to improve efficiency and strategic means to ensure optimal documentation and coding quality. In a prospective study, documentation and coding quality were evaluated in a standardized way by weekly assessment. Clinical data from 1385 inpatients were processed for initial correctness and quality of documentation and coding. Principal diagnoses were found to be accurate in 82.7% of cases, inexact in 7.1%, and wrong in 10.1%. Effects on financial returns occurred in 16%. Based on these findings, an optimized, interdisciplinary, and multiprofessional workflow on medical documentation, coding, and data control was developed. Workflow incorporating regular assessment of documentation and coding quality is required by the DRG system to ensure efficient accounting of hospital services. Interdisciplinary and multiprofessional cooperation is recognized to be an important factor in establishing an efficient workflow in medical documentation and coding.

NG6: Integrated next generation sequencing storage and processing environment.

PubMed

Mariette, Jérôme; Escudié, Frédéric; Allias, Nicolas; Salin, Gérald; Noirot, Céline; Thomas, Sylvain; Klopp, Christophe

2012-09-09

Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads. We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,…) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine. NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data.

Workflow Challenges of Enterprise Imaging: HIMSS-SIIM Collaborative White Paper.

PubMed

Towbin, Alexander J; Roth, Christopher J; Bronkalla, Mark; Cram, Dawn

2016-10-01

With the advent of digital cameras, there has been an explosion in the number of medical specialties using images to diagnose or document disease and guide interventions. In many specialties, these images are not added to the patient's electronic medical record and are not distributed so that other providers caring for the patient can view them. As hospitals begin to develop enterprise imaging strategies, they have found that there are multiple challenges preventing the implementation of systems to manage image capture, image upload, and image management. This HIMSS-SIIM white paper will describe the key workflow challenges related to enterprise imaging and offer suggestions for potential solutions to these challenges.

Problem Management Module: An Innovative System to Improve Problem List Workflow

PubMed Central

Hodge, Chad M.; Kuttler, Kathryn G.; Bowes, Watson A.; Narus, Scott P.

2014-01-01

Electronic problem lists are essential to modern health record systems, with a primary goal to serve as the repository of a patient’s current health issues. Additionally, coded problems can be used to drive downstream activities such as decision support, evidence-based medicine, billing, and cohort generation for research. Meaningful Use also requires use of a coded problem list. Over the course of three years, Intermountain Healthcare developed a problem management module (PMM) that provided innovative functionality to improve clinical workflow and boost problem list adoption, e.g. smart search, user customizable views, problem evolution, and problem timelines. In 23 months of clinical use, clinicians entered over 70,000 health issues, the percentage of free-text items dropped to 1.2%, completeness of problem list items increased by 14%, and more collaborative habits were initiated. PMID:25954372

Towards a Unified Architecture for Data-Intensive Seismology in VERCE

NASA Astrophysics Data System (ADS)

Klampanos, I.; Spinuso, A.; Trani, L.; Krause, A.; Garcia, C. R.; Atkinson, M.

2013-12-01

Modern seismology involves managing, storing and processing large datasets, typically geographically distributed across organisations. Performing computational experiments using these data generates more data, which in turn have to be managed, further analysed and frequently be made available within or outside the scientific community. As part of the EU-funded project VERCE (http://verce.eu), we research and develop a number of use-cases, interfacing technologies to satisfy the data-intensive requirements of modern seismology. Our solution seeks to support: (1) familiar programming environments to develop and execute experiments, in particular via Python/ObsPy, (2) a unified view of heterogeneous computing resources, public or private, through the adoption of workflows, (3) monitoring the experiments and validating the data products at varying granularities, via a comprehensive provenance system, (4) reproducibility of experiments and consistency in collaboration, via a shared registry of processing units and contextual metadata (computing resources, data, etc.) Here, we provide a brief account of these components and their roles in the proposed architecture. Our design integrates heterogeneous distributed systems, while allowing researchers to retain current practices and control data handling and execution via higher-level abstractions. At the core of our solution lies the workflow language Dispel. While Dispel can be used to express workflows at fine detail, it may also be used as part of meta- or job-submission workflows. User interaction can be provided through a visual editor or through custom applications on top of parameterisable workflows, which is the approach VERCE follows. According to our design, the scientist may use versions of Dispel/workflow processing elements offered by the VERCE library or override them introducing custom scientific code, using ObsPy. This approach has the advantage that, while the scientist uses a familiar tool, the resulting workflow can be executed on a number of underlying stream-processing engines, such as STORM or OGSA-DAI, transparently. While making efficient use of arbitrarily distributed resources and large data-sets is of priority, such processing requires adequate provenance tracking and monitoring. Hiding computation and orchestration details via a workflow system, allows us to embed provenance harvesting where appropriate without impeding the user's regular working patterns. Our provenance model is based on the W3C PROV standard and can provide information of varying granularity regarding execution, systems and data consumption/production. A video demonstrating a prototype provenance exploration tool can be found at http://bit.ly/15t0Fz0. Keeping experimental methodology and results open and accessible, as well as encouraging reproducibility and collaboration, is of central importance to modern science. As our users are expected to be based at different geographical locations, to have access to different computing resources and to employ customised scientific codes, the use of a shared registry of workflow components, implementations, data and computing resources is critical.

DEWEY: the DICOM-enabled workflow engine system.

PubMed

Erickson, Bradley J; Langer, Steve G; Blezek, Daniel J; Ryan, William J; French, Todd L

2014-06-01

Workflow is a widely used term to describe the sequence of steps to accomplish a task. The use of workflow technology in medicine and medical imaging in particular is limited. In this article, we describe the application of a workflow engine to improve workflow in a radiology department. We implemented a DICOM-enabled workflow engine system in our department. We designed it in a way to allow for scalability, reliability, and flexibility. We implemented several workflows, including one that replaced an existing manual workflow and measured the number of examinations prepared in time without and with the workflow system. The system significantly increased the number of examinations prepared in time for clinical review compared to human effort. It also met the design goals defined at its outset. Workflow engines appear to have value as ways to efficiently assure that complex workflows are completed in a timely fashion.

MO-D-213-01: Workflow Monitoring for a High Volume Radiation Oncology Center

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laub, S; Dunn, M; Galbreath, G

2015-06-15

Purpose: Implement a center wide communication system that increases interdepartmental transparency and accountability while decreasing redundant work and treatment delays by actively monitoring treatment planning workflow. Methods: Intake Management System (IMS), a program developed by ProCure Treatment Centers Inc., is a multi-function database that stores treatment planning process information. It was devised to work with the oncology information system (Mosaiq) to streamline interdepartmental workflow.Each step in the treatment planning process is visually represented and timelines for completion of individual tasks are established within the software. The currently active step of each patient’s planning process is highlighted either red or greenmore » according to whether the initially allocated amount of time has passed for the given process. This information is displayed as a Treatment Planning Process Monitor (TPPM), which is shown on screens in the relevant departments throughout the center. This display also includes the individuals who are responsible for each task.IMS is driven by Mosaiq’s quality checklist (QCL) functionality. Each step in the workflow is initiated by a Mosaiq user sending the responsible party a QCL assignment. IMS is connected to Mosaiq and the sending or completing of a QCL updates the associated field in the TPPM to the appropriate status. Results: Approximately one patient a week is identified during the workflow process as needing to have his/her treatment start date modified or resources re-allocated to address the most urgent cases. Being able to identify a realistic timeline for planning each patient and having multiple departments communicate their limitations and time constraints allows for quality plans to be developed and implemented without overburdening any one department. Conclusion: Monitoring the progression of the treatment planning process has increased transparency between departments, which enables efficient communication. Having built-in timelines allows easy prioritization of tasks and resources and facilitates effective time management.« less

Laboratory Information Systems Management and Operations.

PubMed

Cucoranu, Ioan C

2015-06-01

The main mission of a laboratory information system (LIS) is to manage workflow and deliver accurate results for clinical management. Successful selection and implementation of an anatomic pathology LIS is not complete unless it is complemented by specialized information technology support and maintenance. LIS is required to remain continuously operational with minimal or no downtime and the LIS team has to ensure that all operations are compliant with the mandated rules and regulations. Copyright © 2015 Elsevier Inc. All rights reserved.

Designing an architectural style for dynamic medical Cross-Organizational Workflow management system: an approach based on agents and web services.

PubMed

Bouzguenda, Lotfi; Turki, Manel

2014-04-01

This paper shows how the combined use of agent and web services technologies can help to design an architectural style for dynamic medical Cross-Organizational Workflow (COW) management system. Medical COW aims at supporting the collaboration between several autonomous and possibly heterogeneous medical processes, distributed over different organizations (Hospitals, Clinic or laboratories). Dynamic medical COW refers to occasional cooperation between these health organizations, free of structural constraints, where the medical partners involved and their number are not pre-defined. More precisely, this paper proposes a new architecture style based on agents and web services technologies to deal with two key coordination issues of dynamic COW: medical partners finding and negotiation between them. It also proposes how the proposed architecture for dynamic medical COW management system can connect to a multi-agent system coupling the Clinical Decision Support System (CDSS) with Computerized Prescriber Order Entry (CPOE). The idea is to assist the health professionals such as doctors, nurses and pharmacists with decision making tasks, as determining diagnosis or patient data analysis without stopping their clinical processes in order to act in a coherent way and to give care to the patient.

Quality Metadata Management for Geospatial Scientific Workflows: from Retrieving to Assessing with Online Tools

NASA Astrophysics Data System (ADS)

Leibovici, D. G.; Pourabdollah, A.; Jackson, M.

2011-12-01

Experts and decision-makers use or develop models to monitor global and local changes of the environment. Their activities require the combination of data and processing services in a flow of operations and spatial data computations: a geospatial scientific workflow. The seamless ability to generate, re-use and modify a geospatial scientific workflow is an important requirement but the quality of outcomes is equally much important [1]. Metadata information attached to the data and processes, and particularly their quality, is essential to assess the reliability of the scientific model that represents a workflow [2]. Managing tools, dealing with qualitative and quantitative metadata measures of the quality associated with a workflow, are, therefore, required for the modellers. To ensure interoperability, ISO and OGC standards [3] are to be adopted, allowing for example one to define metadata profiles and to retrieve them via web service interfaces. However these standards need a few extensions when looking at workflows, particularly in the context of geoprocesses metadata. We propose to fill this gap (i) at first through the provision of a metadata profile for the quality of processes, and (ii) through providing a framework, based on XPDL [4], to manage the quality information. Web Processing Services are used to implement a range of metadata analyses on the workflow in order to evaluate and present quality information at different levels of the workflow. This generates the metadata quality, stored in the XPDL file. The focus is (a) on the visual representations of the quality, summarizing the retrieved quality information either from the standardized metadata profiles of the components or from non-standard quality information e.g., Web 2.0 information, and (b) on the estimated qualities of the outputs derived from meta-propagation of uncertainties (a principle that we have introduced [5]). An a priori validation of the future decision-making supported by the outputs of the workflow once run, is then provided using the meta-propagated qualities, obtained without running the workflow [6], together with the visualization pointing out the need to improve the workflow with better data or better processes on the workflow graph itself. [1] Leibovici, DG, Hobona, G Stock, K Jackson, M (2009) Qualifying geospatial workfow models for adaptive controlled validity and accuracy. In: IEEE 17th GeoInformatics, 1-5 [2] Leibovici, DG, Pourabdollah, A (2010a) Workflow Uncertainty using a Metamodel Framework and Metadata for Data and Processes. OGC TC/PC Meetings, September 2010, Toulouse, France [3] OGC (2011) www.opengeospatial.org [4] XPDL (2008) Workflow Process Definition Interface - XML Process Definition Language.Workflow Management Coalition, Document WfMC-TC-1025, 2008 [5] Leibovici, DG Pourabdollah, A Jackson, M (2011) Meta-propagation of Uncertainties for Scientific Workflow Management in Interoperable Spatial Data Infrastructures. In: Proceedings of the European Geosciences Union (EGU2011), April 2011, Austria [6] Pourabdollah, A Leibovici, DG Jackson, M (2011) MetaPunT: an Open Source tool for Meta-Propagation of uncerTainties in Geospatial Processing. In: Proceedings of OSGIS2011, June 2011, Nottingham, UK

Horizon: The Portable, Scalable, and Reusable Framework for Developing Automated Data Management and Product Generation Systems

NASA Astrophysics Data System (ADS)

Huang, T.; Alarcon, C.; Quach, N. T.

2014-12-01

Capture, curate, and analysis are the typical activities performed at any given Earth Science data center. Modern data management systems must be adaptable to heterogeneous science data formats, scalable to meet the mission's quality of service requirements, and able to manage the life-cycle of any given science data product. Designing a scalable data management doesn't happen overnight. It takes countless hours of refining, refactoring, retesting, and re-architecting. The Horizon data management and workflow framework, developed at the Jet Propulsion Laboratory, is a portable, scalable, and reusable framework for developing high-performance data management and product generation workflow systems to automate data capturing, data curation, and data analysis activities. The NASA's Physical Oceanography Distributed Active Archive Center (PO.DAAC)'s Data Management and Archive System (DMAS) is its core data infrastructure that handles capturing and distribution of hundreds of thousands of satellite observations each day around the clock. DMAS is an application of the Horizon framework. The NASA Global Imagery Browse Services (GIBS) is NASA's Earth Observing System Data and Information System (EOSDIS)'s solution for making high-resolution global imageries available to the science communities. The Imagery Exchange (TIE), an application of the Horizon framework, is a core subsystem for GIBS responsible for data capturing and imagery generation automation to support the EOSDIS' 12 distributed active archive centers and 17 Science Investigator-led Processing Systems (SIPS). This presentation discusses our ongoing effort in refining, refactoring, retesting, and re-architecting the Horizon framework to enable data-intensive science and its applications.

Targeting safety improvements through identification of incident origination and detection in a near-miss incident learning system.

PubMed

Novak, Avrey; Nyflot, Matthew J; Ermoian, Ralph P; Jordan, Loucille E; Sponseller, Patricia A; Kane, Gabrielle M; Ford, Eric C; Zeng, Jing

2016-05-01

Radiation treatment planning involves a complex workflow that has multiple potential points of vulnerability. This study utilizes an incident reporting system to identify the origination and detection points of near-miss errors, in order to guide their departmental safety improvement efforts. Previous studies have examined where errors arise, but not where they are detected or applied a near-miss risk index (NMRI) to gauge severity. From 3/2012 to 3/2014, 1897 incidents were analyzed from a departmental incident learning system. All incidents were prospectively reviewed weekly by a multidisciplinary team and assigned a NMRI score ranging from 0 to 4 reflecting potential harm to the patient (no potential harm to potential critical harm). Incidents were classified by point of incident origination and detection based on a 103-step workflow. The individual steps were divided among nine broad workflow categories (patient assessment, imaging for radiation therapy (RT) planning, treatment planning, pretreatment plan review, treatment delivery, on-treatment quality management, post-treatment completion, equipment/software quality management, and other). The average NMRI scores of incidents originating or detected within each broad workflow area were calculated. Additionally, out of 103 individual process steps, 35 were classified as safety barriers, the process steps whose primary function is to catch errors. The safety barriers which most frequently detected incidents were identified and analyzed. Finally, the distance between event origination and detection was explored by grouping events by the number of broad workflow area events passed through before detection, and average NMRI scores were compared. Near-miss incidents most commonly originated within treatment planning (33%). However, the incidents with the highest average NMRI scores originated during imaging for RT planning (NMRI = 2.0, average NMRI of all events = 1.5), specifically during the documentation of patient positioning and localization of the patient. Incidents were most frequently detected during treatment delivery (30%), and incidents identified at this point also had higher severity scores than other workflow areas (NMRI = 1.6). Incidents identified during on-treatment quality management were also more severe (NMRI = 1.7), and the specific process steps of reviewing portal and CBCT images tended to catch highest-severity incidents. On average, safety barriers caught 46% of all incidents, most frequently at physics chart review, therapist's chart check, and the review of portal images; however, most of the incidents that pass through a particular safety barrier are not designed to be capable of being captured at that barrier. Incident learning systems can be used to assess the most common points of error origination and detection in radiation oncology. This can help tailor safety improvement efforts and target the highest impact portions of the workflow. The most severe near-miss events tend to originate during simulation, with the most severe near-miss events detected at the time of patient treatment. Safety barriers can be improved to allow earlier detection of near-miss events.

Bar Coding and Tracking in Pathology.

PubMed

Hanna, Matthew G; Pantanowitz, Liron

2016-03-01

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology. Copyright © 2016 Elsevier Inc. All rights reserved.

Bar Coding and Tracking in Pathology.

PubMed

Hanna, Matthew G; Pantanowitz, Liron

2015-06-01

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology. Copyright © 2015 Elsevier Inc. All rights reserved.

Essential attributes identified in the design of a Laboratory Information Management System for a high throughput siRNA screening laboratory.

PubMed

Grandjean, Geoffrey; Graham, Ryan; Bartholomeusz, Geoffrey

2011-11-01

In recent years high throughput screening operations have become a critical application in functional and translational research. Although a seemingly unmanageable amount of data is generated by these high-throughput, large-scale techniques, through careful planning, an effective Laboratory Information Management System (LIMS) can be developed and implemented in order to streamline all phases of a workflow. Just as important as data mining and analysis procedures at the end of complex processes is the tracking of individual steps of applications that generate such data. Ultimately, the use of a customized LIMS will enable users to extract meaningful results from large datasets while trusting the robustness of their assays. To illustrate the design of a custom LIMS, this practical example is provided to highlight the important aspects of the design of a LIMS to effectively modulate all aspects of an siRNA screening service. This system incorporates inventory management, control of workflow, data handling and interaction with investigators, statisticians and administrators. All these modules are regulated in a synchronous manner within the LIMS. © 2011 Bentham Science Publishers

Ergatis: a web interface and scalable software system for bioinformatics workflows

PubMed Central

Orvis, Joshua; Crabtree, Jonathan; Galens, Kevin; Gussman, Aaron; Inman, Jason M.; Lee, Eduardo; Nampally, Sreenath; Riley, David; Sundaram, Jaideep P.; Felix, Victor; Whitty, Brett; Mahurkar, Anup; Wortman, Jennifer; White, Owen; Angiuoli, Samuel V.

2010-01-01

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports high-throughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects. Availability: Ergatis is an open-source project and is freely available at http://ergatis.sourceforge.net Contact: jorvis@users.sourceforge.net PMID:20413634

Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

PubMed Central

2012-01-01

Background Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. Results In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Conclusions Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis. The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org. PMID:22559942

User Requirements for a Chronic Kidney Disease Clinical Decision Support Tool to Promote Timely Referral.

PubMed

Gulla, Joy; Neri, Pamela M; Bates, David W; Samal, Lipika

2017-05-01

Timely referral of patients with CKD has been associated with cost and mortality benefits, but referrals are often done too late in the course of the disease. Clinical decision support (CDS) offers a potential solution, but interventions have failed because they were not designed to support the physician workflow. We sought to identify user requirements for a chronic kidney disease (CKD) CDS system to promote timely referral. We interviewed primary care physicians (PCPs) to identify data needs for a CKD CDS system that would encourage timely referral and also gathered information about workflow to assess risk factors for progression of CKD. Interviewees were general internists recruited from a network of 14 primary care clinics affiliated with Brigham and Women's Hospital (BWH). We then performed a qualitative analysis to identify user requirements and system attributes for a CKD CDS system. Of the 12 participants, 25% were women, the mean age was 53 (range 37-82), mean years in clinical practice was 27 (range 11-58). We identified 21 user requirements. Seven of these user requirements were related to support for the referral process workflow, including access to pertinent information and support for longitudinal co-management. Six user requirements were relevant to PCP management of CKD, including management of risk factors for progression, interpretation of biomarkers of CKD severity, and diagnosis of the cause of CKD. Finally, eight user requirements addressed user-centered design of CDS, including the need for actionable information, links to guidelines and reference materials, and visualization of trends. These 21 user requirements can be used to design an intuitive and usable CDS system with the attributes necessary to promote timely referral. Copyright © 2017 Elsevier B.V. All rights reserved.

The Ophidia Stack: Toward Large Scale, Big Data Analytics Experiments for Climate Change

NASA Astrophysics Data System (ADS)

Fiore, S.; Williams, D. N.; D'Anca, A.; Nassisi, P.; Aloisio, G.

2015-12-01

The Ophidia project is a research effort on big data analytics facing scientific data analysis challenges in multiple domains (e.g. climate change). It provides a "datacube-oriented" framework responsible for atomically processing and manipulating scientific datasets, by providing a common way to run distributive tasks on large set of data fragments (chunks). Ophidia provides declarative, server-side, and parallel data analysis, jointly with an internal storage model able to efficiently deal with multidimensional data and a hierarchical data organization to manage large data volumes. The project relies on a strong background on high performance database management and On-Line Analytical Processing (OLAP) systems to manage large scientific datasets. The Ophidia analytics platform provides several data operators to manipulate datacubes (about 50), and array-based primitives (more than 100) to perform data analysis on large scientific data arrays. To address interoperability, Ophidia provides multiple server interfaces (e.g. OGC-WPS). From a client standpoint, a Python interface enables the exploitation of the framework into Python-based eco-systems/applications (e.g. IPython) and the straightforward adoption of a strong set of related libraries (e.g. SciPy, NumPy). The talk will highlight a key feature of the Ophidia framework stack: the "Analytics Workflow Management System" (AWfMS). The Ophidia AWfMS coordinates, orchestrates, optimises and monitors the execution of multiple scientific data analytics and visualization tasks, thus supporting "complex analytics experiments". Some real use cases related to the CMIP5 experiment will be discussed. In particular, with regard to the "Climate models intercomparison data analysis" case study proposed in the EU H2020 INDIGO-DataCloud project, workflows related to (i) anomalies, (ii) trend, and (iii) climate change signal analysis will be presented. Such workflows will be distributed across multiple sites - according to the datasets distribution - and will include intercomparison, ensemble, and outlier analysis. The two-level workflow solution envisioned in INDIGO (coarse grain for distributed tasks orchestration, and fine grain, at the level of a single data analytics cluster instance) will be presented and discussed.

Design of a decision-support architecture for management of remotely monitored patients.

PubMed

Basilakis, Jim; Lovell, Nigel H; Redmond, Stephen J; Celler, Branko G

2010-09-01

Telehealth is the provision of health services at a distance. Typically, this occurs in unsupervised or remote environments, such as a patient's home. We describe one such telehealth system and the integration of extracted clinical measurement parameters with a decision-support system (DSS). An enterprise application-server framework, combined with a rules engine and statistical analysis tools, is used to analyze the acquired telehealth data, searching for trends and shifts in parameter values, as well as identifying individual measurements that exceed predetermined or adaptive thresholds. An overarching business process engine is used to manage the core DSS knowledge base and coordinate workflow outputs of the DSS. The primary role for such a DSS is to provide an effective means to reduce the data overload and to provide a means of health risk stratification to allow appropriate targeting of clinical resources to best manage the health of the patient. In this way, the system may ultimately influence changes in workflow by targeting scarce clinical resources to patients of most need. A single case study extracted from an initial pilot trial of the system, in patients with chronic obstructive pulmonary disease and chronic heart failure, will be reviewed to illustrate the potential benefit of integrating telehealth and decision support in the management of both acute and chronic disease.

Architecture of next-generation information management systems for digital radiology enterprises

NASA Astrophysics Data System (ADS)

Wong, Stephen T. C.; Wang, Huili; Shen, Weimin; Schmidt, Joachim; Chen, George; Dolan, Tom

2000-05-01

Few information systems today offer a clear and flexible means to define and manage the automated part of radiology processes. None of them provide a coherent and scalable architecture that can easily cope with heterogeneity and inevitable local adaptation of applications. Most importantly, they often lack a model that can integrate clinical and administrative information to aid better decisions in managing resources, optimizing operations, and improving productivity. Digital radiology enterprises require cost-effective solutions to deliver information to the right person in the right place and at the right time. We propose a new architecture of image information management systems for digital radiology enterprises. Such a system is based on the emerging technologies in workflow management, distributed object computing, and Java and Web techniques, as well as Philips' domain knowledge in radiology operations. Our design adapts the approach of '4+1' architectural view. In this new architecture, PACS and RIS will become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, it will provide powerful query and statistical functions for managing resources and improving productivity in real time. This work will lead to a new direction of image information management in the next millennium. We will illustrate the innovative design with implemented examples of a working prototype.

Pervasive access to images and data--the use of computing grids and mobile/wireless devices across healthcare enterprises.

PubMed

Pohjonen, Hanna; Ross, Peeter; Blickman, Johan G; Kamman, Richard

2007-01-01

Emerging technologies are transforming the workflows in healthcare enterprises. Computing grids and handheld mobile/wireless devices are providing clinicians with enterprise-wide access to all patient data and analysis tools on a pervasive basis. In this paper, emerging technologies are presented that provide computing grids and streaming-based access to image and data management functions, and system architectures that enable pervasive computing on a cost-effective basis. Finally, the implications of such technologies are investigated regarding the positive impacts on clinical workflows.

Managing healthcare information using short message service (SMS) in wireless broadband networks

NASA Astrophysics Data System (ADS)

Documet, Jorge; Tsao, Sinchai; Documet, Luis; Liu, Brent J.; Zhou, Zheng; Joseph, Anika O.

2007-03-01

Due to the ubiquity of cell phones, SMS (Short Message Service) has become an ideal means to wirelessly manage a Healthcare environment and in particular PACS (Picture Archival and Communications System) data. SMS is a flexible and mobile method for real-time access and control of Healthcare information systems such as HIS (Hospital Information System) or PACS. Unlike conventional wireless access methods, SMS' mobility is not limited by the presence of a WiFi network or any other localized signal. It provides a simple, reliable yet flexible method to communicate with an information system. In addition, SMS services are widely available for low costs from cellular phone service providers and allows for more mobility than other services such as wireless internet. This paper aims to describe a use case of SMS as a means of remotely communicating with a PACS server. Remote access to a PACS server and its Query-Retrieve services allows for a more convenient, flexible and streamlined radiology workflow. Wireless access methods such as SMS will increase dedicated PACS workstation availability for more specialized DICOM (Digital Imaging and Communications in Medicine) workflow management. This implementation will address potential security, performance and cost issues of applying SMS as part of a healthcare information management system. This is in an effort to design a wireless communication system with optimal mobility and flexibility at minimum material and time costs.

It's All About the Data: Workflow Systems and Weather

NASA Astrophysics Data System (ADS)

Plale, B.

2009-05-01

Digital data is fueling new advances in the computational sciences, particularly geospatial research as environmental sensing grows more practical through reduced technology costs, broader network coverage, and better instruments. e-Science research (i.e., cyberinfrastructure research) has responded to data intensive computing with tools, systems, and frameworks that support computationally oriented activities such as modeling, analysis, and data mining. Workflow systems support execution of sequences of tasks on behalf of a scientist. These systems, such as Taverna, Apache ODE, and Kepler, when built as part of a larger cyberinfrastructure framework, give the scientist tools to construct task graphs of execution sequences, often through a visual interface for connecting task boxes together with arcs representing control flow or data flow. Unlike business processing workflows, scientific workflows expose a high degree of detail and control during configuration and execution. Data-driven science imposes unique needs on workflow frameworks. Our research is focused on two issues. The first is the support for workflow-driven analysis over all kinds of data sets, including real time streaming data and locally owned and hosted data. The second is the essential role metadata/provenance collection plays in data driven science, for discovery, determining quality, for science reproducibility, and for long-term preservation. The research has been conducted over the last 6 years in the context of cyberinfrastructure for mesoscale weather research carried out as part of the Linked Environments for Atmospheric Discovery (LEAD) project. LEAD has pioneered new approaches for integrating complex weather data, assimilation, modeling, mining, and cyberinfrastructure systems. Workflow systems have the potential to generate huge volumes of data. Without some form of automated metadata capture, either metadata description becomes largely a manual task that is difficult if not impossible under high-volume conditions, or the searchability and manageability of the resulting data products is disappointingly low. The provenance of a data product is a record of its lineage, or trace of the execution history that resulted in the product. The provenance of a forecast model result, e.g., captures information about the executable version of the model, configuration parameters, input data products, execution environment, and owner. Provenance enables data to be properly attributed and captures critical parameters about the model run so the quality of the result can be ascertained. Proper provenance is essential to providing reproducible scientific computing results. Workflow languages used in science discovery are complete programming languages, and in theory can support any logic expressible by a programming language. The execution environments supporting the workflow engines, on the other hand, are subject to constraints on physical resources, and hence in practice the workflow task graphs used in science utilize relatively few of the cataloged workflow patterns. It is important to note that these workflows are executed on demand, and are executed once. Into this context is introduced the need for science discovery that is responsive to real time information. If we can use simple programming models and abstractions to make scientific discovery involving real-time data accessible to specialists who share and utilize data across scientific domains, we bring science one step closer to solving the largest of human problems.

Wireless-PDA-controlled image workflow from PACS: the next trend in the health care enterprise?

NASA Astrophysics Data System (ADS)

Erberich, Stephan G.; Documet, Jorge; Zhou, Michael Z.; Cao, Fei; Liu, Brent J.; Mogel, Greg T.; Huang, H. K.

2003-05-01

Image workflow in today's Picture Archiving and Communication Systems (PACS) is controlled from fixed Display Workstations (DW) using proprietary control interfaces. A remote access to the Hospital Information System (HIS) and Radiology Information System (RIS) for urgent patient information retrieval does not exist or gradually become available. The lack for remote access and workflow control for HIS and RIS is especially true when it comes to medical images of a PACS on Department or Hospital level. As images become more complex and data sizes expand rapidly with new image techniques like functional MRI, Mammography or routine spiral CT to name a few, the access and manageability becomes an important issue. Long image downloads or incomplete work lists cannot be tolerated in a busy health care environment. In addition, the domain of the PACS is no longer limited to the imaging department and PACS is also being used in the ER and emergency care units. Thus a prompt and secure access and manageability not only by the radiologist, but also from the physician becomes crucial to optimally utilize the PACS in the health care enterprise of the new millennium. The purpose of this paper is to introduce a concept and its implementation of a remote access and workflow control of the PACS combining wireless, Internet and Internet2 technologies. A wireless device, the Personal Digital Assistant (PDA), is used to communicate to a PACS web server that acts as a gateway controlling the commands for which the user has access to the PACS server. The commands implemented for this test-bed are query/retrieve of the patient list and study list including modality, examination, series and image selection and pushing any list items to a selected DW on the PACS network.

Curriculum Online Review System: Proposing Curriculum with Collaboration

ERIC Educational Resources Information Center

Rhinehart, Marilyn; Barlow, Rhonda; Shafer, Stu; Hassur, Debby

2009-01-01

The Curriculum Online Review System (CORS) at Johnson County Community College (JCCC) uses SharePoint as a Web platform for the JCCC Curriculum Proposals Process. The CORS application manages proposals throughout the approval process using collaboration tools and workflows to notify all stakeholders. This innovative new program has changed the way…

Routine Digital Pathology Workflow: The Catania Experience

PubMed Central

Fraggetta, Filippo; Garozzo, Salvatore; Zannoni, Gian Franco; Pantanowitz, Liron; Rossi, Esther Diana

2017-01-01

Introduction: Successful implementation of whole slide imaging (WSI) for routine clinical practice has been accomplished in only a few pathology laboratories worldwide. We report the transition to an effective and complete digital surgical pathology workflow in the pathology laboratory at Cannizzaro Hospital in Catania, Italy. Methods: All (100%) permanent histopathology glass slides were digitized at ×20 using Aperio AT2 scanners. Compatible stain and scanning slide racks were employed to streamline operations. eSlide Manager software was bidirectionally interfaced with the anatomic pathology laboratory information system. Virtual slide trays connected to the two-dimensional (2D) barcode tracking system allowed pathologists to confirm that they were correctly assigned slides and that all tissues on these glass slides were scanned. Results: Over 115,000 glass slides were digitized with a scan fail rate of around 1%. Drying glass slides before scanning minimized them sticking to scanner racks. Implementation required introduction of a 2D barcode tracking system and modification of histology workflow processes. Conclusion: Our experience indicates that effective adoption of WSI for primary diagnostic use was more dependent on optimizing preimaging variables and integration with the laboratory information system than on information technology infrastructure and ensuring pathologist buy-in. Implementation of digital pathology for routine practice not only leveraged the benefits of digital imaging but also creates an opportunity for establishing standardization of workflow processes in the pathology laboratory. PMID:29416914

Routine Digital Pathology Workflow: The Catania Experience.

PubMed

Fraggetta, Filippo; Garozzo, Salvatore; Zannoni, Gian Franco; Pantanowitz, Liron; Rossi, Esther Diana

2017-01-01

Successful implementation of whole slide imaging (WSI) for routine clinical practice has been accomplished in only a few pathology laboratories worldwide. We report the transition to an effective and complete digital surgical pathology workflow in the pathology laboratory at Cannizzaro Hospital in Catania, Italy. All (100%) permanent histopathology glass slides were digitized at ×20 using Aperio AT2 scanners. Compatible stain and scanning slide racks were employed to streamline operations. eSlide Manager software was bidirectionally interfaced with the anatomic pathology laboratory information system. Virtual slide trays connected to the two-dimensional (2D) barcode tracking system allowed pathologists to confirm that they were correctly assigned slides and that all tissues on these glass slides were scanned. Over 115,000 glass slides were digitized with a scan fail rate of around 1%. Drying glass slides before scanning minimized them sticking to scanner racks. Implementation required introduction of a 2D barcode tracking system and modification of histology workflow processes. Our experience indicates that effective adoption of WSI for primary diagnostic use was more dependent on optimizing preimaging variables and integration with the laboratory information system than on information technology infrastructure and ensuring pathologist buy-in. Implementation of digital pathology for routine practice not only leveraged the benefits of digital imaging but also creates an opportunity for establishing standardization of workflow processes in the pathology laboratory.

Automatic system testing of a decision support system for insulin dosing using Google Android.

PubMed

Spat, Stephan; Höll, Bernhard; Petritsch, Georg; Schaupp, Lukas; Beck, Peter; Pieber, Thomas R

2013-01-01

Hyperglycaemia in hospitalized patients is a common and costly health care problem. The GlucoTab system is a mobile workflow and decision support system, aiming to facilitate efficient and safe glycemic control of non-critically ill patients. Being a medical device, the GlucoTab requires extensive and reproducible testing. A framework for high-volume, reproducible and automated system testing of the GlucoTab system was set up applying several Open Source tools for test automation and system time handling. The REACTION insulin titration protocol was investigated in a paper-based clinical trial (PBCT). In order to validate the GlucoTab system, data from this trial was used for simulation and system tests. In total, 1190 decision support action points were identified and simulated. Four data points (0.3%) resulted in a GlucoTab system error caused by a defective implementation. In 144 data points (12.1%), calculation errors of physicians and nurses in the PBCT were detected. The test framework was able to verify manual calculation of insulin doses and detect relatively many user errors and workflow anomalies in the PBCT data. This shows the high potential of the electronic decision support application to improve safety of implementation of an insulin titration protocol and workflow management system in clinical wards.

Pathology economic model tool: a novel approach to workflow and budget cost analysis in an anatomic pathology laboratory.

PubMed

Muirhead, David; Aoun, Patricia; Powell, Michael; Juncker, Flemming; Mollerup, Jens

2010-08-01

The need for higher efficiency, maximum quality, and faster turnaround time is a continuous focus for anatomic pathology laboratories and drives changes in work scheduling, instrumentation, and management control systems. To determine the costs of generating routine, special, and immunohistochemical microscopic slides in a large, academic anatomic pathology laboratory using a top-down approach. The Pathology Economic Model Tool was used to analyze workflow processes at The Nebraska Medical Center's anatomic pathology laboratory. Data from the analysis were used to generate complete cost estimates, which included not only materials, consumables, and instrumentation but also specific labor and overhead components for each of the laboratory's subareas. The cost data generated by the Pathology Economic Model Tool were compared with the cost estimates generated using relative value units. Despite the use of automated systems for different processes, the workflow in the laboratory was found to be relatively labor intensive. The effect of labor and overhead on per-slide costs was significantly underestimated by traditional relative-value unit calculations when compared with the Pathology Economic Model Tool. Specific workflow defects with significant contributions to the cost per slide were identified. The cost of providing routine, special, and immunohistochemical slides may be significantly underestimated by traditional methods that rely on relative value units. Furthermore, a comprehensive analysis may identify specific workflow processes requiring improvement.

wft4galaxy: a workflow testing tool for galaxy.

PubMed

Piras, Marco Enrico; Pireddu, Luca; Zanetti, Gianluigi

2017-12-01

Workflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows effectively comprise specialized computer programs implementing often very complex analysis procedures. To date, no simple way to automatically test Galaxy workflows and ensure their correctness has appeared in the literature. With wft4galaxy we offer a tool to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly. wft4galaxy can be easily installed as a regular Python program or launched directly as a Docker container-the latter reducing installation effort to a minimum. Available at https://github.com/phnmnl/wft4galaxy under the Academic Free License v3.0. marcoenrico.piras@crs4.it. © The Author 2017. Published by Oxford University Press.

SMITH: a LIMS for handling next-generation sequencing workflows

PubMed Central

2014-01-01

Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. Conclusions SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis. PMID:25471934

SMITH: a LIMS for handling next-generation sequencing workflows.

PubMed

Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

2014-01-01

Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis.

Toward a geoinformatics framework for understanding the social and biophysical influences on urban nutrient pollution due to residential impervious service connectivity

NASA Astrophysics Data System (ADS)

Miles, B.; Band, L. E.

2012-12-01

Water sustainability has been recognized as a fundamental problem of science whose solution relies in part on high-performance computing. Stormwater management is a major concern of urban sustainability. Understanding interactions between urban landcover and stormwater nutrient pollution requires consideration of fine-scale residential stormwater management, which in turn requires high-resolution LIDAR and landcover data not provided through national spatial data infrastructure, as well as field observation at the household scale. The objectives of my research are twofold: (1) advance understanding of the relationship between residential stormwater management practices and the export of nutrient pollution from stormwater in urbanized ecosystems; and (2) improve the informatics workflows used in community ecohydrology modeling as applied to heterogeneous urbanized ecosystems. In support of these objectives, I present preliminary results from initial work to: (1) develop an ecohydrology workflow platform that automates data preparation while maintaining data provenance and model metadata to yield reproducible workflows and support model benchmarking; (2) perform field observation of existing patterns of residential rooftop impervious surface connectivity to stormwater networks; and (3) develop Regional Hydro-Ecological Simulation System (RHESSys) models for watersheds in Baltimore, MD (as part of the Baltimore Ecosystem Study (BES) NSF Long-Term Ecological Research (LTER) site) and Durham, NC (as part of the NSF Urban Long-Term Research Area (ULTRA) program); these models will be used to simulate nitrogen loading resulting from both baseline residential rooftop impervious connectivity and for disconnection scenarios (e.g. roof drainage to lawn v. engineered rain garden, upslope v. riparian). This research builds on work done as part of the NSF EarthCube Layered Architecture Concept Award where a RHESSys workflow is being implemented in an iRODS (integrated Rule-Oriented Data System) environment. Modeling the ecohydrology of urban ecosystems in a reliable and reproducible manner requires a flexible scientific workflow platform that allows rapid prototyping with large-scale spatial datasets and model refinement integrating expert knowledge with local datasets and household surveys.

Several considerations with respect to the future of digital photography and photographic printing

NASA Astrophysics Data System (ADS)

Tuijn, Chris; Mahy, Marc F.

2000-12-01

Digital cameras are no longer exotic gadgets being used by a privileged group of early adopters. More and more people realize that there are obvious advantages to the digital solution over the conventional film-based workflow. Claiming that prints on paper are no longer necessary in the digit workflow, however, would be similar to reviving the myth of the paperless office. Often, people still like to share their memories on paper and this for a variety of reasons. There are still some hurdles to be taken in order to make the digital dream com true. In this paper, we will give a survey of the different workflows in digital photography. The local, semi-local and Internet solutions will be discussed as well as the preferred output systems for each of these solutions. When discussing output system, we immediately think of appropriate color management solutions. In the second part of this paper, we will discuss the major color management issues appearing in digital photography. A clear separation between the image acquisition and the image rendering phases will be made. After a quick survey of the different image restoration and enhancement techniques, we will make some reflections on the ideal color exchange space; the enhanced image should be delivered in this exchange space and, from there, the standard color management transformations can be applied to transfer the image from this exchange space to the native color space of the output device. We will also discus some color gamut characteristics and color management problems of different types of photographic printers that can occur during this conversion process.

The Kiel data management infrastructure - arising from a generic data model

NASA Astrophysics Data System (ADS)

Fleischer, D.; Mehrtens, H.; Schirnick, C.; Springer, P.

2010-12-01

The Kiel Data Management Infrastructure (KDMI) started from a cooperation of three large-scale projects (SFB574, SFB754 and Cluster of Excellence The Future Ocean) and the Leibniz Institute of Marine Sciences (IFM-GEOMAR). The common strategy for project data management is a single person collecting and transforming data according to the requirements of the targeted data center(s). The intention of the KDMI cooperation is to avoid redundant and potentially incompatible data management efforts for scientists and data managers and to create a single sustainable infrastructure. An increased level of complexity in the conceptual planing arose from the diversity of marine disciplines and approximately 1000 scientists involved. KDMI key features focus on the data provenance which we consider to comprise the entire workflow from field sampling thru labwork to data calculation and evaluation. Managing the data of each individual project participant in this way yields the data management for the entire project and warrants the reusability of (meta)data. Accordingly scientists provide a workflow definition of their data creation procedures resulting in their target variables. The central idea in the development of the KDMI presented here is based on the object oriented programming concept which allows to have one object definition (workflow) and infinite numbers of object instances (data). Each definition is created by a graphical user interface and produces XML output stored in a database using a generic data model. On creation of a data instance the KDMI translates the definition into web forms for the scientist, the generic data model then accepts all information input following the given data provenance definition. An important aspect of the implementation phase is the possibility of a successive transition from daily measurement routines resulting in single spreadsheet files with well known points of failure and limited reuseability to a central infrastructure as a single point of truth. The data provenance approach has the following positive side effects: (1) the scientist designs the extend and timing of data and metadata prompts by workflow definitions himself while (2) consistency and completeness (mandatory information) of metadata in the resulting XML document can be checked by XML validation. (3) Storage of the entire data creation process (including raw data and processing steps) provides a multidimensional quality history accessible by all researchers in addition to the commonly applied one dimensional quality flag system. (4) The KDMI can be extended to other scientific disciplines by adding new workflows and domain specific outputs assisted by the KDMI-Team. The KDMI is a social network inspired system but instead of sharing privacy it is a sharing platform for daily scientific work, data and their provenance.

Ergonomic design for dental offices.

PubMed

Ahearn, David J; Sanders, Martha J; Turcotte, Claudia

2010-01-01

The increasing complexity of the dental office environment influences productivity and workflow for dental clinicians. Advances in technology, and with it the range of products needed to provide services, have led to sprawl in operatory setups and the potential for awkward postures for dental clinicians during the delivery of oral health services. Although ergonomics often addresses the prevention of musculoskeletal disorders for specific populations of workers, concepts of workflow and productivity are integral to improved practice in work environments. This article provides suggestions for improving workflow and productivity for dental clinicians. The article applies ergonomic principles to dental practice issues such as equipment and supply management, office design, and workflow management. Implications for improved ergonomic processes and future research are explored.

Git Replacement for the

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, P.

2014-09-23

GRAPE is a tool for managing software project workflows for the Git version control system. It provides a suite of tools to simplify and configure branch based development, integration with a project's testing suite, and integration with the Atlassian Stash repository hosting tool.

The impact of using an intravenous workflow management system (IVWMS) on cost and patient safety.

PubMed

Lin, Alex C; Deng, Yihong; Thaibah, Hilal; Hingl, John; Penm, Jonathan; Ivey, Marianne F; Thomas, Mark

2018-07-01

The aim of this study was to determine the financial costs associated with wasted and missing doses before and after the implementation of an intravenous workflow management system (IVWMS) and to quantify the number and the rate of detected intravenous (IV) preparation errors. A retrospective analysis of the sample hospital information system database was conducted using three months of data before and after the implementation of an IVWMS System (DoseEdge ® ) which uses barcode scanning and photographic technologies to track and verify each step of the preparation process. The financial impact associated with wasted and missing >IV doses was determined by combining drug acquisition, labor, accessory, and disposal costs. The intercepted error reports and pharmacist detected error reports were drawn from the IVWMS to quantify the number of errors by defined error categories. The total number of IV doses prepared before and after the implementation of the IVWMS system were 110,963 and 101,765 doses, respectively. The adoption of the IVWMS significantly reduced the amount of wasted and missing IV doses by 14,176 and 2268 doses, respectively (p < 0.001). The overall cost savings of using the system was $144,019 over 3 months. The total number of errors detected was 1160 (1.14%) after using the IVWMS. The implementation of the IVWMS facilitated workflow changes that led to a positive impact on cost and patient safety. The implementation of the IVWMS increased patient safety by enforcing standard operating procedures and bar code verifications. Published by Elsevier B.V.

Using the CMS threaded framework in a production environment

DOE PAGES

Jones, C. D.; Contreras, L.; Gartung, P.; ...

2015-12-23

During 2014, the CMS Offline and Computing Organization completed the necessary changes to use the CMS threaded framework in the full production environment. We will briefly discuss the design of the CMS Threaded Framework, in particular how the design affects scaling performance. We will then cover the effort involved in getting both the CMSSW application software and the workflow management system ready for using multiple threads for production. Finally, we will present metrics on the performance of the application and workflow system as well as the difficulties which were uncovered. As a result, we will end with CMS' plans formore » using the threaded framework to do production for LHC Run 2.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novak, Avrey; Nyflot, Matthew J.; Ermoian, Ralph P.

Purpose: Radiation treatment planning involves a complex workflow that has multiple potential points of vulnerability. This study utilizes an incident reporting system to identify the origination and detection points of near-miss errors, in order to guide their departmental safety improvement efforts. Previous studies have examined where errors arise, but not where they are detected or applied a near-miss risk index (NMRI) to gauge severity. Methods: From 3/2012 to 3/2014, 1897 incidents were analyzed from a departmental incident learning system. All incidents were prospectively reviewed weekly by a multidisciplinary team and assigned a NMRI score ranging from 0 to 4 reflectingmore » potential harm to the patient (no potential harm to potential critical harm). Incidents were classified by point of incident origination and detection based on a 103-step workflow. The individual steps were divided among nine broad workflow categories (patient assessment, imaging for radiation therapy (RT) planning, treatment planning, pretreatment plan review, treatment delivery, on-treatment quality management, post-treatment completion, equipment/software quality management, and other). The average NMRI scores of incidents originating or detected within each broad workflow area were calculated. Additionally, out of 103 individual process steps, 35 were classified as safety barriers, the process steps whose primary function is to catch errors. The safety barriers which most frequently detected incidents were identified and analyzed. Finally, the distance between event origination and detection was explored by grouping events by the number of broad workflow area events passed through before detection, and average NMRI scores were compared. Results: Near-miss incidents most commonly originated within treatment planning (33%). However, the incidents with the highest average NMRI scores originated during imaging for RT planning (NMRI = 2.0, average NMRI of all events = 1.5), specifically during the documentation of patient positioning and localization of the patient. Incidents were most frequently detected during treatment delivery (30%), and incidents identified at this point also had higher severity scores than other workflow areas (NMRI = 1.6). Incidents identified during on-treatment quality management were also more severe (NMRI = 1.7), and the specific process steps of reviewing portal and CBCT images tended to catch highest-severity incidents. On average, safety barriers caught 46% of all incidents, most frequently at physics chart review, therapist’s chart check, and the review of portal images; however, most of the incidents that pass through a particular safety barrier are not designed to be capable of being captured at that barrier. Conclusions: Incident learning systems can be used to assess the most common points of error origination and detection in radiation oncology. This can help tailor safety improvement efforts and target the highest impact portions of the workflow. The most severe near-miss events tend to originate during simulation, with the most severe near-miss events detected at the time of patient treatment. Safety barriers can be improved to allow earlier detection of near-miss events.« less

ProcessGene-Connect: SOA Integration between Business Process Models and Enactment Transactions of Enterprise Software Systems

NASA Astrophysics Data System (ADS)

Wasser, Avi; Lincoln, Maya

In recent years, both practitioners and applied researchers have become increasingly interested in methods for integrating business process models and enterprise software systems through the deployment of enabling middleware. Integrative BPM research has been mainly focusing on the conversion of workflow notations into enacted application procedures, and less effort has been invested in enhancing the connectivity between design level, non-workflow business process models and related enactment systems such as: ERP, SCM and CRM. This type of integration is useful at several stages of an IT system lifecycle, from design and implementation through change management, upgrades and rollout. The paper presents an integration method that utilizes SOA for connecting business process models with corresponding enterprise software systems. The method is then demonstrated through an Oracle E-Business Suite procurement process and its ERP transactions.

Grid-based platform for training in Earth Observation

NASA Astrophysics Data System (ADS)

Petcu, Dana; Zaharie, Daniela; Panica, Silviu; Frincu, Marc; Neagul, Marian; Gorgan, Dorian; Stefanut, Teodor

2010-05-01

GiSHEO platform [1] providing on-demand services for training and high education in Earth Observation is developed, in the frame of an ESA funded project through its PECS programme, to respond to the needs of powerful education resources in remote sensing field. It intends to be a Grid-based platform of which potential for experimentation and extensibility are the key benefits compared with a desktop software solution. Near-real time applications requiring simultaneous multiple short-time-response data-intensive tasks, as in the case of a short time training event, are the ones that are proved to be ideal for this platform. The platform is based on Globus Toolkit 4 facilities for security and process management, and on the clusters of four academic institutions involved in the project. The authorization uses a VOMS service. The main public services are the followings: the EO processing services (represented through special WSRF-type services); the workflow service exposing a particular workflow engine; the data indexing and discovery service for accessing the data management mechanisms; the processing services, a collection allowing easy access to the processing platform. The WSRF-type services for basic satellite image processing are reusing free image processing tools, OpenCV and GDAL. New algorithms and workflows were develop to tackle with challenging problems like detecting the underground remains of old fortifications, walls or houses. More details can be found in [2]. Composed services can be specified through workflows and are easy to be deployed. The workflow engine, OSyRIS (Orchestration System using a Rule based Inference Solution), is based on DROOLS, and a new rule-based workflow language, SILK (SImple Language for worKflow), has been built. Workflow creation in SILK can be done with or without a visual designing tools. The basics of SILK are the tasks and relations (rules) between them. It is similar with the SCUFL language, but not relying on XML in order to allow the introduction of more workflow specific issues. Moreover, an event-condition-action (ECA) approach allows a greater flexibility when expressing data and task dependencies, as well as the creation of adaptive workflows which can react to changes in the configuration of the Grid or in the workflow itself. Changes inside the grid are handled by creating specific rules which allow resource selection based on various task scheduling criteria. Modifications of the workflow are usually accomplished either by inserting or retracting at runtime rules belonging to it or by modifying the executor of the task in case a better one is found. The former implies changes in its structure while the latter does not necessarily mean changes of the resource but more precisely changes of the algorithm used for solving the task. More details can be found in [3]. Another important platform component is the data indexing and storage service, GDIS, providing features for data storage, indexing data using a specialized RDBMS, finding data by various conditions, querying external services and keeping track of temporary data generated by other components. The data storage component part of GDIS is responsible for storing the data by using available storage backends such as local disk file systems (ext3), local cluster storage (GFS) or distributed file systems (HDFS). A front-end GridFTP service is capable of interacting with the storage domains on behalf of the clients and in a uniform way and also enforces the security restrictions provided by other specialized services and related with data access. The data indexing is performed by PostGIS. An advanced and flexible interface for searching the project's geographical repository is built around a custom query language (LLQL - Lisp Like Query Language) designed to provide fine grained access to the data in the repository and to query external services (e.g. for exploiting the connection with GENESI-DR catalog). More details can be found in [4]. The Workload Management System (WMS) provides two types of resource managers. The first one will be based on Condor HTC and use Condor as a job manager for task dispatching and working nodes (for development purposes) while the second one will use GT4 GRAM (for production purposes). The WMS main component, the Grid Task Dispatcher (GTD), is responsible for the interaction with other internal services as the composition engine in order to facilitate access to the processing platform. Its main responsibilities are to receive tasks from the workflow engine or directly from user interface, to use a task description language (the ClassAd meta language in case of Condor HTC) for job units, to submit and check the status of jobs inside the workload management system and to retrieve job logs for debugging purposes. More details can be found in [4]. A particular component of the platform is eGLE, the eLearning environment. It provides the functionalities necessary to create the visual appearance of the lessons through the usage of visual containers like tools, patterns and templates. The teacher uses the platform for testing the already created lessons, as well as for developing new lesson resources, such as new images and workflows describing graph-based processing. The students execute the lessons or describe and experiment with new workflows or different data. The eGLE database includes several workflow-based lesson descriptions, teaching materials and lesson resources, selected satellite and spatial data. More details can be found in [5]. A first training event of using the platform was organized in September 2009 during 11th SYNASC symposium (links to the demos, testing interface, and exercises are available on project site [1]). The eGLE component was presented at 4th GPC conference in May 2009. Moreover, the functionality of the platform will be presented as demo in April 2010 at 5th EGEE User forum. References: [1] GiSHEO consortium, Project site, http://gisheo.info.uvt.ro [2] D. Petcu, D. Zaharie, M. Neagul, S. Panica, M. Frincu, D. Gorgan, T. Stefanut, V. Bacu, Remote Sensed Image Processing on Grids for Training in Earth Observation. In Image Processing, V. Kordic (ed.), In-Tech, January 2010. [3] M. Neagul, S. Panica, D. Petcu, D. Zaharie, D. Gorgan, Web and Grid Services for Training in Earth Observation, IDAACS 2009, IEEE Computer Press, 241-246 [4] M. Frincu, S. Panica, M. Neagul, D. Petcu, Gisheo: On Demand Grid Service Based Platform for EO Data Processing. HiperGrid 2009, Politehnica Press, 415-422. [5] D. Gorgan, T. Stefanut, V. Bacu, Grid Based Training Environment for Earth Observation, GPC 2009, LNCS 5529, 98-109

Quality data collection and management technology of aerospace complex product assembly process

NASA Astrophysics Data System (ADS)

Weng, Gang; Liu, Jianhua; He, Yongxi; Zhuang, Cunbo

2017-04-01

Aiming at solving problems of difficult management and poor traceability for discrete assembly process quality data, a data collection and management method is proposed which take the assembly process and BOM as the core. Data collection method base on workflow technology, data model base on BOM and quality traceability of assembly process is included in the method. Finally, assembly process quality data management system is developed and effective control and management of quality information for complex product assembly process is realized.

SISYPHUS: A high performance seismic inversion factory

NASA Astrophysics Data System (ADS)

Gokhberg, Alexey; Simutė, Saulė; Boehm, Christian; Fichtner, Andreas

2016-04-01

In the recent years the massively parallel high performance computers became the standard instruments for solving the forward and inverse problems in seismology. The respective software packages dedicated to forward and inverse waveform modelling specially designed for such computers (SPECFEM3D, SES3D) became mature and widely available. These packages achieve significant computational performance and provide researchers with an opportunity to solve problems of bigger size at higher resolution within a shorter time. However, a typical seismic inversion process contains various activities that are beyond the common solver functionality. They include management of information on seismic events and stations, 3D models, observed and synthetic seismograms, pre-processing of the observed signals, computation of misfits and adjoint sources, minimization of misfits, and process workflow management. These activities are time consuming, seldom sufficiently automated, and therefore represent a bottleneck that can substantially offset performance benefits provided by even the most powerful modern supercomputers. Furthermore, a typical system architecture of modern supercomputing platforms is oriented towards the maximum computational performance and provides limited standard facilities for automation of the supporting activities. We present a prototype solution that automates all aspects of the seismic inversion process and is tuned for the modern massively parallel high performance computing systems. We address several major aspects of the solution architecture, which include (1) design of an inversion state database for tracing all relevant aspects of the entire solution process, (2) design of an extensible workflow management framework, (3) integration with wave propagation solvers, (4) integration with optimization packages, (5) computation of misfits and adjoint sources, and (6) process monitoring. The inversion state database represents a hierarchical structure with branches for the static process setup, inversion iterations, and solver runs, each branch specifying information at the event, station and channel levels. The workflow management framework is based on an embedded scripting engine that allows definition of various workflow scenarios using a high-level scripting language and provides access to all available inversion components represented as standard library functions. At present the SES3D wave propagation solver is integrated in the solution; the work is in progress for interfacing with SPECFEM3D. A separate framework is designed for interoperability with an optimization module; the workflow manager and optimization process run in parallel and cooperate by exchanging messages according to a specially designed protocol. A library of high-performance modules implementing signal pre-processing, misfit and adjoint computations according to established good practices is included. Monitoring is based on information stored in the inversion state database and at present implements a command line interface; design of a graphical user interface is in progress. The software design fits well into the common massively parallel system architecture featuring a large number of computational nodes running distributed applications under control of batch-oriented resource managers. The solution prototype has been implemented on the "Piz Daint" supercomputer provided by the Swiss Supercomputing Centre (CSCS).

PACS for surgery and interventional radiology: features of a Therapy Imaging and Model Management System (TIMMS).

PubMed

Lemke, Heinz U; Berliner, Leonard

2011-05-01

Appropriate use of information and communication technology (ICT) and mechatronic (MT) systems is viewed by many experts as a means to improve workflow and quality of care in the operating room (OR). This will require a suitable information technology (IT) infrastructure, as well as communication and interface standards, such as specialized extensions of DICOM, to allow data interchange between surgical system components in the OR. A design of such an infrastructure, sometimes referred to as surgical PACS, but better defined as a Therapy Imaging and Model Management System (TIMMS), will be introduced in this article. A TIMMS should support the essential functions that enable and advance image guided therapy, and in the future, a more comprehensive form of patient-model guided therapy. Within this concept, the "image-centric world view" of the classical PACS technology is complemented by an IT "model-centric world view". Such a view is founded in the special patient modelling needs of an increasing number of modern surgical interventions as compared to the imaging intensive working mode of diagnostic radiology, for which PACS was originally conceptualised and developed. The modelling aspects refer to both patient information and workflow modelling. Standards for creating and integrating information about patients, equipment, and procedures are vitally needed when planning for an efficient OR. The DICOM Working Group 24 (WG-24) has been established to develop DICOM objects and services related to image and model guided surgery. To determine these standards, it is important to define step-by-step surgical workflow practices and create interventional workflow models per procedures or per variable cases. As the boundaries between radiation therapy, surgery and interventional radiology are becoming less well-defined, precise patient models will become the greatest common denominator for all therapeutic disciplines. In addition to imaging, the focus of WG-24 is to serve the therapeutic disciplines by enabling modelling technology to be based on standards. Copyright © 2011. Published by Elsevier Ireland Ltd.

Overcoming Barriers to Technology Adoption in Small Manufacturing Enterprises (SMEs)

DTIC Science & Technology

2003-06-01

automates quote-generation, order - processing workflow management, perform- ance analysis, and accounting functions. Ultimately, it will enable Magdic...that Magdic imple- ment an MES instead. The MES, in addition to solving the problem of document manage- ment, would automate quote-generation, order ... processing , workflow management, perform- ance analysis, and accounting functions. To help Magdic personnel learn about the MES, TIDE personnel provided

Research on a dynamic workflow access control model

NASA Astrophysics Data System (ADS)

Liu, Yiliang; Deng, Jinxia

2007-12-01

In recent years, the access control technology has been researched widely in workflow system, two typical technologies of that are RBAC (Role-Based Access Control) and TBAC (Task-Based Access Control) model, which has been successfully used in the role authorizing and assigning in a certain extent. However, during the process of complicating a system's structure, these two types of technology can not be used in minimizing privileges and separating duties, and they are inapplicable when users have a request of frequently changing on the workflow's process. In order to avoid having these weakness during the applying, a variable flow dynamic role_task_view (briefly as DRTVBAC) of fine-grained access control model is constructed on the basis existed model. During the process of this model applying, an algorithm is constructed to solve users' requirements of application and security needs on fine-grained principle of privileges minimum and principle of dynamic separation of duties. The DRTVBAC model is implemented in the actual system, the figure shows that the task associated with the dynamic management of role and the role assignment is more flexible on authority and recovery, it can be met the principle of least privilege on the role implement of a specific task permission activated; separated the authority from the process of the duties completing in the workflow; prevented sensitive information discovering from concise and dynamic view interface; satisfied with the requirement of the variable task-flow frequently.

Information systems for administration, clinical documentation and quality assurance in an Austrian disease management programme.

PubMed

Beck, Peter; Truskaller, Thomas; Rakovac, Ivo; Bruner, Fritz; Zanettin, Dominik; Pieber, Thomas R

2009-01-01

5.9% of the Austrian population is affected by diabetes mellitus. Disease Management is a structured treatment approach that is suitable for application to the diabetes mellitus area and often is supported by information technology. This article describes the information systems developed and implemented in the Austrian disease management programme for type 2 diabetes. Several workflows for administration as well as for clinical documentation have been implemented utilizing the Austrian e-Health infrastructure. De-identified clinical data is available for creating feedback reports for providers and programme evaluation.

A Web Interface for Eco System Modeling

NASA Astrophysics Data System (ADS)

McHenry, K.; Kooper, R.; Serbin, S. P.; LeBauer, D. S.; Desai, A. R.; Dietze, M. C.

2012-12-01

We have developed the Predictive Ecosystem Analyzer (PEcAn) as an open-source scientific workflow system and ecoinformatics toolbox that manages the flow of information in and out of regional-scale terrestrial biosphere models, facilitates heterogeneous data assimilation, tracks data provenance, and enables more effective feedback between models and field research. The over-arching goal of PEcAn is to make otherwise complex analyses transparent, repeatable, and accessible to a diverse array of researchers, allowing both novice and expert users to focus on using the models to examine complex ecosystems rather than having to deal with complex computer system setup and configuration questions in order to run the models. Through the developed web interface we hide much of the data and model details and allow the user to simply select locations, ecosystem models, and desired data sources as inputs to the model. Novice users are guided by the web interface through setting up a model execution and plotting the results. At the same time expert users are given enough freedom to modify specific parameters before the model gets executed. This will become more important as more and more models are added to the PEcAn workflow as well as more and more data that will become available as NEON comes online. On the backend we support the execution of potentially computationally expensive models on different High Performance Computers (HPC) and/or clusters. The system can be configured with a single XML file that gives it the flexibility needed for configuring and running the different models on different systems using a combination of information stored in a database as well as pointers to files on the hard disk. While the web interface usually creates this configuration file, expert users can still directly edit it to fine tune the configuration.. Once a workflow is finished the web interface will allow for the easy creation of plots over result data while also allowing the user to download the results for further processing. The current workflow in the web interface is a simple linear workflow, but will be expanded to allow for more complex workflows. We are working with Kepler and Cyberintegrator to allow for these more complex workflows as well as collecting provenance of the workflow being executed. This provenance regarding model executions is stored in a database along with the derived results. All of this information is then accessible using the BETY database web frontend. The PEcAn interface.

Leadership characteristics and business management in modern academic surgery.

PubMed

Büchler, Peter; Martin, David; Knaebel, Hanns-Peter; Büchler, Markus W

2006-04-01

Management skills are necessary to successfully lead a surgical department in future. This article focuses on practical aspects of surgical management, leadership and training. It demonstrates how the implementation of business management concepts changes workflow management and surgical training. A systematic Medline search was performed and business management publications were analysed. Neither management nor leadership skills are inborn but acquired. Management is about planning, controlling and putting appropriate structures in place. Leadership is anticipating and coping with change and people, and adopting a visionary stance. More change requires more leadership. Changes in surgery occur with unprecedented speed because of a growing demand for surgical procedures with limited financial resources. Modern leadership and management theories have to be tailored to surgery. It is clear that not all of them are applicable but some of them are essential for surgeons. In business management, common traits of successful leaders include team orientation and communication skills. As the most important character, however, appears to be the emotional intelligence. Novel training concepts for surgeons include on-the-job training and introduction of improved workflow management systems, e.g. the central case management. The need for surgeons with advanced skills in business, finance and organisational management is evident and will require systematic and tailored training.

A Customized Workflow-Driven Instant Messaging System Support Team Communication in the Hospital.

PubMed

Lee, Ying-Li; Chien, Tsai-Feng; Chen, Hsiu-Chin

2016-01-01

Effective communication among the healthcare team is a very important skill to support team resource management (TRM). However, we take too much effort to connect with other team members by using traditional telephone communication. In this study, we developed an instant messaging system embedded in the original hospital information system and evaluated the preliminary outcome and the usage of the system.

MyGeoHub: A Collaborative Geospatial Research and Education Platform

NASA Astrophysics Data System (ADS)

Kalyanam, R.; Zhao, L.; Biehl, L. L.; Song, C. X.; Merwade, V.; Villoria, N.

2017-12-01

Scientific research is increasingly collaborative and globally distributed; research groups now rely on web-based scientific tools and data management systems to simplify their day-to-day collaborative workflows. However, such tools often lack seamless interfaces, requiring researchers to contend with manual data transfers, annotation and sharing. MyGeoHub is a web platform that supports out-of-the-box, seamless workflows involving data ingestion, metadata extraction, analysis, sharing and publication. MyGeoHub is built on the HUBzero cyberinfrastructure platform and adds general-purpose software building blocks (GABBs), for geospatial data management, visualization and analysis. A data management building block iData, processes geospatial files, extracting metadata for keyword and map-based search while enabling quick previews. iData is pervasive, allowing access through a web interface, scientific tools on MyGeoHub or even mobile field devices via a data service API. GABBs includes a Python map library as well as map widgets that in a few lines of code, generate complete geospatial visualization web interfaces for scientific tools. GABBs also includes powerful tools that can be used with no programming effort. The GeoBuilder tool provides an intuitive wizard for importing multi-variable, geo-located time series data (typical of sensor readings, GPS trackers) to build visualizations supporting data filtering and plotting. MyGeoHub has been used in tutorials at scientific conferences and educational activities for K-12 students. MyGeoHub is also constantly evolving; the recent addition of Jupyter and R Shiny notebook environments enable reproducible, richly interactive geospatial analyses and applications ranging from simple pre-processing to published tools. MyGeoHub is not a monolithic geospatial science gateway, instead it supports diverse needs ranging from just a feature-rich data management system, to complex scientific tools and workflows.

A Proposed Set of Metrics to Reduce Patient Safety Risk From Within the Anatomic Pathology Laboratory

PubMed Central

Banks, Peter; Brown, Richard; Laslowski, Alex; Daniels, Yvonne; Branton, Phil; Carpenter, John; Zarbo, Richard; Forsyth, Ramses; Liu, Yan-hui; Kohl, Shane; Diebold, Joachim; Masuda, Shinobu; Plummer, Tim

2017-01-01

Background: Anatomic pathology laboratory workflow consists of 3 major specimen handling processes. Among the workflow are preanalytic, analytic, and postanalytic phases that contain multistep subprocesses with great impact on patient care. A worldwide representation of experts came together to create a system of metrics, as a basis for laboratories worldwide, to help them evaluate and improve specimen handling to reduce patient safety risk. Method: Members of the Initiative for Anatomic Pathology Laboratory Patient Safety (IAPLPS) pooled their extensive expertise to generate a list of metrics highlighting processes with high and low risk for adverse patient outcomes. Results: Our group developed a universal, comprehensive list of 47 metrics for patient specimen handling in the anatomic pathology laboratory. Steps within the specimen workflow sequence are categorized as high or low risk. In general, steps associated with the potential for specimen misidentification correspond to the high-risk grouping and merit greater focus within quality management systems. Primarily workflow measures related to operational efficiency can be considered low risk. Conclusion: Our group intends to advance the widespread use of these metrics in anatomic pathology laboratories to reduce patient safety risk and improve patient care with development of best practices and interlaboratory error reporting programs. PMID:28340232

A Proposed Set of Metrics to Reduce Patient Safety Risk From Within the Anatomic Pathology Laboratory.

PubMed

Banks, Peter; Brown, Richard; Laslowski, Alex; Daniels, Yvonne; Branton, Phil; Carpenter, John; Zarbo, Richard; Forsyth, Ramses; Liu, Yan-Hui; Kohl, Shane; Diebold, Joachim; Masuda, Shinobu; Plummer, Tim; Dennis, Eslie

2017-05-01

Anatomic pathology laboratory workflow consists of 3 major specimen handling processes. Among the workflow are preanalytic, analytic, and postanalytic phases that contain multistep subprocesses with great impact on patient care. A worldwide representation of experts came together to create a system of metrics, as a basis for laboratories worldwide, to help them evaluate and improve specimen handling to reduce patient safety risk. Members of the Initiative for Anatomic Pathology Laboratory Patient Safety (IAPLPS) pooled their extensive expertise to generate a list of metrics highlighting processes with high and low risk for adverse patient outcomes. : Our group developed a universal, comprehensive list of 47 metrics for patient specimen handling in the anatomic pathology laboratory. Steps within the specimen workflow sequence are categorized as high or low risk. In general, steps associated with the potential for specimen misidentification correspond to the high-risk grouping and merit greater focus within quality management systems. Primarily workflow measures related to operational efficiency can be considered low risk. Our group intends to advance the widespread use of these metrics in anatomic pathology laboratories to reduce patient safety risk and improve patient care with development of best practices and interlaboratory error reporting programs. © American Society for Clinical Pathology 2017.

Real-Time Electronic Dashboard Technology and Its Use to Improve Pediatric Radiology Workflow.

PubMed

Shailam, Randheer; Botwin, Ariel; Stout, Markus; Gee, Michael S

The purpose of our study was to create a real-time electronic dashboard in the pediatric radiology reading room providing a visual display of updated information regarding scheduled and in-progress radiology examinations that could help radiologists to improve clinical workflow and efficiency. To accomplish this, a script was set up to automatically send real-time HL7 messages from the radiology information system (Epic Systems, Verona, WI) to an Iguana Interface engine, with relevant data regarding examinations stored in an SQL Server database for visual display on the dashboard. Implementation of an electronic dashboard in the reading room of a pediatric radiology academic practice has led to several improvements in clinical workflow, including decreasing the time interval for radiologist protocol entry for computed tomography or magnetic resonance imaging examinations as well as fewer telephone calls related to unprotocoled examinations. Other advantages include enhanced ability of radiologists to anticipate and attend to examinations requiring radiologist monitoring or scanning, as well as to work with technologists and operations managers to optimize scheduling in radiology resources. We foresee increased utilization of electronic dashboard technology in the future as a method to improve radiology workflow and quality of patient care. Copyright © 2017 Elsevier Inc. All rights reserved.

Climate Data Analytics Workflow Management

NASA Astrophysics Data System (ADS)

Zhang, J.; Lee, S.; Pan, L.; Mattmann, C. A.; Lee, T. J.

2016-12-01

In this project we aim to pave a novel path to create a sustainable building block toward Earth science big data analytics and knowledge sharing. Closely studying how Earth scientists conduct data analytics research in their daily work, we have developed a provenance model to record their activities, and to develop a technology to automatically generate workflows for scientists from the provenance. On top of it, we have built the prototype of a data-centric provenance repository, and establish a PDSW (People, Data, Service, Workflow) knowledge network to support workflow recommendation. To ensure the scalability and performance of the expected recommendation system, we have leveraged the Apache OODT system technology. The community-approved, metrics-based performance evaluation web-service will allow a user to select a metric from the list of several community-approved metrics and to evaluate model performance using the metric as well as the reference dataset. This service will facilitate the use of reference datasets that are generated in support of the model-data intercomparison projects such as Obs4MIPs and Ana4MIPs. The data-centric repository infrastructure will allow us to catch richer provenance to further facilitate knowledge sharing and scientific collaboration in the Earth science community. This project is part of Apache incubator CMDA project.

MO-B-BRB-03: Systems Engineering Tools for Treatment Planning Process Optimization in Radiation Medicine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kapur, A.

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

DOE PAGES

Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; ...

2015-01-01

Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-end NGS analysis requirements. The Globus Genomicsmore » system is built on Amazon's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.« less

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

PubMed Central

Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; Rodriguez, Alex; Madduri, Ravi; Dave, Utpal; Lacinski, Lukasz; Foster, Ian; Gusev, Yuriy; Madhavan, Subha

2014-01-01

Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon 's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research. PMID:26925205

Optimization of business processes in banks through flexible workflow

NASA Astrophysics Data System (ADS)

Postolache, V.

2017-08-01

This article describes an integrated business model of a commercial bank. There are examples of components that go into its composition: wooden models and business processes, strategic goals, organizational structure, system architecture, operational and marketing risk models, etc. The practice has shown that the development and implementation of the integrated business model of the bank significantly increase operating efficiency and its management, ensures organizational and technology stable development. Considering the evolution of business processes in the banking sector, should be analysed their common characteristics. From the author’s point of view, a business process is a set of various activities of a commercial bank in which “Input” is one or more financial and material resources, as a result of this activity and “output” is created by banking product, which is some value to consumer. Using workflow technology, management business process efficiency issue is a matter of managing the integration of resources and sequence of actions aimed at achieving this goal. In turn, it implies management of jobs or functions’ interaction, synchronizing of the assignments periods, reducing delays in the transmission of the results etc. Workflow technology is very important for managers at all levels, as they can use it to easily strengthen the control over what is happening in a particular unit, and in the bank as a whole. The manager is able to plan, to implement rules, to interact within the framework of the company’s procedures and tasks entrusted to the system of the distribution function and execution control, alert on the implementation and issuance of the statistical data on the effectiveness of operating procedures. Development and active use of the integrated bank business model is one of the key success factors that contribute to long-term and stable development of the bank, increase employee efficiency and business processes, implement the strategic objectives.

Process improvement for the safe delivery of multidisciplinary-executed treatments-A case in Y-90 microspheres therapy.

PubMed

Cai, Bin; Altman, Michael B; Garcia-Ramirez, Jose; LaBrash, Jason; Goddu, S Murty; Mutic, Sasa; Parikh, Parag J; Olsen, Jeffrey R; Saad, Nael; Zoberi, Jacqueline E

To develop a safe and robust workflow for yttrium-90 (Y-90) radioembolization procedures in a multidisciplinary team environment. A generalized Define-Measure-Analyze-Improve-Control (DMAIC)-based approach to process improvement was applied to a Y-90 radioembolization workflow. In the first DMAIC cycle, events with the Y-90 workflow were defined and analyzed. To improve the workflow, a web-based interactive electronic white board (EWB) system was adopted as the central communication platform and information processing hub. The EWB-based Y-90 workflow then underwent a second DMAIC cycle. Out of 245 treatments, three misses that went undetected until treatment initiation were recorded over a period of 21 months, and root-cause-analysis was performed to determine causes of each incident and opportunities for improvement. The EWB-based Y-90 process was further improved via new rules to define reliable sources of information as inputs into the planning process, as well as new check points to ensure this information was communicated correctly throughout the process flow. After implementation of the revised EWB-based Y-90 workflow, after two DMAIC-like cycles, there were zero misses out of 153 patient treatments in 1 year. The DMAIC-based approach adopted here allowed the iterative development of a robust workflow to achieve an adaptable, event-minimizing planning process despite a complex setting which requires the participation of multiple teams for Y-90 microspheres therapy. Implementation of such a workflow using the EWB or similar platform with a DMAIC-based process improvement approach could be expanded to other treatment procedures, especially those requiring multidisciplinary management. Copyright © 2016 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Integration, acceptance testing, and clinical operation of the Medical Information, Communication and Archive System, phase II.

PubMed

Smith, E M; Wandtke, J; Robinson, A

1999-05-01

The Medical Information, Communication and Archive System (MICAS) is a multivendor incremental approach to picture archiving and communications system (PACS). It is a multimodality integrated image management system that is seamlessly integrated with the radiology information system (RIS). Phase II enhancements of MICAS include a permanent archive, automated workflow, study caches, Microsoft (Redmond, WA) Windows NT diagnostic workstations with all components adhering to Digital Information Communications in Medicine (DICOM) standards. MICAS is designed as an enterprise-wide PACS to provide images and reports throughout the Strong Health healthcare network. Phase II includes the addition of a Cemax-Icon (Fremont, CA) archive, PACS broker (Mitra, Waterloo, Canada), an interface (IDX PACSlink, Burlington, VT) to the RIS (IDXrad) plus the conversion of the UNIX-based redundant array of inexpensive disks (RAID) 5 temporary archives in phase I to NT-based RAID 0 DICOM modality-specific study caches (ImageLabs, Bedford, MA). The phase I acquisition engines and workflow management software was uninstalled and the Cemax archive manager (AM) assumed these functions. The existing ImageLabs UNIX-based viewing software was enhanced and converted to an NT-based DICOM viewer. Installation of phase II hardware and software and integration with existing components began in July 1998. Phase II of MICAS demonstrates that a multivendor open-system incremental approach to PACS is feasible, cost-effective, and has significant advantages over a single-vendor implementation.

To Image...or Not to Image?

ERIC Educational Resources Information Center

Bruley, Karina

1996-01-01

Provides a checklist of considerations for installing document image processing with an electronic document management system. Other topics include scanning; indexing; the image file life cycle; benefits of imaging; document-driven workflow; and planning for workplace changes like postsorting, creating a scanning room, redeveloping job tasks and…

Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow.

PubMed

Stockton, David B; Santamaria, Fidel

2017-10-01

We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features. Finally, to maximize automation, we extended our NeuroManager workflow automation suite to include these tools plus a separate investigation database. The extended suite allows the user to integrate ABI experimental and modeling data into an automated workflow deployed on heterogeneous computer infrastructures, from local servers, to high performance computing environments, to the cloud. Since our approach is focused on workflow procedures our tools can be modified to interact with the increasing number of neuroscience databases being developed to cover all scales and properties of the nervous system.

Efficient Workflows for Curation of Heterogeneous Data Supporting Modeling of U-Nb Alloy Aging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, Logan Timothy; Hackenberg, Robert Errol

These are slides from a presentation summarizing a graduate research associate's summer project. The following topics are covered in these slides: data challenges in materials, aging in U-Nb Alloys, Building an Aging Model, Different Phase Trans. in U-Nb, the Challenge, Storing Materials Data, Example Data Source, Organizing Data: What is a Schema?, What does a "XML Schema" look like?, Our Data Schema: Nice and Simple, Storing Data: Materials Data Curation System (MDCS), Problem with MDCS: Slow Data Entry, Getting Literature into MDCS, Staging Data in Excel Document, Final Result: MDCS Records, Analyzing Image Data, Process for Making TTT Diagram, Bottleneckmore » Number 1: Image Analysis, Fitting a TTP Boundary, Fitting a TTP Curve: Comparable Results, How Does it Compare to Our Data?, Image Analysis Workflow, Curating Hardness Records, Hardness Data: Two Key Decisions, Before Peak Age? - Automation, Interactive Viz, Which Transformation?, Microstructure-Informed Model, Tracking the Entire Process, General Problem with Property Models, Pinyon: Toolkit for Managing Model Creation, Tracking Individual Decisions, Jupyter: Docs and Code in One File, Hardness Analysis Workflow, Workflow for Aging Models, and conclusions.« less

Diabetes Information Technology: Designing Informatics Systems to Catalyze Change in Clinical Care

PubMed Central

Lester, William T.; Zai, Adrian H.; Chueh, Henry C.; Grant, Richard W.

2008-01-01

Current computerized reminder and decision support systems intended to improve diabetes care have had a limited effect on clinical outcomes. Increasing pressures on health care networks to meet standards of diabetes care have created an environment where information technology systems for diabetes management are often created under duress, appended to existing clinical systems, and poorly integrated into the existing workflow. After defining the components of diabetes disease management, the authors present an eight-step conceptual framework to guide the development of more effective diabetes information technology systems for translating clinical information into clinical action. PMID:19885355

Using R in Taverna: RShell v1.2

PubMed Central

Wassink, Ingo; Rauwerda, Han; Neerincx, Pieter BT; Vet, Paul E van der; Breit, Timo M; Leunissen, Jack AM; Nijholt, Anton

2009-01-01

Background R is the statistical language commonly used by many life scientists in (omics) data analysis. At the same time, these complex analyses benefit from a workflow approach, such as used by the open source workflow management system Taverna. However, Taverna had limited support for R, because it supported just a few data types and only a single output. Also, there was no support for graphical output and persistent sessions. Altogether this made using R in Taverna impractical. Findings We have developed an R plugin for Taverna: RShell, which provides R functionality within workflows designed in Taverna. In order to fully support the R language, our RShell plugin directly uses the R interpreter. The RShell plugin consists of a Taverna processor for R scripts and an RShell Session Manager that communicates with the R server. We made the RShell processor highly configurable allowing the user to define multiple inputs and outputs. Also, various data types are supported, such as strings, numeric data and images. To limit data transport between multiple RShell processors, the RShell plugin also supports persistent sessions. Here, we will describe the architecture of RShell and the new features that are introduced in version 1.2, i.e.: i) Support for R up to and including R version 2.9; ii) Support for persistent sessions to limit data transfer; iii) Support for vector graphics output through PDF; iv)Syntax highlighting of the R code; v) Improved usability through fewer port types. Our new RShell processor is backwards compatible with workflows that use older versions of the RShell processor. We demonstrate the value of the RShell processor by a use-case workflow that maps oligonucleotide probes designed with DNA sequence information from Vega onto the Ensembl genome assembly. Conclusion Our RShell plugin enables Taverna users to employ R scripts within their workflows in a highly configurable way. PMID:19607662

Building a Culture of Continuous Improvement and Employee Engagement Using a Daily Management System Part 1: Overview.

PubMed

Maurer, Marsha; Canacari, Elena; Eng, Kimberly; Foley, Jane; Phelan, Cynthia; Sulmonte, Kimberlyann; Wandel, Jane

2018-03-01

A daily management system (DMS) can be used to implement continuous quality improvement and advance employee engagement. It can empower staff to identify problems in the care environment that impact quality or workflow and to address them on a daily basis. Through DMS, improvement becomes the work of everyone, every day. The authors of this 2-part series describe their work to develop a DMS. Part 1 describes the background and organizing framework of the program.

Echo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, Dustin Yewell

This document is a white paper marketing proposal for Echo™ is a data analysis platform designed for efficient, robust, and scalable creation and execution of complex workflows. Echo’s analysis management system refers to the ability to track, understand, and reproduce workflows used for arriving at results and decisions. Echo improves on traditional scripted data analysis in MATLAB, Python, R, and other languages to allow analysts to make better use of their time. Additionally, the Echo platform provides a powerful data management and curation solution allowing analysts to quickly find, access, and consume datasets. After two years of development and amore » first release in early 2016, Echo is now available for use with many data types in a wide range of application domains. Echo provides tools that allow users to focus on data analysis and decisions with confidence that results are reported accurately.« less

Improve wildlife species tracking—Implementing an enhanced global positioning system data management system for California condors

USGS Publications Warehouse

Waltermire, Robert G.; Emmerich, Christopher U.; Mendenhall, Laura C.; Bohrer, Gil; Weinzierl, Rolf P.; McGann, Andrew J.; Lineback, Pat K.; Kern, Tim J.; Douglas, David C.

2016-05-03

U.S. Fish and Wildlife Service (USFWS) staff in the Pacific Southwest Region and at the Hopper Mountain National Wildlife Refuge Complex requested technical assistance to improve their global positioning system (GPS) data acquisition, management, and archive in support of the California Condor Recovery Program. The USFWS deployed and maintained GPS units on individual Gymnogyps californianus (California condor) in support of long-term research and daily operational monitoring and management of California condors. The U.S. Geological Survey (USGS) obtained funding through the Science Support Program to provide coordination among project participants, provide GPS Global System for Mobile Communication (GSM) transmitters for testing, and compare GSM/GPS with existing Argos satellite GPS technology. The USFWS staff worked with private companies to design, develop, and fit condors with GSM/GPS transmitters. The Movebank organization, an online database of animal tracking data, coordinated with each of these companies to automatically stream their GPS data into Movebank servers and coordinated with USFWS to improve Movebank software for managing transmitter data, including proofing/error checking of incoming GPS data. The USGS arranged to pull raw GPS data from Movebank into the USGS California Condor Management and Analysis Portal (CCMAP) (https://my.usgs.gov/ccmap) for production and dissemination of a daily map of condor movements including various automated alerts. Further, the USGS developed an automatic archiving system for pulling raw and proofed Movebank data into USGS ScienceBase to comply with the Federal Information Security Management Act of 2002. This improved data management system requires minimal manual intervention resulting in more efficient data flow from GPS data capture to archive status. As a result of the project’s success, Pinnacles National Park and the Ventana Wildlife Society California condor programs became partners and adopted the same workflow, tracking, and data archive system. This GPS tracking data management model and workflow should be applicable and beneficial to other wildlife tracking programs.

BioPartsDB: a synthetic biology workflow web-application for education and research.

PubMed

Stracquadanio, Giovanni; Yang, Kun; Boeke, Jef D; Bader, Joel S

2016-11-15

Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones. BioPartsDB is released under the MIT license and available for download at https://github.com/baderzone/biopartsdb Additional documentation and video tutorials are available at https://github.com/baderzone/biopartsdb/wiki An Amazon Web Services image is available from the AWS Market Place (ami-a01d07c8). joel.bader@jhu.edu. © The Author 2016. Published by Oxford University Press.

Improving Clinical Workflow in Ambulatory Care: Implemented Recommendations in an Innovation Prototype for the Veteran’s Health Administration

PubMed Central

Patterson, Emily S.; Lowry, Svetlana Z.; Ramaiah, Mala; Gibbons, Michael C.; Brick, David; Calco, Robert; Matton, Greg; Miller, Anne; Makar, Ellen; Ferrer, Jorge A.

2015-01-01

Introduction: Human factors workflow analyses in healthcare settings prior to technology implemented are recommended to improve workflow in ambulatory care settings. In this paper we describe how insights from a workflow analysis conducted by NIST were implemented in a software prototype developed for a Veteran’s Health Administration (VHA) VAi2 innovation project and associated lessons learned. Methods: We organize the original recommendations and associated stages and steps visualized in process maps from NIST and the VA’s lessons learned from implementing the recommendations in the VAi2 prototype according to four stages: 1) before the patient visit, 2) during the visit, 3) discharge, and 4) visit documentation. NIST recommendations to improve workflow in ambulatory care (outpatient) settings and process map representations were based on reflective statements collected during one-hour discussions with three physicians. The development of the VAi2 prototype was conducted initially independently from the NIST recommendations, but at a midpoint in the process development, all of the implementation elements were compared with the NIST recommendations and lessons learned were documented. Findings: Story-based displays and templates with default preliminary order sets were used to support scheduling, time-critical notifications, drafting medication orders, and supporting a diagnosis-based workflow. These templates enabled customization to the level of diagnostic uncertainty. Functionality was designed to support cooperative work across interdisciplinary team members, including shared documentation sessions with tracking of text modifications, medication lists, and patient education features. Displays were customized to the role and included access for consultants and site-defined educator teams. Discussion: Workflow, usability, and patient safety can be enhanced through clinician-centered design of electronic health records. The lessons learned from implementing NIST recommendations to improve workflow in ambulatory care using an EHR provide a first step in moving from a billing-centered perspective on how to maintain accurate, comprehensive, and up-to-date information about a group of patients to a clinician-centered perspective. These recommendations point the way towards a “patient visit management system,” which incorporates broader notions of supporting workload management, supporting flexible flow of patients and tasks, enabling accountable distributed work across members of the clinical team, and supporting dynamic tracking of steps in tasks that have longer time distributions. PMID:26290887

Data Management System

NASA Technical Reports Server (NTRS)

1997-01-01

CENTRA 2000 Inc., a wholly owned subsidiary of Auto-trol technology, obtained permission to use software originally developed at Johnson Space Center for the Space Shuttle and early Space Station projects. To support their enormous information-handling needs, a product data management, electronic document management and work-flow system was designed. Initially, just 33 database tables comprised the original software, which was later expanded to about 100 tables. This system, now called CENTRA 2000, is designed for quick implementation and supports the engineering process from preliminary design through release-to-production. CENTRA 2000 can also handle audit histories and provides a means to ensure new information is distributed. The product has 30 production sites worldwide.

Database management systems for process safety.

PubMed

Early, William F

2006-03-17

Several elements of the process safety management regulation (PSM) require tracking and documentation of actions; process hazard analyses, management of change, process safety information, operating procedures, training, contractor safety programs, pre-startup safety reviews, incident investigations, emergency planning, and compliance audits. These elements can result in hundreds of actions annually that require actions. This tracking and documentation commonly is a failing identified in compliance audits, and is difficult to manage through action lists, spreadsheets, or other tools that are comfortably manipulated by plant personnel. This paper discusses the recent implementation of a database management system at a chemical plant and chronicles the improvements accomplished through the introduction of a customized system. The system as implemented modeled the normal plant workflows, and provided simple, recognizable user interfaces for ease of use.

Implementation and evaluation of an integrated computerized asthma management system in a pediatric emergency department: a randomized clinical trial.

PubMed

Dexheimer, Judith W; Abramo, Thomas J; Arnold, Donald H; Johnson, Kevin; Shyr, Yu; Ye, Fei; Fan, Kang-Hsien; Patel, Neal; Aronsky, Dominik

2014-11-01

The use of evidence-based guidelines can improve the care for asthma patients. We implemented a computerized asthma management system in a pediatric emergency department (ED) to integrate national guidelines. Our objective was to determine whether patient eligibility identification by a probabilistic disease detection system (Bayesian network) combined with an asthma management system embedded in the workflow decreases time to disposition decision. We performed a prospective, randomized controlled trial in an urban, tertiary care pediatric ED. All patients 2-18 years of age presenting to the ED between October 2010 and February 2011 were screened for inclusion by the disease detection system. Patients identified to have an asthma exacerbation were randomized to intervention or control. For intervention patients, asthma management was computer-driven and workflow-integrated including computer-based asthma scoring in triage, and time-driven display of asthma-related reminders for re-scoring on the electronic patient status board combined with guideline-compliant order sets. Control patients received standard asthma management. The primary outcome measure was the time from triage to disposition decision. The Bayesian network identified 1339 patients with asthma exacerbations, of which 788 had an asthma diagnosis determined by an ED physician-established reference standard (positive predictive value 69.9%). The median time to disposition decision did not differ among the intervention (228 min; IQR=(141, 326)) and control group (223 min; IQR=(129, 316)); (p=0.362). The hospital admission rate was unchanged between intervention (25%) and control groups (26%); (p=0.867). ED length of stay did not differ among intervention (262 min; IQR=(165, 410)) and control group (247 min; IQR=(163, 379)); (p=0.818). The control and intervention groups were similar in regards to time to disposition; the computerized management system did not add additional wait time. The time to disposition decision did not change; however the management system integrated several different information systems to support clinicians' communication. Copyright © 2014. Published by Elsevier Ireland Ltd.

Using aerial images for establishing a workflow for the quantification of water management measures

NASA Astrophysics Data System (ADS)

Leuschner, Annette; Merz, Christoph; van Gasselt, Stephan; Steidl, Jörg

2017-04-01

Quantified landscape characteristics, such as morphology, land use or hydrological conditions, play an important role for hydrological investigations as landscape parameters directly control the overall water balance. A powerful assimilation and geospatial analysis of remote sensing datasets in combination with hydrological modeling allows to quantify landscape parameters and water balances efficiently. This study focuses on the development of a workflow to extract hydrologically relevant data from aerial image datasets and derived products in order to allow an effective parametrization of a hydrological model. Consistent and self-contained data source are indispensable for achieving reasonable modeling results. In order to minimize uncertainties and inconsistencies, input parameters for modeling should be extracted from one remote-sensing dataset mainly if possbile. Here, aerial images have been chosen because of their high spatial and spectral resolution that permits the extraction of various model relevant parameters, like morphology, land-use or artificial drainage-systems. The methodological repertoire to extract environmental parameters range from analyses of digital terrain models, multispectral classification and segmentation of land use distribution maps and mapping of artificial drainage-systems based on spectral and visual inspection. The workflow has been tested for a mesoscale catchment area which forms a characteristic hydrological system of a young moraine landscape located in the state of Brandenburg, Germany. These dataset were used as input-dataset for multi-temporal hydrological modelling of water balances to detect and quantify anthropogenic and meteorological impacts. ArcSWAT, as a GIS-implemented extension and graphical user input interface for the Soil Water Assessment Tool (SWAT) was chosen. The results of this modeling approach provide the basis for anticipating future development of the hydrological system, and regarding system changes for the adaption of water resource management decisions.

Scientific Data Management (SDM) Center for Enabling Technologies. 2007-2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ludascher, Bertram; Altintas, Ilkay

Over the past five years, our activities have both established Kepler as a viable scientific workflow environment and demonstrated its value across multiple science applications. We have published numerous peer-reviewed papers on the technologies highlighted in this short paper and have given Kepler tutorials at SC06,SC07,SC08,and SciDAC 2007. Our outreach activities have allowed scientists to learn best practices and better utilize Kepler to address their individual workflow problems. Our contributions to advancing the state-of-the-art in scientific workflows have focused on the following areas. Progress in each of these areas is described in subsequent sections. Workflow development. The development of amore » deeper understanding of scientific workflows "in the wild" and of the requirements for support tools that allow easy construction of complex scientific workflows; Generic workflow components and templates. The development of generic actors (i.e.workflow components and processes) which can be broadly applied to scientific problems; Provenance collection and analysis. The design of a flexible provenance collection and analysis infrastructure within the workflow environment; and, Workflow reliability and fault tolerance. The improvement of the reliability and fault-tolerance of workflow environments.« less

Innovations in clinical trials informatics.

PubMed

Summers, Ron; Vyas, Hiten; Dudhal, Nilesh; Doherty, Neil F; Coombs, Crispin R; Hepworth, Mark

2008-01-01

This paper will investigate innovations in information management for use in clinical trials. The application typifies a complex, adaptive, distributed and information-rich environment for which continuous innovation is necessary. Organisational innovation is highlighted as well as the technical innovations in workflow processes and their representation as an integrated set of web services. Benefits realization uncovers further innovations in the business strand of the work undertaken. Following the description of the development of this information management system, the semantic web is postulated as a possible solution to tame the complexity related to information management issues found within clinical trials support systems.

A Mixed-Methods Research Framework for Healthcare Process Improvement.

PubMed

Bastian, Nathaniel D; Munoz, David; Ventura, Marta

2016-01-01

The healthcare system in the United States is spiraling out of control due to ever-increasing costs without significant improvements in quality, access to care, satisfaction, and efficiency. Efficient workflow is paramount to improving healthcare value while maintaining the utmost standards of patient care and provider satisfaction in high stress environments. This article provides healthcare managers and quality engineers with a practical healthcare process improvement framework to assess, measure and improve clinical workflow processes. The proposed mixed-methods research framework integrates qualitative and quantitative tools to foster the improvement of processes and workflow in a systematic way. The framework consists of three distinct phases: 1) stakeholder analysis, 2a) survey design, 2b) time-motion study, and 3) process improvement. The proposed framework is applied to the pediatric intensive care unit of the Penn State Hershey Children's Hospital. The implementation of this methodology led to identification and categorization of different workflow tasks and activities into both value-added and non-value added in an effort to provide more valuable and higher quality patient care. Based upon the lessons learned from the case study, the three-phase methodology provides a better, broader, leaner, and holistic assessment of clinical workflow. The proposed framework can be implemented in various healthcare settings to support continuous improvement efforts in which complexity is a daily element that impacts workflow. We proffer a general methodology for process improvement in a healthcare setting, providing decision makers and stakeholders with a useful framework to help their organizations improve efficiency. Published by Elsevier Inc.

Future Software Sizing Metrics and Estimation Challenges

DTIC Science & Technology

2011-07-01

systems 4. Ultrahigh software system assurance 5. Legacy maintenance and Brownfield development 6. Agile and Lean/ Kanban development. This paper...refined as the design of the maintenance modifications or Brownfield re-engineering is determined. VII. 6. AGILE AND LEAN/ KANBAN DEVELOPMENT The...difficulties of software maintenance estimation can often be mitigated by using lean workflow management techniques such as Kanban [25]. In Kanban

Supply chain optimization at an academic medical center.

PubMed

Labuhn, Jonathan; Almeter, Philip; McLaughlin, Christopher; Fields, Philip; Turner, Benjamin

2017-08-01

A successful supply chain optimization project that leveraged technology, engineering principles, and a technician workflow redesign in the setting of a growing health system is described. With continued rises in medication costs, medication inventory management is increasingly important. Proper management of central pharmacy inventory and floor-stock inventory in automated dispensing cabinets (ADCs) can be challenging. In an effort to improve control of inventory costs in the central pharmacy of a large academic medical center, the pharmacy department implemented a supply chain optimization project in collaboration with the medical center's inhouse team of experts on process improvement and industrial engineering. The project had 2 main components: (1) upgrading and reconfiguring carousel technology within an expanded central pharmacy footprint to generate accurate floor-stock inventory replenishment reports, which resulted in efficiencies within the medication-use system, and (2) implementing a technician workflow redesign and algorithm to right-size the ADC inventory, which decreased inventory stockouts (i.e., incidents of depletion of medication stock) and improved ADC user satisfaction. Through a multifaceted approach to inventory management, the number of stockouts per month was decreased and ADC inventory was optimized, resulting in a one-time inventory cost savings of $220,500. Copyright © 2017 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

DOE PAGES

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi; ...

2016-07-21

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

Challenges to effective crisis management: using information and communication technologies to coordinate emergency medical services and emergency department teams.

PubMed

Reddy, Madhu C; Paul, Sharoda A; Abraham, Joanna; McNeese, Michael; DeFlitch, Christopher; Yen, John

2009-04-01

The purpose of this study is to identify the major challenges to coordination between emergency department (ED) teams and emergency medical services (EMS) teams. We conducted a series of focus groups involving both ED and EMS team members using a crisis scenario as the basis of the focus group discussion. We also collected organizational workflow data. We identified three major challenges to coordination between ED and EMS teams including ineffectiveness of current information and communication technologies, lack of common ground, and breakdowns in information flow. The three challenges highlight the importance of designing systems from socio-technical perspective. In particular, these inter-team coordination systems must support socio-technical issues such as awareness, context, and workflow between the two teams.

Thinking beyond "the Way We've Always Done It"

ERIC Educational Resources Information Center

Ohler, Lila

2013-01-01

In this article, the author discusses the future potential of electronic resources management (ERM) organization, within the development of the next-generation integrated library systems (ILS), as a very promising strategy. This also presents enormous challenges to ERM librarians though, especially on how to determine standards and workflows. The…

48 CFR 252.232-7006 - Wide Area WorkFlow Payment Instructions.

Code of Federal Regulations, 2013 CFR

2013-10-01

...— (1) Have a designated electronic business point of contact in the System for Award Management at... submission. Document submissions may be via Web entry, Electronic Data Interchange, or File Transfer Protocol... that uniquely identifies a unit, activity, or organization. Document type means the type of payment...

48 CFR 252.232-7006 - Wide Area WorkFlow Payment Instructions.

Code of Federal Regulations, 2014 CFR

2014-10-01

...— (1) Have a designated electronic business point of contact in the System for Award Management at... submission. Document submissions may be via Web entry, Electronic Data Interchange, or File Transfer Protocol... that uniquely identifies a unit, activity, or organization. Document type means the type of payment...

Workflow based framework for life science informatics.

PubMed

Tiwari, Abhishek; Sekhar, Arvind K T

2007-10-01

Workflow technology is a generic mechanism to integrate diverse types of available resources (databases, servers, software applications and different services) which facilitate knowledge exchange within traditionally divergent fields such as molecular biology, clinical research, computational science, physics, chemistry and statistics. Researchers can easily incorporate and access diverse, distributed tools and data to develop their own research protocols for scientific analysis. Application of workflow technology has been reported in areas like drug discovery, genomics, large-scale gene expression analysis, proteomics, and system biology. In this article, we have discussed the existing workflow systems and the trends in applications of workflow based systems.

Closha: bioinformatics workflow system for the analysis of massive sequencing data.

PubMed

Ko, GunHwan; Kim, Pan-Gyu; Yoon, Jongcheol; Han, Gukhee; Park, Seong-Jin; Song, Wangho; Lee, Byungwook

2018-02-19

While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rapidly increasing amounts of data available from the new high-throughput methods have made data processing infeasible without automated pipelines. The integration of data and analytic resources into workflow systems provides a solution to the problem by simplifying the task of data analysis. To address this challenge, we developed a cloud-based workflow management system, Closha, to provide fast and cost-effective analysis of massive genomic data. We implemented complex workflows making optimal use of high-performance computing clusters. Closha allows users to create multi-step analyses using drag and drop functionality and to modify the parameters of pipeline tools. Users can also import the Galaxy pipelines into Closha. Closha is a hybrid system that enables users to use both analysis programs providing traditional tools and MapReduce-based big data analysis programs simultaneously in a single pipeline. Thus, the execution of analytics algorithms can be parallelized, speeding up the whole process. We also developed a high-speed data transmission solution, KoDS, to transmit a large amount of data at a fast rate. KoDS has a file transfer speed of up to 10 times that of normal FTP and HTTP. The computer hardware for Closha is 660 CPU cores and 800 TB of disk storage, enabling 500 jobs to run at the same time. Closha is a scalable, cost-effective, and publicly available web service for large-scale genomic data analysis. Closha supports the reliable and highly scalable execution of sequencing analysis workflows in a fully automated manner. Closha provides a user-friendly interface to all genomic scientists to try to derive accurate results from NGS platform data. The Closha cloud server is freely available for use from http://closha.kobic.re.kr/ .

A web accessible scientific workflow system for vadoze zone performance monitoring: design and implementation examples

NASA Astrophysics Data System (ADS)

Mattson, E.; Versteeg, R.; Ankeny, M.; Stormberg, G.

2005-12-01

Long term performance monitoring has been identified by DOE, DOD and EPA as one of the most challenging and costly elements of contaminated site remedial efforts. Such monitoring should provide timely and actionable information relevant to a multitude of stakeholder needs. This information should be obtained in a manner which is auditable, cost effective and transparent. Over the last several years INL staff has designed and implemented a web accessible scientific workflow system for environmental monitoring. This workflow environment integrates distributed, automated data acquisition from diverse sensors (geophysical, geochemical and hydrological) with server side data management and information visualization through flexible browser based data access tools. Component technologies include a rich browser-based client (using dynamic javascript and html/css) for data selection, a back-end server which uses PHP for data processing, user management, and result delivery, and third party applications which are invoked by the back-end using webservices. This system has been implemented and is operational for several sites, including the Ruby Gulch Waste Rock Repository (a capped mine waste rock dump on the Gilt Edge Mine Superfund Site), the INL Vadoze Zone Research Park and an alternative cover landfill. Implementations for other vadoze zone sites are currently in progress. These systems allow for autonomous performance monitoring through automated data analysis and report generation. This performance monitoring has allowed users to obtain insights into system dynamics, regulatory compliance and residence times of water. Our system uses modular components for data selection and graphing and WSDL compliant webservices for external functions such as statistical analyses and model invocations. Thus, implementing this system for novel sites and extending functionality (e.g. adding novel models) is relatively straightforward. As system access requires a standard webbrowser and uses intuitive functionality, stakeholders with diverse degrees of technical insight can use this system with little or no training.

Automation is key to managing a population's health.

PubMed

Matthews, Michael B; Hodach, Richard

2012-04-01

Online tools for automating population health management can help healthcare organizations meet their patients' needs both during and between encounters with the healthcare system. These tools can facilitate: The use of registries to track patients' health status and care gaps. Outbound messaging to notify patients when they need care. Care team management of more patients at different levels of risk. Automation of workflows related to case management and transitions of care. Online educational and mobile health interventions to engage patients in their care. Analytics programs to identify opportunities for improvement.

Implementing chronic care for COPD: planned visits, care coordination, and patient empowerment for improved outcomes.

PubMed

Fromer, Len

2011-01-01

Current primary care patterns for chronic obstructive pulmonary disease (COPD) focus on reactive care for acute exacerbations, often neglecting ongoing COPD management to the detriment of patient experience and outcomes. Proactive diagnosis and ongoing multifactorial COPD management, comprising smoking cessation, influenza and pneumonia vaccinations, pulmonary rehabilitation, and symptomatic and maintenance pharmacotherapy according to severity, can significantly improve a patient's health-related quality of life, reduce exacerbations and their consequences, and alleviate the functional, utilization, and financial burden of COPD. Redesign of primary care according to principles of the chronic care model, which is implemented in the patient-centered medical home, can shift COPD management from acute rescue to proactive maintenance. The chronic care model and patient-centered medical home combine delivery system redesign, clinical information systems, decision support, and self-management support within a practice, linked with health care organization and community resources beyond the practice. COPD care programs implementing two or more chronic care model components effectively reduce emergency room and inpatient utilization. This review guides primary care practices in improving COPD care workflows, highlighting the contributions of multidisciplinary collaborative team care, care coordination, and patient engagement. Each primary care practice can devise a COPD care workflow addressing risk awareness, spirometric diagnosis, guideline-based treatment and rehabilitation, and self-management support, to improve patient outcomes in COPD.

a Real-Time GIS Platform for High Sour Gas Leakage Simulation, Evaluation and Visualization

NASA Astrophysics Data System (ADS)

Li, M.; Liu, H.; Yang, C.

2015-07-01

The development of high-sulfur gas fields, also known as sour gas field, is faced with a series of safety control and emergency management problems. The GIS-based emergency response system is placed high expectations under the consideration of high pressure, high content, complex terrain and highly density population in Sichuan Basin, southwest China. The most researches on high hydrogen sulphide gas dispersion simulation and evaluation are used for environmental impact assessment (EIA) or emergency preparedness planning. This paper introduces a real-time GIS platform for high-sulfur gas emergency response. Combining with real-time data from the leak detection systems and the meteorological monitoring stations, GIS platform provides the functions of simulating, evaluating and displaying of the different spatial-temporal toxic gas distribution patterns and evaluation results. This paper firstly proposes the architecture of Emergency Response/Management System, secondly explains EPA's Gaussian dispersion model CALPUFF simulation workflow under high complex terrain and real-time data, thirdly explains the emergency workflow and spatial analysis functions of computing the accident influencing areas, population and the optimal evacuation routes. Finally, a well blow scenarios is used for verify the system. The study shows that GIS platform which integrates the real-time data and CALPUFF models will be one of the essential operational platforms for high-sulfur gas fields emergency management.

The Rising Frequency of IT Blackouts Indicates the Increasing Relevance of IT Emergency Concepts to Ensure Patient Safety

PubMed Central

Sax, U.; Lipprandt, M.

2016-01-01

Summary Introduction As many medical workflows depend vastly on IT support, great demands are placed on the availability and accuracy of the applications involved. The cases of IT failure through ransomware at the beginning of 2016 are impressive examples of the dependence of clinical processes on IT. Although IT risk management attempts to reduce the risk of IT blackouts, the probability of partial/total data loss, or even worse, data falsification, is not zero. The objective of this paper is to present the state of the art with respect to strategies, processes, and governance to deal with the failure of IT systems. Methods This article is conducted as a narrative review. Results Worst case scenarios are needed, dealing with methods as to how to survive the downtime of clinical systems, for example through alternative workflows. These workflows have to be trained regularly. We categorize the most important types of IT system failure, assess the usefulness of classic counter measures, and state that most risk management approaches fall short on exactly this matter. Conclusion To ensure that continuous, evidence-based improvements to the recommendations for IT emergency concepts are made, it is essential that IT blackouts and IT disasters are reported, analyzed, and critically discussed. This requires changing from a culture of shame and blame to one of error and safety in healthcare IT. This change is finding its way into other disciplines in medicine. In addition, systematically planned and analyzed simulations of IT disaster may assist in IT emergency concept development. PMID:27830241

The Rising Frequency of IT Blackouts Indicates the Increasing Relevance of IT Emergency Concepts to Ensure Patient Safety.

PubMed

Sax, Ulrich; Lipprandt, M; Röhrig, R

2016-11-10

As many medical workflows depend vastly on IT support, great demands are placed on the availability and accuracy of the applications involved. The cases of IT failure through ransomware at the beginning of 2016 are impressive examples of the dependence of clinical processes on IT. Although IT risk management attempts to reduce the risk of IT blackouts, the probability of partial/total data loss, or even worse, data falsification, is not zero. The objective of this paper is to present the state of the art with respect to strategies, processes, and governance to deal with the failure of IT systems. This article is conducted as a narrative review. Worst case scenarios are needed, dealing with methods as to how to survive the downtime of clinical systems, for example through alternative workflows. These workflows have to be trained regularly. We categorize the most important types of IT system failure, assess the usefulness of classic counter measures, and state that most risk management approaches fall short on exactly this matter. To ensure that continuous, evidence-based improvements to the recommendations for IT emergency concepts are made, it is essential that IT blackouts and IT disasters are reported, analyzed, and critically discussed. This requires changing from a culture of shame and blame to one of error and safety in healthcare IT. This change is finding its way into other disciplines in medicine. In addition, systematically planned and analyzed simulations of IT disaster may assist in IT emergency concept development.

The standard-based open workflow system in GeoBrain (Invited)

NASA Astrophysics Data System (ADS)

Di, L.; Yu, G.; Zhao, P.; Deng, M.

2013-12-01

GeoBrain is an Earth science Web-service system developed and operated by the Center for Spatial Information Science and Systems, George Mason University. In GeoBrain, a standard-based open workflow system has been implemented to accommodate the automated processing of geospatial data through a set of complex geo-processing functions for advanced production generation. The GeoBrain models the complex geoprocessing at two levels, the conceptual and concrete. At the conceptual level, the workflows exist in the form of data and service types defined by ontologies. The workflows at conceptual level are called geo-processing models and cataloged in GeoBrain as virtual product types. A conceptual workflow is instantiated into a concrete, executable workflow when a user requests a product that matches a virtual product type. Both conceptual and concrete workflows are encoded in Business Process Execution Language (BPEL). A BPEL workflow engine, called BPELPower, has been implemented to execute the workflow for the product generation. A provenance capturing service has been implemented to generate the ISO 19115-compliant complete product provenance metadata before and after the workflow execution. The generation of provenance metadata before the workflow execution allows users to examine the usability of the final product before the lengthy and expensive execution takes place. The three modes of workflow executions defined in the ISO 19119, transparent, translucent, and opaque, are available in GeoBrain. A geoprocessing modeling portal has been developed to allow domain experts to develop geoprocessing models at the type level with the support of both data and service/processing ontologies. The geoprocessing models capture the knowledge of the domain experts and are become the operational offering of the products after a proper peer review of models is conducted. An automated workflow composition has been experimented successfully based on ontologies and artificial intelligence technology. The GeoBrain workflow system has been used in multiple Earth science applications, including the monitoring of global agricultural drought, the assessment of flood damage, the derivation of national crop condition and progress information, and the detection of nuclear proliferation facilities and events.

IceProd 2: A Next Generation Data Analysis Framework for the IceCube Neutrino Observatory

NASA Astrophysics Data System (ADS)

Schultz, D.

2015-12-01

We describe the overall structure and new features of the second generation of IceProd, a data processing and management framework. IceProd was developed by the IceCube Neutrino Observatory for processing of Monte Carlo simulations, detector data, and analysis levels. It runs as a separate layer on top of grid and batch systems. This is accomplished by a set of daemons which process job workflow, maintaining configuration and status information on the job before, during, and after processing. IceProd can also manage complex workflow DAGs across distributed computing grids in order to optimize usage of resources. IceProd is designed to be very light-weight; it runs as a python application fully in user space and can be set up easily. For the initial completion of this second version of IceProd, improvements have been made to increase security, reliability, scalability, and ease of use.

Automated lattice data generation

NASA Astrophysics Data System (ADS)

Ayyar, Venkitesh; Hackett, Daniel C.; Jay, William I.; Neil, Ethan T.

2018-03-01

The process of generating ensembles of gauge configurations (and measuring various observables over them) can be tedious and error-prone when done "by hand". In practice, most of this procedure can be automated with the use of a workflow manager. We discuss how this automation can be accomplished using Taxi, a minimal Python-based workflow manager built for generating lattice data. We present a case study demonstrating this technology.

Flexible guideline-based patient careflow systems.

PubMed

Quaglini, S; Stefanelli, M; Lanzola, G; Caporusso, V; Panzarasa, S

2001-04-01

Workflow Management Systems integrate domain and organisational knowledge to support business processes. When applied to the medical environment, they can be termed "Careflow Management Systems", and may be used to manage care delivery by enhancing co-operation among healthcare professionals. This paper focuses on care delivery based on clinical practice guidelines. Healthcare organisations are very different from industrial or commercial companies: their main goal is not profit, but maintaining and improving the health of the public. Therefore, outcomes are difficult to measure. Firstly, physicians, while playing a variety of roles, are quite independent decision-makers; secondly, the object of the process, i.e. the patient, may be involved in choosing treatment options, and may be treated by different institutions. For these reasons, the standard functionality of typical Workflow Management Systems must be strongly enhanced in order to cope with healthcare delivery needs. A major issue is accounting for exceptions. In most non-clinical settings this is not a problem because processes are very well defined and can often be easily controlled by some higher authority. As explained above, this does not happen in healthcare organisations. Responsibilities are widely shared, and health care professionals may be non-compliant with guidelines for a variety of reasons. The paper presents a classification of possible exceptions, and shows how the sequence of tasks described by a guideline may be altered, at the implementation level, in order to meet actual user needs, while maintaining guideline intentions as much as possible. A terminology server is also exploited towards this end. This work illustrates a prototype of a Careflow Management System based on an international guideline for ischemic stroke treatment, developed by the American Heart Association.

A healthcare Lean Six Sigma System for postanesthesia care unit workflow improvement.

PubMed

Kuo, Alex Mu-Hsing; Borycki, Elizabeth; Kushniruk, Andre; Lee, Te-Shu

2011-01-01

The aim of this article is to propose a new model called Healthcare Lean Six Sigma System that integrates Lean and Six Sigma methodologies to improve workflow in a postanesthesia care unit. The methodology of the proposed model is fully described. A postanesthesia care unit case study is also used to demonstrate the benefits of using the Healthcare Lean Six Sigma System model by combining Lean and Six Sigma methodologies together. The new model bridges the service gaps between health care providers and patients, balances the requirements of health care managers, and delivers health care services to patients by taking the benefits of the Lean speed and Six Sigma high-quality principles. The full benefits of the new model will be realized when applied at both strategic and operational levels. For further research, we will examine how the proposed model is used in different real-world case studies.

Informatics applied to cytology

PubMed Central

Hornish, Maryanne; Goulart, Robert A.

2008-01-01

Automation and emerging information technologies are being adopted by cytology laboratories to augment Pap test screening and improve diagnostic accuracy. As a result, informatics, the application of computers and information systems to information management, has become essential for the successful operation of the cytopathology laboratory. This review describes how laboratory information management systems can be used to achieve an automated and seamless workflow process. The utilization of software, electronic databases and spreadsheets to perform necessary quality control measures are discussed, as well as a Lean production system and Six Sigma approach, to reduce errors in the cytopathology laboratory. PMID:19495402

A PDA study management tool (SMT) utilizing wireless broadband and full DICOM viewing capability

NASA Astrophysics Data System (ADS)

Documet, Jorge; Liu, Brent; Zhou, Zheng; Huang, H. K.; Documet, Luis

2007-03-01

During the last 4 years IPI (Image Processing and Informatics) Laboratory has been developing a web-based Study Management Tool (SMT) application that allows Radiologists, Film librarians and PACS-related (Picture Archiving and Communication System) users to dynamically and remotely perform Query/Retrieve operations in a PACS network. The users utilizing a regular PDA (Personal Digital Assistant) can remotely query a PACS archive to distribute any study to an existing DICOM (Digital Imaging and Communications in Medicine) node. This application which has proven to be convenient to manage the Study Workflow [1, 2] has been extended to include a DICOM viewing capability in the PDA. With this new feature, users can take a quick view of DICOM images providing them mobility and convenience at the same time. In addition, we are extending this application to Metropolitan-Area Wireless Broadband Networks. This feature requires Smart Phones that are capable of working as a PDA and have access to Broadband Wireless Services. With the extended application to wireless broadband technology and the preview of DICOM images, the Study Management Tool becomes an even more powerful tool for clinical workflow management.

Night of the living color: horror scenarios in color management land

NASA Astrophysics Data System (ADS)

Lammens, Johan M.

1998-12-01

An ICC-based color management is becoming increasingly feasible and its picking up support from all the major high end design and pre-press applications as well as hardware manufacturers. In addition, the new sRGB standard is emerging as a way to effectively do 'color management for the masses', and is being supported by many leading manufacturers as well. While there certainly remain serious technical issues to address for both ICC and sRGB color management, it seems that the main problem users are facing today is how to integrate all components of their workflow into a seamless system, and how to configured each component to work well with all the others. This paper takes a brief look at the history of color management for a workflow perspective, and attempts to analyze how to compose and configured a quadruple color conversions can become a terrific nightmare. Some of the many ways to get the wrong results are briefly illustrated, as well as a few ways to get the right results. Finally, some technical recommendations are offered for how to improve the situation from a user point of view.

Using CyberShake Workflows to Manage Big Seismic Hazard Data on Large-Scale Open-Science HPC Resources

NASA Astrophysics Data System (ADS)

Callaghan, S.; Maechling, P. J.; Juve, G.; Vahi, K.; Deelman, E.; Jordan, T. H.

2015-12-01

The CyberShake computational platform, developed by the Southern California Earthquake Center (SCEC), is an integrated collection of scientific software and middleware that performs 3D physics-based probabilistic seismic hazard analysis (PSHA) for Southern California. CyberShake integrates large-scale and high-throughput research codes to produce probabilistic seismic hazard curves for individual locations of interest and hazard maps for an entire region. A recent CyberShake calculation produced about 500,000 two-component seismograms for each of 336 locations, resulting in over 300 million synthetic seismograms in a Los Angeles-area probabilistic seismic hazard model. CyberShake calculations require a series of scientific software programs. Early computational stages produce data used as inputs by later stages, so we describe CyberShake calculations using a workflow definition language. Scientific workflow tools automate and manage the input and output data and enable remote job execution on large-scale HPC systems. To satisfy the requests of broad impact users of CyberShake data, such as seismologists, utility companies, and building code engineers, we successfully completed CyberShake Study 15.4 in April and May 2015, calculating a 1 Hz urban seismic hazard map for Los Angeles. We distributed the calculation between the NSF Track 1 system NCSA Blue Waters, the DOE Leadership-class system OLCF Titan, and USC's Center for High Performance Computing. This study ran for over 5 weeks, burning about 1.1 million node-hours and producing over half a petabyte of data. The CyberShake Study 15.4 results doubled the maximum simulated seismic frequency from 0.5 Hz to 1.0 Hz as compared to previous studies, representing a factor of 16 increase in computational complexity. We will describe how our workflow tools supported splitting the calculation across multiple systems. We will explain how we modified CyberShake software components, including GPU implementations and migrating from file-based communication to MPI messaging, to greatly reduce the I/O demands and node-hour requirements of CyberShake. We will also present performance metrics from CyberShake Study 15.4, and discuss challenges that producers of Big Data on open-science HPC resources face moving forward.

Beyond health information technology: critical factors necessary for effective diabetes disease management.

PubMed

Ciemins, Elizabeth L; Coon, Patricia J; Fowles, Jinnet Briggs; Min, Sung-joon

2009-05-01

Electronic health records (EHRs) have been implemented throughout the United States with varying degrees of success. Past EHR implementation experiences can inform health systems planning to initiate new or expand existing EHR systems. Key "critical success factors," e.g., use of disease registries, workflow integration, and real-time clinical guideline support, have been identified but not fully tested in practice. A pre/postintervention cohort analysis was conducted on 495 adult patients selected randomly from a diabetes registry and followed for 6 years. Two intervention phases were evaluated: a "low-dose" period targeting primary care provider (PCP) and patient education followed by a "high-dose" EHR diabetes management implementation period, including a diabetes disease registry and office workflow changes, e.g., diabetes patient preidentification to facilitate real-time diabetes preventive care, disease management, and patient education. Across baseline, "low-dose," and "high-dose" postintervention periods, a significantly greater proportion of patients (a) achieved American Diabetes Association (ADA) guidelines for control of blood pressure (26.9 to 33.1 to 43.9%), glycosylated hemoglobin (48.5 to 57.5 to 66.8%), and low-density lipoprotein cholesterol (33.1 to 44.4 to 56.6%) and (b) received recommended preventive eye (26.2 to 36.4 to 58%), foot (23.4 to 40.3 to 66.9%), and renal (38.5 to 53.9 to 71%) examinations or screens. Implementation of a fully functional, specialized EHR combined with tailored office workflow process changes was associated with increased adherence to ADA guidelines, including risk factor control, by PCPs and their patients with diabetes. Incorporation of previously identified "critical success factors" potentially contributed to the success of the program, as did use of a two-phase approach. 2009 Diabetes Technology Society.

A Cloud-based Infrastructure and Architecture for Environmental System Research

NASA Astrophysics Data System (ADS)

Wang, D.; Wei, Y.; Shankar, M.; Quigley, J.; Wilson, B. E.

2016-12-01

The present availability of high-capacity networks, low-cost computers and storage devices, and the widespread adoption of hardware virtualization and service-oriented architecture provide a great opportunity to enable data and computing infrastructure sharing between closely related research activities. By taking advantage of these approaches, along with the world-class high computing and data infrastructure located at Oak Ridge National Laboratory, a cloud-based infrastructure and architecture has been developed to efficiently deliver essential data and informatics service and utilities to the environmental system research community, and will provide unique capabilities that allows terrestrial ecosystem research projects to share their software utilities (tools), data and even data submission workflow in a straightforward fashion. The infrastructure will minimize large disruptions from current project-based data submission workflows for better acceptances from existing projects, since many ecosystem research projects already have their own requirements or preferences for data submission and collection. The infrastructure will eliminate scalability problems with current project silos by provide unified data services and infrastructure. The Infrastructure consists of two key components (1) a collection of configurable virtual computing environments and user management systems that expedite data submission and collection from environmental system research community, and (2) scalable data management services and system, originated and development by ORNL data centers.

MO-B-BRB-01: Optimize Treatment Planning Process in Clinical Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, W.

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

MO-B-BRB-00: Optimizing the Treatment Planning Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

MO-B-BRB-02: Maintain the Quality of Treatment Planning for Time-Constraint Cases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, J.

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

Online time and resource management based on surgical workflow time series analysis.

PubMed

Maktabi, M; Neumuth, T

2017-02-01

Hospitals' effectiveness and efficiency can be enhanced by automating the resource and time management of the most cost-intensive unit in the hospital: the operating room (OR). The key elements required for the ideal organization of hospital staff and technical resources (such as instruments in the OR) are an exact online forecast of both the surgeon's resource usage and the remaining intervention time. This paper presents a novel online approach relying on time series analysis and the application of a linear time-variant system. We calculated the power spectral density and the spectrogram of surgical perspectives (e.g., used instrument) of interest to compare several surgical workflows. Considering only the use of the surgeon's right hand during an intervention, we were able to predict the remaining intervention time online with an error of 21 min 45 s ±9 min 59 s for lumbar discectomy. Furthermore, the performance of forecasting of technical resource usage in the next 20 min was calculated for a combination of spectral analysis and the application of a linear time-variant system (sensitivity: 74 %; specificity: 75 %) focusing on just the use of surgeon's instrument in question. The outstanding benefit of these methods is that the automated recording of surgical workflows has minimal impact during interventions since the whole set of surgical perspectives need not be recorded. The resulting predictions can help various stakeholders such as OR staff and hospital technicians. Moreover, reducing resource conflicts could well improve patient care.

Toward server-side, high performance climate change data analytics in the Earth System Grid Federation (ESGF) eco-system

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Williams, Dean; Aloisio, Giovanni

2016-04-01

In many scientific domains such as climate, data is often n-dimensional and requires tools that support specialized data types and primitives to be properly stored, accessed, analysed and visualized. Moreover, new challenges arise in large-scale scenarios and eco-systems where petabytes (PB) of data can be available and data can be distributed and/or replicated (e.g., the Earth System Grid Federation (ESGF) serving the Coupled Model Intercomparison Project, Phase 5 (CMIP5) experiment, providing access to 2.5PB of data for the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5). Most of the tools currently available for scientific data analysis in the climate domain fail at large scale since they: (1) are desktop based and need the data locally; (2) are sequential, so do not benefit from available multicore/parallel machines; (3) do not provide declarative languages to express scientific data analysis tasks; (4) are domain-specific, which ties their adoption to a specific domain; and (5) do not provide a workflow support, to enable the definition of complex "experiments". The Ophidia project aims at facing most of the challenges highlighted above by providing a big data analytics framework for eScience. Ophidia provides declarative, server-side, and parallel data analysis, jointly with an internal storage model able to efficiently deal with multidimensional data and a hierarchical data organization to manage large data volumes ("datacubes"). The project relies on a strong background of high performance database management and OLAP systems to manage large scientific data sets. It also provides a native workflow management support, to define processing chains and workflows with tens to hundreds of data analytics operators to build real scientific use cases. With regard to interoperability aspects, the talk will present the contribution provided both to the RDA Working Group on Array Databases, and the Earth System Grid Federation (ESGF) Compute Working Team. Also highlighted will be the results of large scale climate model intercomparison data analysis experiments, for example: (1) defined in the context of the EU H2020 INDIGO-DataCloud project; (2) implemented in a real geographically distributed environment involving CMCC (Italy) and LLNL (US) sites; (3) exploiting Ophidia as server-side, parallel analytics engine; and (4) applied on real CMIP5 data sets available through ESGF.

Wireless remote control of clinical image workflow: using a PDA for off-site distribution and disaster recovery.

PubMed

Documet, Jorge; Liu, Brent J; Documet, Luis; Huang, H K

2006-07-01

This paper describes a picture archiving and communication system (PACS) tool based on Web technology that remotely manages medical images between a PACS archive and remote destinations. Successfully implemented in a clinical environment and also demonstrated for the past 3 years at the conferences of various organizations, including the Radiological Society of North America, this tool provides a very practical and simple way to manage a PACS, including off-site image distribution and disaster recovery. The application is robust and flexible and can be used on a standard PC workstation or a Tablet PC, but more important, it can be used with a personal digital assistant (PDA). With a PDA, the Web application becomes a powerful wireless and mobile image management tool. The application's quick and easy-to-use features allow users to perform Digital Imaging and Communications in Medicine (DICOM) queries and retrievals with a single interface, without having to worry about the underlying configuration of DICOM nodes. In addition, this frees up dedicated PACS workstations to perform their specialized roles within the PACS workflow. This tool has been used at Saint John's Health Center in Santa Monica, California, for 2 years. The average number of queries per month is 2,021, with 816 C-MOVE retrieve requests. Clinical staff members can use PDAs to manage image workflow and PACS examination distribution conveniently for off-site consultations by referring physicians and radiologists and for disaster recovery. This solution also improves radiologists' effectiveness and efficiency in health care delivery both within radiology departments and for off-site clinical coverage.

Rethinking Clinical Workflow.

PubMed

Schlesinger, Joseph J; Burdick, Kendall; Baum, Sarah; Bellomy, Melissa; Mueller, Dorothee; MacDonald, Alistair; Chern, Alex; Chrouser, Kristin; Burger, Christie

2018-03-01

The concept of clinical workflow borrows from management and leadership principles outside of medicine. The only way to rethink clinical workflow is to understand the neuroscience principles that underlie attention and vigilance. With any implementation to improve practice, there are human factors that can promote or impede progress. Modulating the environment and working as a team to take care of patients is paramount. Clinicians must continually rethink clinical workflow, evaluate progress, and understand that other industries have something to offer. Then, novel approaches can be implemented to take the best care of patients. Copyright © 2017 Elsevier Inc. All rights reserved.

MASCAL: RFID Tracking of Patients, Staff and Equipment to Enhance Hospital Response to Mass Casualty Events

PubMed Central

Fry, Emory A.; Lenert, Leslie A.

2005-01-01

Most medical facilities practice managing the large numbers of seriously injured patients expected during catastrophic events. As the demands on the healthcare team increase, however, the challenges faced by managers escalate, workflow bottlenecks develop and system capacity decreases. This paper describes MASCAL, an integrated software–hardware system designed to enhance management of resources at a hospital during a mass casualty situation. MASCAL uses active 802.11b asset tags to track patients, equipment and staff during the response to a disaster. The system integrates tag position information with data from personnel databases, medical information systems, registration applications and the US Navy’s TACMEDCS triage application in a custom visual disaster management environment. MASCAL includes interfaces for a hospital command center, local area managers (emergency room, operating suites, radiology, etc.) and registration personnel. MASCAL is an operational system undergoing functional evaluation at the Naval Medical Center, San Diego, CA. PMID:16779042

Anatomy of an anesthesia information management system.

PubMed

Shah, Nirav J; Tremper, Kevin K; Kheterpal, Sachin

2011-09-01

Anesthesia information management systems (AIMS) have become more prevalent as more sophisticated hardware and software have increased usability and reliability. National mandates and incentives have driven adoption as well. AIMS can be developed in one of several software models (Web based, client/server, or incorporated into a medical device). Irrespective of the development model, the best AIMS have a feature set that allows for comprehensive management of workflow for an anesthesiologist. Key features include preoperative, intraoperative, and postoperative documentation; quality assurance; billing; compliance and operational reporting; patient and operating room tracking; and integration with hospital electronic medical records. Copyright © 2011 Elsevier Inc. All rights reserved.

CyberShake: Running Seismic Hazard Workflows on Distributed HPC Resources

NASA Astrophysics Data System (ADS)

Callaghan, S.; Maechling, P. J.; Graves, R. W.; Gill, D.; Olsen, K. B.; Milner, K. R.; Yu, J.; Jordan, T. H.

2013-12-01

As part of its program of earthquake system science research, the Southern California Earthquake Center (SCEC) has developed a simulation platform, CyberShake, to perform physics-based probabilistic seismic hazard analysis (PSHA) using 3D deterministic wave propagation simulations. CyberShake performs PSHA by simulating a tensor-valued wavefield of Strain Green Tensors, and then using seismic reciprocity to calculate synthetic seismograms for about 415,000 events per site of interest. These seismograms are processed to compute ground motion intensity measures, which are then combined with probabilities from an earthquake rupture forecast to produce a site-specific hazard curve. Seismic hazard curves for hundreds of sites in a region can be used to calculate a seismic hazard map, representing the seismic hazard for a region. We present a recently completed PHSA study in which we calculated four CyberShake seismic hazard maps for the Southern California area to compare how CyberShake hazard results are affected by different SGT computational codes (AWP-ODC and AWP-RWG) and different community velocity models (Community Velocity Model - SCEC (CVM-S4) v11.11 and Community Velocity Model - Harvard (CVM-H) v11.9). We present our approach to running workflow applications on distributed HPC resources, including systems without support for remote job submission. We show how our approach extends the benefits of scientific workflows, such as job and data management, to large-scale applications on Track 1 and Leadership class open-science HPC resources. We used our distributed workflow approach to perform CyberShake Study 13.4 on two new NSF open-science HPC computing resources, Blue Waters and Stampede, executing over 470 million tasks to calculate physics-based hazard curves for 286 locations in the Southern California region. For each location, we calculated seismic hazard curves with two different community velocity models and two different SGT codes, resulting in over 1100 hazard curves. We will report on the performance of this CyberShake study, four times larger than previous studies. Additionally, we will examine the challenges we face applying these workflow techniques to additional open-science HPC systems and discuss whether our workflow solutions continue to provide value to our large-scale PSHA calculations.

A task-based support architecture for developing point-of-care clinical decision support systems for the emergency department.

PubMed

Wilk, S; Michalowski, W; O'Sullivan, D; Farion, K; Sayyad-Shirabad, J; Kuziemsky, C; Kukawka, B

2013-01-01

The purpose of this study was to create a task-based support architecture for developing clinical decision support systems (CDSSs) that assist physicians in making decisions at the point-of-care in the emergency department (ED). The backbone of the proposed architecture was established by a task-based emergency workflow model for a patient-physician encounter. The architecture was designed according to an agent-oriented paradigm. Specifically, we used the O-MaSE (Organization-based Multi-agent System Engineering) method that allows for iterative translation of functional requirements into architectural components (e.g., agents). The agent-oriented paradigm was extended with ontology-driven design to implement ontological models representing knowledge required by specific agents to operate. The task-based architecture allows for the creation of a CDSS that is aligned with the task-based emergency workflow model. It facilitates decoupling of executable components (agents) from embedded domain knowledge (ontological models), thus supporting their interoperability, sharing, and reuse. The generic architecture was implemented as a pilot system, MET3-AE--a CDSS to help with the management of pediatric asthma exacerbation in the ED. The system was evaluated in a hospital ED. The architecture allows for the creation of a CDSS that integrates support for all tasks from the task-based emergency workflow model, and interacts with hospital information systems. Proposed architecture also allows for reusing and sharing system components and knowledge across disease-specific CDSSs.

Digitization workflows for flat sheets and packets of plants, algae, and fungi1

PubMed Central

Nelson, Gil; Sweeney, Patrick; Wallace, Lisa E.; Rabeler, Richard K.; Allard, Dorothy; Brown, Herrick; Carter, J. Richard; Denslow, Michael W.; Ellwood, Elizabeth R.; Germain-Aubrey, Charlotte C.; Gilbert, Ed; Gillespie, Emily; Goertzen, Leslie R.; Legler, Ben; Marchant, D. Blaine; Marsico, Travis D.; Morris, Ashley B.; Murrell, Zack; Nazaire, Mare; Neefus, Chris; Oberreiter, Shanna; Paul, Deborah; Ruhfel, Brad R.; Sasek, Thomas; Shaw, Joey; Soltis, Pamela S.; Watson, Kimberly; Weeks, Andrea; Mast, Austin R.

2015-01-01

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation’s (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7–36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged. PMID:26421256

Workflow and Electronic Health Records in Small Medical Practices

PubMed Central

Ramaiah, Mala; Subrahmanian, Eswaran; Sriram, Ram D; Lide, Bettijoyce B

2012-01-01

This paper analyzes the workflow and implementation of electronic health record (EHR) systems across different functions in small physician offices. We characterize the differences in the offices based on the levels of computerization in terms of workflow, sources of time delay, and barriers to using EHR systems to support the entire workflow. The study was based on a combination of questionnaires, interviews, in situ observations, and data collection efforts. This study was not intended to be a full-scale time-and-motion study with precise measurements but was intended to provide an overview of the potential sources of delays while performing office tasks. The study follows an interpretive model of case studies rather than a large-sample statistical survey of practices. To identify time-consuming tasks, workflow maps were created based on the aggregated data from the offices. The results from the study show that specialty physicians are more favorable toward adopting EHR systems than primary care physicians are. The barriers to adoption of EHR systems by primary care physicians can be attributed to the complex workflows that exist in primary care physician offices, leading to nonstandardized workflow structures and practices. Also, primary care physicians would benefit more from EHR systems if the systems could interact with external entities. PMID:22737096

Leveraging workflow control patterns in the domain of clinical practice guidelines.

PubMed

Kaiser, Katharina; Marcos, Mar

2016-02-10

Clinical practice guidelines (CPGs) include recommendations describing appropriate care for the management of patients with a specific clinical condition. A number of representation languages have been developed to support executable CPGs, with associated authoring/editing tools. Even with tool assistance, authoring of CPG models is a labor-intensive task. We aim at facilitating the early stages of CPG modeling task. In this context, we propose to support the authoring of CPG models based on a set of suitable procedural patterns described in an implementation-independent notation that can be then semi-automatically transformed into one of the alternative executable CPG languages. We have started with the workflow control patterns which have been identified in the fields of workflow systems and business process management. We have analyzed the suitability of these patterns by means of a qualitative analysis of CPG texts. Following our analysis we have implemented a selection of workflow patterns in the Asbru and PROforma CPG languages. As implementation-independent notation for the description of patterns we have chosen BPMN 2.0. Finally, we have developed XSLT transformations to convert the BPMN 2.0 version of the patterns into the Asbru and PROforma languages. We showed that although a significant number of workflow control patterns are suitable to describe CPG procedural knowledge, not all of them are applicable in the context of CPGs due to their focus on single-patient care. Moreover, CPGs may require additional patterns not included in the set of workflow control patterns. We also showed that nearly all the CPG-suitable patterns can be conveniently implemented in the Asbru and PROforma languages. Finally, we demonstrated that individual patterns can be semi-automatically transformed from a process specification in BPMN 2.0 to executable implementations in these languages. We propose a pattern and transformation-based approach for the development of CPG models. Such an approach can form the basis of a valid framework for the authoring of CPG models. The identification of adequate patterns and the implementation of transformations to convert patterns from a process specification into different executable implementations are the first necessary steps for our approach.

The impact of computerized provider order entry systems on inpatient clinical workflow: a literature review.

PubMed

Niazkhani, Zahra; Pirnejad, Habibollah; Berg, Marc; Aarts, Jos

2009-01-01

Previous studies have shown the importance of workflow issues in the implementation of CPOE systems and patient safety practices. To understand the impact of CPOE on clinical workflow, we developed a conceptual framework and conducted a literature search for CPOE evaluations between 1990 and June 2007. Fifty-one publications were identified that disclosed mixed effects of CPOE systems. Among the frequently reported workflow advantages were the legible orders, remote accessibility of the systems, and the shorter order turnaround times. Among the frequently reported disadvantages were the time-consuming and problematic user-system interactions, and the enforcement of a predefined relationship between clinical tasks and between providers. Regarding the diversity of findings in the literature, we conclude that more multi-method research is needed to explore CPOE's multidimensional and collective impact on especially collaborative workflow.

Workflow continuity--moving beyond business continuity in a multisite 24-7 healthcare organization.

PubMed

Kolowitz, Brian J; Lauro, Gonzalo Romero; Barkey, Charles; Black, Harry; Light, Karen; Deible, Christopher

2012-12-01

As hospitals move towards providing in-house 24 × 7 services, there is an increasing need for information systems to be available around the clock. This study investigates one organization's need for a workflow continuity solution that provides around the clock availability for information systems that do not provide highly available services. The organization investigated is a large multifacility healthcare organization that consists of 20 hospitals and more than 30 imaging centers. A case analysis approach was used to investigate the organization's efforts. The results show an overall reduction in downtimes where radiologists could not continue their normal workflow on the integrated Picture Archiving and Communications System (PACS) solution by 94 % from 2008 to 2011. The impact of unplanned downtimes was reduced by 72 % while the impact of planned downtimes was reduced by 99.66 % over the same period. Additionally more than 98 h of radiologist impact due to a PACS upgrade in 2008 was entirely eliminated in 2011 utilizing the system created by the workflow continuity approach. Workflow continuity differs from high availability and business continuity in its design process and available services. Workflow continuity only ensures that critical workflows are available when the production system is unavailable due to scheduled or unscheduled downtimes. Workflow continuity works in conjunction with business continuity and highly available system designs. The results of this investigation revealed that this approach can add significant value to organizations because impact on users is minimized if not eliminated entirely.

Software to Manage the Unmanageable

NASA Technical Reports Server (NTRS)

2005-01-01

In 1995, NASA s Jet Propulsion Laboratory (JPL) contracted Redmond, Washington-based Lucidoc Corporation, to design a technology infrastructure to automate the intersection between policy management and operations management with advanced software that automates document workflow, document status, and uniformity of document layout. JPL had very specific parameters for the software. It expected to store and catalog over 8,000 technical and procedural documents integrated with hundreds of processes. The project ended in 2000, but NASA still uses the resulting highly secure document management system, and Lucidoc has managed to help other organizations, large and small, with integrating document flow and operations management to ensure a compliance-ready culture.

Realizing what's essential: a case study on integrating electronic journal management into a print-centric technical services department.

PubMed

Dollar, Daniel M; Gallagher, John; Glover, Janis; Marone, Regina Kenny; Crooker, Cynthia

2007-04-01

To support migration from print to electronic resources, the Cushing/Whitney Medical Library at Yale University reorganized its Technical Services Department to focus on managing electronic resources. The library hired consultants to help plan the changes and to present recommendations for integrating electronic resource management into every position. The library task force decided to focus initial efforts on the periodical collection. To free staff time to devote to electronic journals, most of the print subscriptions were switched to online only and new workflows were developed for e-journals. Staff learned new responsibilities such as activating e-journals, maintaining accurate holdings information in the online public access catalog and e-journals database ("electronic shelf reading"), updating the link resolver knowledgebase, and troubleshooting. All of the serials team members now spend significant amounts of time managing e-journals. The serials staff now spends its time managing the materials most important to the library's clientele (e-journals and databases). The team's proactive approach to maintenance work and rapid response to reported problems should improve patrons' experiences using e-journals. The library is taking advantage of new technologies such as an electronic resource management system, and library workflows and procedures will continue to evolve as technology changes.

Realizing what's essential: a case study on integrating electronic journal management into a print-centric technicalservices department

PubMed Central

Dollar, Daniel M.; Gallagher, John; Glover, Janis; Marone, Regina Kenny; Crooker, Cynthia

2007-01-01

Objective: To support migration from print to electronic resources, the Cushing/Whitney Medical Library at Yale University reorganized its Technical Services Department to focus on managing electronic resources. Methods: The library hired consultants to help plan the changes and to present recommendations for integrating electronic resource management into every position. The library task force decided to focus initial efforts on the periodical collection. To free staff time to devote to electronic journals, most of the print subscriptions were switched to online only and new workflows were developed for e-journals. Results: Staff learned new responsibilities such as activating e-journals, maintaining accurate holdings information in the online public access catalog and e-journals database (“electronic shelf reading”), updating the link resolver knowledgebase, and troubleshooting. All of the serials team members now spend significant amounts of time managing e-journals. Conclusions: The serials staff now spends its time managing the materials most important to the library's clientele (e-journals and databases). The team's proactive approach to maintenance work and rapid response to reported problems should improve patrons' experiences using e-journals. The library is taking advantage of new technologies such as an electronic resource management system, and library workflows and procedures will continue to evolve as technology changes. PMID:17443247

Everware toolkit. Supporting reproducible science and challenge-driven education.

NASA Astrophysics Data System (ADS)

Ustyuzhanin, A.; Head, T.; Babuschkin, I.; Tiunov, A.

2017-10-01

Modern science clearly demands for a higher level of reproducibility and collaboration. To make research fully reproducible one has to take care of several aspects: research protocol description, data access, environment preservation, workflow pipeline, and analysis script preservation. Version control systems like git help with the workflow and analysis scripts part. Virtualization techniques like Docker or Vagrant can help deal with environments. Jupyter notebooks are a powerful platform for conducting research in a collaborative manner. We present project Everware that seamlessly integrates git repository management systems such as Github or Gitlab, Docker and Jupyter helping with a) sharing results of real research and b) boosts education activities. With the help of Everware one can not only share the final artifacts of research but all the depth of the research process. This been shown to be extremely helpful during organization of several data analysis hackathons and machine learning schools. Using Everware participants could start from an existing solution instead of starting from scratch. They could start contributing immediately. Everware allows its users to make use of their own computational resources to run the workflows they are interested in, which leads to higher scalability of the toolkit.

Executing SADI services in Galaxy.

PubMed

Aranguren, Mikel Egaña; González, Alejandro Rodríguez; Wilkinson, Mark D

2014-01-01

In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. SADI-Galaxy bridges the gap between Galaxy, an easy to use but "static" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.

Process-driven information management system at a biotech company: concept and implementation.

PubMed

Gobbi, Alberto; Funeriu, Sandra; Ioannou, John; Wang, Jinyi; Lee, Man-Ling; Palmer, Chris; Bamford, Bob; Hewitt, Robin

2004-01-01

While established pharmaceutical companies have chemical information systems in place to manage their compounds and the associated data, new startup companies need to implement these systems from scratch. Decisions made early in the design phase usually have long lasting effects on the expandability, maintenance effort, and costs associated with the information management system. Careful analysis of work and data flows, both inter- and intradepartmental, and identification of existing dependencies between activities are important. This knowledge is required to implement an information management system, which enables the research community to work efficiently by avoiding redundant registration and processing of data and by timely provision of the data whenever needed. This paper first presents the workflows existing at Anadys, then ARISE, the research information management system developed in-house at Anadys. ARISE was designed to support the preclinical drug discovery process and covers compound registration, analytical quality control, inventory management, high-throughput screening, lower throughput screening, and data reporting.

Digital disruption ?syndromes.

PubMed

Sullivan, Clair; Staib, Andrew

2017-05-18

The digital transformation of hospitals in Australia is occurring rapidly in order to facilitate innovation and improve efficiency. Rapid transformation can cause temporary disruption of hospital workflows and staff as processes are adapted to the new digital workflows. The aim of this paper is to outline various types of digital disruption and some strategies for effective management. A large tertiary university hospital recently underwent a rapid, successful roll-out of an integrated electronic medical record (EMR). We observed this transformation and propose several digital disruption "syndromes" to assist with understanding and management during digital transformation: digital deceleration, digital transparency, digital hypervigilance, data discordance, digital churn and post-digital 'depression'. These 'syndromes' are defined and discussed in detail. Successful management of this temporary digital disruption is important to ensure a successful transition to a digital platform. What is known about this topic? Digital disruption is defined as the changes facilitated by digital technologies that occur at a pace and magnitude that disrupt established ways of value creation, social interactions, doing business and more generally our thinking. Increasing numbers of Australian hospitals are implementing digital solutions to replace traditional paper-based systems for patient care in order to create opportunities for improved care and efficiencies. Such large scale change has the potential to create transient disruption to workflows and staff. Managing this temporary disruption effectively is an important factor in the successful implementation of an EMR. What does this paper add? A large tertiary university hospital recently underwent a successful rapid roll-out of an integrated electronic medical record (EMR) to become Australia's largest digital hospital over a 3-week period. We observed and assisted with the management of several cultural, behavioural and operational forms of digital disruption which lead us to propose some digital disruption 'syndromes'. The definition and management of these 'syndromes' are discussed in detail. What are the implications for practitioners? Minimising the temporary effects of digital disruption in hospitals requires an understanding that these digital 'syndromes' are to be expected and actively managed during large-scale transformation.

Evidence for electronic health record systems in physical therapy.

PubMed

Vreeman, Daniel J; Taggard, Samuel L; Rhine, Michael D; Worrell, Teddy W

2006-03-01

With increasing pressures to better manage clinical information, we investigated the role of electronic health record (EHR) systems in physical therapist practice through a critical review of the literature. We reviewed studies that met our predefined criteria after independent review by 3 authors. The investigators in all of the reviewed studies reported benefits, including improved reporting, operational efficiency, interdepartmental communication, data accuracy, and capability for future research. In 7 studies, the investigators reported barriers, including challenges with behavior modification, equipment inadequacy, and training. The investigators in all studies reported key success factors, including end-user participation, adequate training, workflow analysis, and data standardization. This review suggests that EHRs have potential benefits for physical therapists. The authors formed the following recommendations based on the studies' themes: (1) incorporate workflow analysis into system design and implementation; (2) include end users, especially clinicians, in system development; (3) devote significant resources for training; (4) plan and test carefully to ensure adequate software and hardware performance; and (5) commit to data standards.

Selecting a Laboratory Information Management System for Biorepositories in Low- and Middle-Income Countries: The H3Africa Experience and Lessons Learned

PubMed Central

Musinguzi, Henry; Lwanga, Newton; Kezimbira, Dafala; Kigozi, Edgar; Katabazi, Fred Ashaba; Wayengera, Misaki; Joloba, Moses Lutaakome; Abayomi, Emmanuel Akin; Swanepoel, Carmen; Croxton, Talishiea; Ozumba, Petronilla; Thankgod, Anazodo; van Zyl, Lizelle; Mayne, Elizabeth Sarah; Kader, Mukthar; Swartz, Garth

2017-01-01

Biorepositories in Africa need significant infrastructural support to meet International Society for Biological and Environmental Repositories (ISBER) Best Practices to support population-based genomics research. ISBER recommends a biorepository information management system which can manage workflows from biospecimen receipt to distribution. The H3Africa Initiative set out to develop regional African biorepositories where Uganda, Nigeria, and South Africa were successfully awarded grants to develop the state-of-the-art biorepositories. The biorepositories carried out an elaborate process to evaluate and choose a laboratory information management system (LIMS) with the aim of integrating the three geographically distinct sites. In this article, we review the processes, African experience, lessons learned, and make recommendations for choosing a biorepository LIMS in the African context.

Implementation of Cyberinfrastructure and Data Management Workflow for a Large-Scale Sensor Network

NASA Astrophysics Data System (ADS)

Jones, A. S.; Horsburgh, J. S.

2014-12-01

Monitoring with in situ environmental sensors and other forms of field-based observation presents many challenges for data management, particularly for large-scale networks consisting of multiple sites, sensors, and personnel. The availability and utility of these data in addressing scientific questions relies on effective cyberinfrastructure that facilitates transformation of raw sensor data into functional data products. It also depends on the ability of researchers to share and access the data in useable formats. In addition to addressing the challenges presented by the quantity of data, monitoring networks need practices to ensure high data quality, including procedures and tools for post processing. Data quality is further enhanced if practitioners are able to track equipment, deployments, calibrations, and other events related to site maintenance and associate these details with observational data. In this presentation we will describe the overall workflow that we have developed for research groups and sites conducting long term monitoring using in situ sensors. Features of the workflow include: software tools to automate the transfer of data from field sites to databases, a Python-based program for data quality control post-processing, a web-based application for online discovery and visualization of data, and a data model and web interface for managing physical infrastructure. By automating the data management workflow, the time from collection to analysis is reduced and sharing and publication is facilitated. The incorporation of metadata standards and descriptions and the use of open-source tools enhances the sustainability and reusability of the data. We will describe the workflow and tools that we have developed in the context of the iUTAH (innovative Urban Transitions and Aridregion Hydrosustainability) monitoring network. The iUTAH network consists of aquatic and climate sensors deployed in three watersheds to monitor Gradients Along Mountain to Urban Transitions (GAMUT). The variety of environmental sensors and the multi-watershed, multi-institutional nature of the network necessitate a well-planned and efficient workflow for acquiring, managing, and sharing sensor data, which should be useful for similar large-scale and long-term networks.

An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64.

PubMed

Winkler, Robert

2015-01-01

In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because of too specific computing platforms. This effect, known as 'workflow decay', can be diminished by using a standardized informatic infrastructure. Thus, we compiled an integrated platform, which contains ready-to-use tools and workflows for mass spectrometry data analysis. Apart from general unit operations, such as peak picking and identification of proteins and metabolites, we put a strong emphasis on the statistical validation of results and Data Mining. MASSyPup64 includes e.g., the OpenMS/TOPPAS framework, the Trans-Proteomic-Pipeline programs, the ProteoWizard tools, X!Tandem, Comet and SpiderMass. The statistical computing language R is installed with packages for MS data analyses, such as XCMS/metaXCMS and MetabR. The R package Rattle provides a user-friendly access to multiple Data Mining methods. Further, we added the non-conventional spreadsheet program teapot for editing large data sets and a command line tool for transposing large matrices. Individual programs, console commands and modules can be integrated using the Workflow Management System (WMS) taverna. We explain the useful combination of the tools by practical examples: (1) A workflow for protein identification and validation, with subsequent Association Analysis of peptides, (2) Cluster analysis and Data Mining in targeted Metabolomics, and (3) Raw data processing, Data Mining and identification of metabolites in untargeted Metabolomics. Association Analyses reveal relationships between variables across different sample sets. We present its application for finding co-occurring peptides, which can be used for target proteomics, the discovery of alternative biomarkers and protein-protein interactions. Data Mining derived models displayed a higher robustness and accuracy for classifying sample groups in targeted Metabolomics than cluster analyses. Random Forest models do not only provide predictive models, which can be deployed for new data sets, but also the variable importance. We demonstrate that the later is especially useful for tracking down significant signals and affected pathways in untargeted Metabolomics. Thus, Random Forest modeling supports the unbiased search for relevant biological features in Metabolomics. Our results clearly manifest the importance of Data Mining methods to disclose non-obvious information in biological mass spectrometry . The application of a Workflow Management System and the integration of all required programs and data in a consistent platform makes the presented data analyses strategies reproducible for non-expert users. The simple remastering process and the Open Source licenses of MASSyPup64 (http://www.bioprocess.org/massypup/) enable the continuous improvement of the system.

End-to-end interoperability and workflows from building architecture design to one or more simulations

DOEpatents

Chao, Tian-Jy; Kim, Younghun

2015-02-10

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented that communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.

Identification and Management of Information Problems by Emergency Department Staff

PubMed Central

Murphy, Alison R.; Reddy, Madhu C.

2014-01-01

Patient-care teams frequently encounter information problems during their daily activities. These information problems include wrong, outdated, conflicting, incomplete, or missing information. Information problems can negatively impact the patient-care workflow, lead to misunderstandings about patient information, and potentially lead to medical errors. Existing research focuses on understanding the cause of these information problems and the impact that they can have on the hospital’s workflow. However, there is limited research on how patient-care teams currently identify and manage information problems that they encounter during their work. Through qualitative observations and interviews in an emergency department (ED), we identified the types of information problems encountered by ED staff, and examined how they identified and managed the information problems. We also discuss the impact that these information problems can have on the patient-care teams, including the cascading effects of information problems on workflow and the ambiguous accountability for fixing information problems within collaborative teams. PMID:25954457

Workarounds to Intended Use of Health Information Technology: A Narrative Review of the Human Factors Engineering Literature.

PubMed

Patterson, Emily S

2018-05-01

Objective To integrate and synthesize insights from recent studies of workarounds to the intended use of health information technology (HIT) by health care professionals. Background Systems are safest when the documentation of how work is done in policies and procedures closely matches what people actually do when they are working. Proactively identifying and managing workarounds to the intended use of technology, including deviations from expected workflows, can improve system safety. Method A narrative review of studies of workarounds with HIT was conducted to identify themes in the literature. Results Three themes were identified: (1) Users circumvented new additional steps in the workflow when using HIT, (2) interdisciplinary team members communicated via HIT in text fields that were intended for other purposes, and (3) locally developed paper-based and manual whiteboard systems were used instead of HIT to support situation awareness of individuals and groups; an example of a locally developed system was handwritten notes about a patient on a piece of paper folded up and carried in a nurse's pocket. Conclusion Workarounds were employed to avoid changes to workflow, enable interdisciplinary communication, coordinate activities, and have real-time portable access to summarized and synthesized information. Application Implications for practice include providing summary overview displays, explicitly supporting role-based communication and coordination through HIT, and reducing the risk to reputation due to electronic monitoring of individual performance.

Improving clinical laboratory efficiency: a time-motion evaluation of the Abbott m2000 RealTime and Roche COBAS AmpliPrep/COBAS TaqMan PCR systems for the simultaneous quantitation of HIV-1 RNA and HCV RNA.

PubMed

Amendola, Alessandra; Coen, Sabrina; Belladonna, Stefano; Pulvirenti, F Renato; Clemens, John M; Capobianchi, M Rosaria

2011-08-01

Diagnostic laboratories need automation that facilitates efficient processing and workflow management to meet today's challenges for expanding services and reducing cost, yet maintaining the highest levels of quality. Processing efficiency of two commercially available automated systems for quantifying HIV-1 and HCV RNA, Abbott m2000 system and Roche COBAS Ampliprep/COBAS TaqMan 96 (docked) systems (CAP/CTM), was evaluated in a mid/high throughput workflow laboratory using a representative daily workload of 24 HCV and 72 HIV samples. Three test scenarios were evaluated: A) one run with four batches on the CAP/CTM system, B) two runs on the Abbott m2000 and C) one run using the Abbott m2000 maxCycle feature (maxCycle) for co-processing these assays. Cycle times for processing, throughput and hands-on time were evaluated. Overall processing cycle time was 10.3, 9.1 and 7.6 h for Scenarios A), B) and C), respectively. Total hands-on time for each scenario was, in order, 100.0 (A), 90.3 (B) and 61.4 min (C). The interface of an automated analyzer to the laboratory workflow, notably system set up for samples and reagents and clean up functions, are as important as the automation capability of the analyzer for the overall impact to processing efficiency and operator hands-on time.

Integration of implant planning workflows into the PACS infrastructure

NASA Astrophysics Data System (ADS)

Gessat, Michael; Strauß, Gero; Burgert, Oliver

2008-03-01

The integration of imaging devices, diagnostic workstations, and image servers into Picture Archiving and Communication Systems (PACS) has had an enormous effect on the efficiency of radiology workflows. The standardization of the information exchange between the devices with the DICOM standard has been an essential precondition for that development. For surgical procedures, no such infrastructure exists. With the increasingly important role computerized planning and assistance systems play in the surgical domain, an infrastructure that unifies the communication between devices becomes necessary. In recent publications, the need for a modularized system design has been established. A reference architecture for a Therapy Imaging and Model Management System (TIMMS) has been proposed. It was accepted by the DICOM Working Group 6 as the reference architecture for DICOM developments for surgery. In this paper we propose the inclusion of implant planning systems into the PACS infrastructure. We propose a generic information model for the patient specific selection and positioning of implants from a repository according to patient image data. The information models are based on clinical workflows from ENT, cardiac, and orthopedic surgery as well as technical requirements derived from different use cases and systems. We show an exemplary implementation of the model for application in ENT surgery: the selection and positioning of an ossicular implant in the middle ear. An implant repository is stored in the PACS. It makes use of an experimental implementation of the Surface Mesh Module that is currently being developed as extension to the DICOM standard.

Scientific Workflows and the Sensor Web for Virtual Environmental Observatories

NASA Astrophysics Data System (ADS)

Simonis, I.; Vahed, A.

2008-12-01

Virtual observatories mature from their original domain and become common practice for earth observation research and policy building. The term Virtual Observatory originally came from the astronomical research community. Here, virtual observatories provide universal access to the available astronomical data archives of space and ground-based observatories. Further on, as those virtual observatories aim at integrating heterogeneous ressources provided by a number of participating organizations, the virtual observatory acts as a coordinating entity that strives for common data analysis techniques and tools based on common standards. The Sensor Web is on its way to become one of the major virtual observatories outside of the astronomical research community. Like the original observatory that consists of a number of telescopes, each observing a specific part of the wave spectrum and with a collection of astronomical instruments, the Sensor Web provides a multi-eyes perspective on the current, past, as well as future situation of our planet and its surrounding spheres. The current view of the Sensor Web is that of a single worldwide collaborative, coherent, consistent and consolidated sensor data collection, fusion and distribution system. The Sensor Web can perform as an extensive monitoring and sensing system that provides timely, comprehensive, continuous and multi-mode observations. This technology is key to monitoring and understanding our natural environment, including key areas such as climate change, biodiversity, or natural disasters on local, regional, and global scales. The Sensor Web concept has been well established with ongoing global research and deployment of Sensor Web middleware and standards and represents the foundation layer of systems like the Global Earth Observation System of Systems (GEOSS). The Sensor Web consists of a huge variety of physical and virtual sensors as well as observational data, made available on the Internet at standardized interfaces. All data sets and sensor communication follow well-defined abstract models and corresponding encodings, mostly developed by the OGC Sensor Web Enablement initiative. Scientific progress is currently accelerated by an emerging new concept called scientific workflows, which organize and manage complex distributed computations. A scientific workflow represents and records the highly complex processes that a domain scientist typically would follow in exploration, discovery and ultimately, transformation of raw data to publishable results. The challenge is now to integrate the benefits of scientific workflows with those provided by the Sensor Web in order to leverage all resources for scientific exploration, problem solving, and knowledge generation. Scientific workflows for the Sensor Web represent the next evolutionary step towards efficient, powerful, and flexible earth observation frameworks and platforms. Those platforms support the entire process from capturing data, sharing and integrating, to requesting additional observations. Multiple sites and organizations will participate on single platforms and scientists from different countries and organizations interact and contribute to large-scale research projects. Simultaneously, the data- and information overload becomes manageable, as multiple layers of abstraction will free scientists to deal with underlying data-, processing or storage peculiarities. The vision are automated investigation and discovery mechanisms that allow scientists to pose queries to the system, which in turn would identify potentially related resources, schedules processing tasks and assembles all parts in workflows that may satisfy the query.

Workflows for Full Waveform Inversions

NASA Astrophysics Data System (ADS)

Boehm, Christian; Krischer, Lion; Afanasiev, Michael; van Driel, Martin; May, Dave A.; Rietmann, Max; Fichtner, Andreas

2017-04-01

Despite many theoretical advances and the increasing availability of high-performance computing clusters, full seismic waveform inversions still face considerable challenges regarding data and workflow management. While the community has access to solvers which can harness modern heterogeneous computing architectures, the computational bottleneck has fallen to these often manpower-bounded issues that need to be overcome to facilitate further progress. Modern inversions involve huge amounts of data and require a tight integration between numerical PDE solvers, data acquisition and processing systems, nonlinear optimization libraries, and job orchestration frameworks. To this end we created a set of libraries and applications revolving around Salvus (http://salvus.io), a novel software package designed to solve large-scale full waveform inverse problems. This presentation focuses on solving passive source seismic full waveform inversions from local to global scales with Salvus. We discuss (i) design choices for the aforementioned components required for full waveform modeling and inversion, (ii) their implementation in the Salvus framework, and (iii) how it is all tied together by a usable workflow system. We combine state-of-the-art algorithms ranging from high-order finite-element solutions of the wave equation to quasi-Newton optimization algorithms using trust-region methods that can handle inexact derivatives. All is steered by an automated interactive graph-based workflow framework capable of orchestrating all necessary pieces. This naturally facilitates the creation of new Earth models and hopefully sparks new scientific insights. Additionally, and even more importantly, it enhances reproducibility and reliability of the final results.

Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

PubMed Central

Morisawa, Hiraku; Hirota, Mikako; Toda, Tosifusa

2006-01-01

Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved. PMID:17018156

TAMEE: data management and analysis for tissue microarrays.

PubMed

Thallinger, Gerhard G; Baumgartner, Kerstin; Pirklbauer, Martin; Uray, Martina; Pauritsch, Elke; Mehes, Gabor; Buck, Charles R; Zatloukal, Kurt; Trajanoski, Zlatko

2007-03-07

With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator. We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from http://genome.tugraz.at/Software/TAMEE.

Patient handling system for carbon ion beam scanning therapy

PubMed Central

Shirai, Toshiyuki; Takei, Yuka; Furukawa, Takuji; Inaniwa, Taku; Matsuzaki, Yuka; Kumagai, Motoki; Murakami, Takeshi; Noda, Koji

2012-01-01

Our institution established a new treatment facility for carbon ion beam scanning therapy in 2010. The major advantages of scanning beam treatment compared to the passive beam treatment are the following: high dose conformation with less excessive dose to the normal tissues, no bolus compensator and patient collimator/ multi‐leaf collimator, better dose efficiency by reducing the number of scatters. The new facility was designed to solve several problems encountered in the existing facility, at which several thousand patients were treated over more than 15 years. Here, we introduce the patient handling system in the new treatment facility. The new facility incorporates three main systems, a scanning irradiation system (S‐IR), treatment planning system (TPS), and patient handling system (PTH). The PTH covers a wide range of functions including imaging, geometrical/position accuracy including motion management (immobilization, robotic arm treatment bed), layout of the treatment room, treatment workflow, software, and others. The first clinical trials without respiratory gating have been successfully started. The PTH allows a reduction in patient stay in the treatment room to as few as 7 min. The PTH plays an important role in carbon ion beam scanning therapy at the new institution, particularly in the management of patient handling, application of image‐guided therapy, and improvement of treatment workflow, and thereby allows substantially better treatment at minimum cost. PACS numbers: 87.56.‐v; 87.57.‐s; 87.55.‐x PMID:23149784

An information management system for patients with tuberculosis: usability assessment with end-users.

PubMed

Darby, Jonathan; Black, Jim; Morrison, David; Buising, Kirsty

2012-01-01

Information systems with clinical decision support (CDS) offer great potential to assist the co-ordination of patients with chronic diseases and to improve patient care. Despite this, few have entered routine clinical use. Tuberculosis (TB) is an infection of public health importance. It has complex interactions with many comorbid conditions, requires close supervised care and prolonged treatment for effective cure. These features make it suitable for use with an information management system with CDS features. In close consultation with key stakeholders, a clinical application was developed for the management of TB patients in Victoria. A formal usability assessment using semi-structured case-scenario based exercises was performed. Subjects were 12 individuals closely involved in the care of TB patients, including Infectious Diseases and Respiratory Physicians, and Public Health Nurses. Two researchers conducted the sessions, independently analysed responses and discrepancies compared to the voice record for validity. Despite varied computer experience, responses were positive regarding user interface and content. Data location was not always intuitive, however this improved with familiarity of the program. Decision support was considered valuable, with useful suggestions for expansion of these features. Automated reporting for correspondence and notification to the Health Department were felt worth the initial investment in data entry. An important workflow-based issue regarding dismissal of alerts and several errors were detected. Usability assessment validated many design elements of the system, provided a unique insight into workflow issues faced by users and hopefully will impact on its ultimate clinical utility.

Embracing the Archives: How NPR Librarians Turned Their Collection into a Workflow Tool

ERIC Educational Resources Information Center

Sin, Lauren; Daugert, Katie

2013-01-01

Several years ago, National Public Radio (NPR) librarians began developing a new content management system (CMS). It was intended to offer desktop access for all NPR-produced content, including transcripts, audio, and metadata. Fast-forward to 2011, and their shiny, new database, Artemis, was ready for debut. Their next challenge: to teach a staff…

JAX Colony Management System (JCMS): an extensible colony and phenotype data management system.

PubMed

Donnelly, Chuck J; McFarland, Mike; Ames, Abigail; Sundberg, Beth; Springer, Dave; Blauth, Peter; Bult, Carol J

2010-04-01

The Jackson Laboratory Colony Management System (JCMS) is a software application for managing data and information related to research mouse colonies, associated biospecimens, and experimental protocols. JCMS runs directly on computers that run one of the PC Windows operating systems, but can be accessed via web browser interfaces from any computer running a Windows, Macintosh, or Linux operating system. JCMS can be configured for a single user or multiple users in small- to medium-size work groups. The target audience for JCMS includes laboratory technicians, animal colony managers, and principal investigators. The application provides operational support for colony management and experimental workflows, sample and data tracking through transaction-based data entry forms, and date-driven work reports. Flexible query forms allow researchers to retrieve database records based on user-defined criteria. Recent advances in handheld computers with integrated barcode readers, middleware technologies, web browsers, and wireless networks add to the utility of JCMS by allowing real-time access to the database from any networked computer.

Streamling the Change Management with Business Rules

NASA Technical Reports Server (NTRS)

Savela, Christopher

2015-01-01

Will discuss how their organization is trying to streamline workflows and the change management process with business rules. In looking for ways to make things more efficient and save money one way is to reduce the work the workflow task approvers have to do when reviewing affected items. Will share the technical details of the business rules, how to implement them, how to speed up the development process by using the API to demonstrate the rules in action.

gProcess and ESIP Platforms for Satellite Imagery Processing over the Grid

NASA Astrophysics Data System (ADS)

Bacu, Victor; Gorgan, Dorian; Rodila, Denisa; Pop, Florin; Neagu, Gabriel; Petcu, Dana

2010-05-01

The Environment oriented Satellite Data Processing Platform (ESIP) is developed through the SEE-GRID-SCI (SEE-GRID eInfrastructure for regional eScience) co-funded by the European Commission through FP7 [1]. The gProcess Platform [2] is a set of tools and services supporting the development and the execution over the Grid of the workflow based processing, and particularly the satelite imagery processing. The ESIP [3], [4] is build on top of the gProcess platform by adding a set of satellite image processing software modules and meteorological algorithms. The satellite images can reveal and supply important information on earth surface parameters, climate data, pollution level, weather conditions that can be used in different research areas. Generally, the processing algorithms of the satellite images can be decomposed in a set of modules that forms a graph representation of the processing workflow. Two types of workflows can be defined in the gProcess platform: abstract workflow (PDG - Process Description Graph), in which the user defines conceptually the algorithm, and instantiated workflow (iPDG - instantiated PDG), which is the mapping of the PDG pattern on particular satellite image and meteorological data [5]. The gProcess platform allows the definition of complex workflows by combining data resources, operators, services and sub-graphs. The gProcess platform is developed for the gLite middleware that is available in EGEE and SEE-GRID infrastructures [6]. gProcess exposes the specific functionality through web services [7]. The Editor Web Service retrieves information on available resources that are used to develop complex workflows (available operators, sub-graphs, services, supported resources, etc.). The Manager Web Service deals with resources management (uploading new resources such as workflows, operators, services, data, etc.) and in addition retrieves information on workflows. The Executor Web Service manages the execution of the instantiated workflows on the Grid infrastructure. In addition, this web service monitors the execution and generates statistical data that are important to evaluate performances and to optimize execution. The Viewer Web Service allows access to input and output data. To prove and to validate the utility of the gProcess and ESIP platforms there were developed the GreenView and GreenLand applications. The GreenView related functionality includes the refinement of some meteorological data such as temperature, and the calibration of the satellite images based on field measurements. The GreenLand application performs the classification of the satellite images by using a set of vegetation indices. The gProcess and ESIP platforms are used as well in GiSHEO project [8] to support the processing of Earth Observation data over the Grid in eGLE (GiSHEO eLearning Environment). Experiments of performance assessment were conducted and they have revealed that the workflow-based execution could improve the execution time of a satellite image processing algorithm [9]. It is not a reliable solution to execute all the workflow nodes on different machines. The execution of some nodes can be more time consuming and they will be performed in a longer time than other nodes. The total execution time will be affected because some nodes will slow down the execution. It is important to correctly balance the workflow nodes. Based on some optimization strategy the workflow nodes can be grouped horizontally, vertically or in a hybrid approach. In this way, those operators will be executed on one machine and also the data transfer between workflow nodes will be lower. The dynamic nature of the Grid infrastructure makes it more exposed to the occurrence of failures. These failures can occur at worker node, services availability, storage element, etc. Currently gProcess has support for some basic error prevention and error management solutions. In future, some more advanced error prevention and management solutions will be integrated in the gProcess platform. References [1] SEE-GRID-SCI Project, http://www.see-grid-sci.eu/ [2] Bacu V., Stefanut T., Rodila D., Gorgan D., Process Description Graph Composition by gProcess Platform. HiPerGRID - 3rd International Workshop on High Performance Grid Middleware, 28 May, Bucharest. Proceedings of CSCS-17 Conference, Vol.2., ISSN 2066-4451, pp. 423-430, (2009). [3] ESIP Platform, http://wiki.egee-see.org/index.php/JRA1_Commonalities [4] Gorgan D., Bacu V., Rodila D., Pop Fl., Petcu D., Experiments on ESIP - Environment oriented Satellite Data Processing Platform. SEE-GRID-SCI User Forum, 9-10 Dec 2009, Bogazici University, Istanbul, Turkey, ISBN: 978-975-403-510-0, pp. 157-166 (2009). [5] Radu, A., Bacu, V., Gorgan, D., Diagrammatic Description of Satellite Image Processing Workflow. Workshop on Grid Computing Applications Development (GridCAD) at the SYNASC Symposium, 28 September 2007, Timisoara, IEEE Computer Press, ISBN 0-7695-3078-8, 2007, pp. 341-348 (2007). [6] Gorgan D., Bacu V., Stefanut T., Rodila D., Mihon D., Grid based Satellite Image Processing Platform for Earth Observation Applications Development. IDAACS'2009 - IEEE Fifth International Workshop on "Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications", 21-23 September, Cosenza, Italy, IEEE Published in Computer Press, 247-252 (2009). [7] Rodila D., Bacu V., Gorgan D., Integration of Satellite Image Operators as Workflows in the gProcess Application. Proceedings of ICCP2009 - IEEE 5th International Conference on Intelligent Computer Communication and Processing, 27-29 Aug, 2009 Cluj-Napoca. ISBN: 978-1-4244-5007-7, pp. 355-358 (2009). [8] GiSHEO consortium, Project site, http://gisheo.info.uvt.ro [9] Bacu V., Gorgan D., Graph Based Evaluation of Satellite Imagery Processing over Grid. ISPDC 2008 - 7th International Symposium on Parallel and Distributed Computing, July 1-5, 2008, Krakow, Poland. IEEE Computer Society 2008, ISBN: 978-0-7695-3472-5, pp. 147-154.

Data Provenance Hybridization Supporting Extreme-Scale Scientific WorkflowApplications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elsethagen, Todd O.; Stephan, Eric G.; Raju, Bibi

As high performance computing (HPC) infrastructures continue to grow in capability and complexity, so do the applications that they serve. HPC and distributed-area computing (DAC) (e.g. grid and cloud) users are looking increasingly toward workflow solutions to orchestrate their complex application coupling, pre- and post-processing needs To gain insight and a more quantitative understanding of a workflow’s performance our method includes not only the capture of traditional provenance information, but also the capture and integration of system environment metrics helping to give context and explanation for a workflow’s execution. In this paper, we describe IPPD’s provenance management solution (ProvEn) andmore » its hybrid data store combining both of these data provenance perspectives.« less

Game engines and immersive displays

NASA Astrophysics Data System (ADS)

Chang, Benjamin; Destefano, Marc

2014-02-01

While virtual reality and digital games share many core technologies, the programming environments, toolkits, and workflows for developing games and VR environments are often distinct. VR toolkits designed for applications in visualization and simulation often have a different feature set or design philosophy than game engines, while popular game engines often lack support for VR hardware. Extending a game engine to support systems such as the CAVE gives developers a unified development environment and the ability to easily port projects, but involves challenges beyond just adding stereo 3D visuals. In this paper we outline the issues involved in adapting a game engine for use with an immersive display system including stereoscopy, tracking, and clustering, and present example implementation details using Unity3D. We discuss application development and workflow approaches including camera management, rendering synchronization, GUI design, and issues specific to Unity3D, and present examples of projects created for a multi-wall, clustered, stereoscopic display.

Development of a digital clinical pathway for emergency medicine: Lessons from usability testing and implementation failure.

PubMed

Gutenstein, Marc; Pickering, John W; Than, Martin

2018-06-01

Clinical pathways are used to support the management of patients in emergency departments. An existing document-based clinical pathway was used as the foundation on which to design and build a digital clinical pathway for acute chest pain, with the aim of improving clinical calculations, clinician decision-making, documentation, and data collection. Established principles of decision support system design were used to build an application within the existing electronic health record, before testing with a multidisciplinary team of doctors using a think-aloud protocol. Technical authoring was successful, however, usability testing revealed that the user experience and the flexibility of workflow within the application were critical barriers to implementation. Emergency medicine and acute care decision support systems face particular challenges to existing models of linear workflow that should be deliberately addressed in digital pathway design. We make key recommendations regarding digital pathway design in emergency medicine.

Business process re-engineering a cardiology department.

PubMed

Bakshi, Syed Murtuza Hussain

2014-01-01

The health care sector is the world's third largest industry and is facing several problems such as excessive waiting times for patients, lack of access to information, high costs of delivery and medical errors. Health care managers seek the help of process re-engineering methods to discover the best processes and to re-engineer existing processes to optimize productivity without compromising on quality. Business process re-engineering refers to the fundamental rethinking and radical redesign of business processes to achieve dramatic improvements in critical, contemporary measures of performance, such as cost, quality and speed. The present study is carried out at a tertiary care corporate hospital with 1000-plus-bed facility. A descriptive study and case study method is used with intensive, careful and complete observation of patient flow, delays, short comings in patient movement and workflow. Data is collected through observations, informal interviews and analyzed by matrix analysis. Flowcharts were drawn for the various work activities of the cardiology department including workflow of the admission process, workflow in the ward and ICCU, workflow of the patient for catheterization laboratory procedure, and in the billing and discharge process. The problems of the existing system were studied and necessary suggestions were recommended to cardiology department module with an illustrated flowchart.

Improved compliance by BPM-driven workflow automation.

PubMed

Holzmüller-Laue, Silke; Göde, Bernd; Fleischer, Heidi; Thurow, Kerstin

2014-12-01

Using methods and technologies of business process management (BPM) for the laboratory automation has important benefits (i.e., the agility of high-level automation processes, rapid interdisciplinary prototyping and implementation of laboratory tasks and procedures, and efficient real-time process documentation). A principal goal of the model-driven development is the improved transparency of processes and the alignment of process diagrams and technical code. First experiences of using the business process model and notation (BPMN) show that easy-to-read graphical process models can achieve and provide standardization of laboratory workflows. The model-based development allows one to change processes quickly and an easy adaption to changing requirements. The process models are able to host work procedures and their scheduling in compliance with predefined guidelines and policies. Finally, the process-controlled documentation of complex workflow results addresses modern laboratory needs of quality assurance. BPMN 2.0 as an automation language to control every kind of activity or subprocess is directed to complete workflows in end-to-end relationships. BPMN is applicable as a system-independent and cross-disciplinary graphical language to document all methods in laboratories (i.e., screening procedures or analytical processes). That means, with the BPM standard, a communication method of sharing process knowledge of laboratories is also available. © 2014 Society for Laboratory Automation and Screening.

Extensible Open-Source Zero-Footprint Web Viewer for Oncologic Imaging Research | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The Tumor Imaging Metrics Core (TIMC), a CCSG Shared-Resource of the Dana-Farber/Harvard Cancer Center, has developed software for managing the workflow and image measurements for oncology clinical trials. This system currently is in use across the five Harvard hospitals to manage over 600 active clinical trials, with 800 users, and has been licensed and implemented at several other Cancer Centers, including Yale, Utah/Huntsman Cancer Institute, and UW/Seattle Cancer Care Alliance.

ERM Ideas and Innovations

ERIC Educational Resources Information Center

Schmidt, Kari

2012-01-01

In this column, the author discusses how the management of e-books has introduced, at many libraries and in varying degrees, the challenges of maintaining effective technical services workflows. Four different e-book workflows are identified and explored, and the author takes a closer look at how particular variables for each are affected, such as…

Scientist-Centered Workflow Abstractions via Generic Actors, Workflow Templates, and Context-Awareness for Groundwater Modeling and Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chin, George; Sivaramakrishnan, Chandrika; Critchlow, Terence J.

2011-07-04

A drawback of existing scientific workflow systems is the lack of support to domain scientists in designing and executing their own scientific workflows. Many domain scientists avoid developing and using workflows because the basic objects of workflows are too low-level and high-level tools and mechanisms to aid in workflow construction and use are largely unavailable. In our research, we are prototyping higher-level abstractions and tools to better support scientists in their workflow activities. Specifically, we are developing generic actors that provide abstract interfaces to specific functionality, workflow templates that encapsulate workflow and data patterns that can be reused and adaptedmore » by scientists, and context-awareness mechanisms to gather contextual information from the workflow environment on behalf of the scientist. To evaluate these scientist-centered abstractions on real problems, we apply them to construct and execute scientific workflows in the specific domain area of groundwater modeling and analysis.« less

Agile based "Semi-"Automated Data ingest process : ORNL DAAC example

NASA Astrophysics Data System (ADS)

Santhana Vannan, S. K.; Beaty, T.; Cook, R. B.; Devarakonda, R.; Hook, L.; Wei, Y.; Wright, D.

2015-12-01

The ORNL DAAC archives and publishes data and information relevant to biogeochemical, ecological, and environmental processes. The data archived at the ORNL DAAC must be well formatted, self-descriptive, and documented, as well as referenced in a peer-reviewed publication. The ORNL DAAC ingest team curates diverse data sets from multiple data providers simultaneously. To streamline the ingest process, the data set submission process at the ORNL DAAC has been recently updated to use an agile process and a semi-automated workflow system has been developed to provide a consistent data provider experience and to create a uniform data product. The goals of semi-automated agile ingest process are to: 1.Provide the ability to track a data set from acceptance to publication 2. Automate steps that can be automated to improve efficiencies and reduce redundancy 3.Update legacy ingest infrastructure 4.Provide a centralized system to manage the various aspects of ingest. This talk will cover the agile methodology, workflow, and tools developed through this system.

Decaf: Decoupled Dataflows for In Situ High-Performance Workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreher, M.; Peterka, T.

Decaf is a dataflow system for the parallel communication of coupled tasks in an HPC workflow. The dataflow can perform arbitrary data transformations ranging from simply forwarding data to complex data redistribution. Decaf does this by allowing the user to allocate resources and execute custom code in the dataflow. All communication through the dataflow is efficient parallel message passing over MPI. The runtime for calling tasks is entirely message-driven; Decaf executes a task when all messages for the task have been received. Such a messagedriven runtime allows cyclic task dependencies in the workflow graph, for example, to enact computational steeringmore » based on the result of downstream tasks. Decaf includes a simple Python API for describing the workflow graph. This allows Decaf to stand alone as a complete workflow system, but Decaf can also be used as the dataflow layer by one or more other workflow systems to form a heterogeneous task-based computing environment. In one experiment, we couple a molecular dynamics code with a visualization tool using the FlowVR and Damaris workflow systems and Decaf for the dataflow. In another experiment, we test the coupling of a cosmology code with Voronoi tessellation and density estimation codes using MPI for the simulation, the DIY programming model for the two analysis codes, and Decaf for the dataflow. Such workflows consisting of heterogeneous software infrastructures exist because components are developed separately with different programming models and runtimes, and this is the first time that such heterogeneous coupling of diverse components was demonstrated in situ on HPC systems.« less

Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

PubMed

Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

2016-03-01

Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

Tools for automated acoustic monitoring within the R package monitoR

USGS Publications Warehouse

Katz, Jonathan; Hafner, Sasha D.; Donovan, Therese

2016-01-01

The R package monitoR contains tools for managing an acoustic-monitoring program including survey metadata, template creation and manipulation, automated detection and results management. These tools are scalable for use with small projects as well as larger long-term projects and those with expansive spatial extents. Here, we describe typical workflow when using the tools in monitoR. Typical workflow utilizes a generic sequence of functions, with the option for either binary point matching or spectrogram cross-correlation detectors.

Requirements for Workflow-Based EHR Systems - Results of a Qualitative Study.

PubMed

Schweitzer, Marco; Lasierra, Nelia; Hoerbst, Alexander

2016-01-01

Today's high quality healthcare delivery strongly relies on efficient electronic health records (EHR). These EHR systems or in general healthcare IT-systems are usually developed in a static manner according to a given workflow. Hence, they are not flexible enough to enable access to EHR data and to execute individual actions within a consultation. This paper reports on requirements pointed by experts in the domain of diabetes mellitus to design a system for supporting dynamic workflows to serve personalization within a medical activity. Requirements were collected by means of expert interviews. These interviews completed a conducted triangulation approach, aimed to gather requirements for workflow-based EHR interactions. The data from the interviews was analyzed through a qualitative approach resulting in a set of requirements enhancing EHR functionality from the user's perspective. Requirements were classified according to four different categorizations: (1) process-related requirements, (2) information needs, (3) required functions, (4) non-functional requirements. Workflow related requirements were identified which should be considered when developing and deploying EHR systems.

ERP (enterprise resource planning) systems can streamline healthcare business functions.

PubMed

Jenkins, E K; Christenson, E

2001-05-01

Enterprise resource planning (ERP) software applications are designed to facilitate the systemwide integration of complex processes and functions across a large enterprise consisting of many internal and external constituents. Although most currently available ERP applications generally are tailored to the needs of the manufacturing industry, many large healthcare systems are investigating these applications. Due to the significant differences between manufacturing and patient care, ERP-based systems do not easily translate to the healthcare setting. In particular, the lack of clinical standardization impedes the use of ERP systems for clinical integration. Nonetheless, an ERP-based system can help a healthcare organization integrate many functions, including patient scheduling, human resources management, workload forecasting, and management of workflow, that are not directly dependent on clinical decision making.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Yingssu; Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080; McPhillips, Scott E.

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data,more » performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.« less

Developing an Automatic Crawling System for Populating a Digital Repository of Professional Development Resources: A Pilot Study

ERIC Educational Resources Information Center

Park, Jung-ran; Yang, Chris; Tosaka, Yuji; Ping, Qing; Mimouni, Houda El

2016-01-01

This study is a part of the larger project that develops a sustainable digital repository of professional development resources on emerging data standards and technologies for data organization and management in libraries. Toward that end, the project team developed an automated workflow to crawl for, monitor, and classify relevant web objects…

Using an ePortfolio System as an Electronic Laboratory Notebook in Undergraduate Biochemistry and Molecular Biology Practical Classes

ERIC Educational Resources Information Center

Johnston, Jill; Kant, Sashi; Gysbers, Vanessa; Hancock, Dale; Denyer, Gareth

2014-01-01

Despite many apparent advantages, including security, back-up, remote access, workflow, and data management, the use of electronic laboratory notebooks (ELNs) in the modern research laboratory is still developing. This presents a challenge to instructors who want to give undergraduate students an introduction to the kinds of data curation and…

Going fully digital: Perspective of a Dutch academic pathology lab

PubMed Central

Stathonikos, Nikolas; Veta, Mitko; Huisman, André; van Diest, Paul J.

2013-01-01

During the last years, whole slide imaging has become more affordable and widely accepted in pathology labs. Digital slides are increasingly being used for digital archiving of routinely produced clinical slides, remote consultation and tumor boards, and quantitative image analysis for research purposes and in education. However, the implementation of a fully digital Pathology Department requires an in depth look into the suitability of digital slides for routine clinical use (the image quality of the produced digital slides and the factors that affect it) and the required infrastructure to support such use (the storage requirements and integration with lab management and hospital information systems). Optimization of digital pathology workflow requires communication between several systems, which can be facilitated by the use of open standards for digital slide storage and scanner management. Consideration of these aspects along with appropriate validation of the use of digital slides for routine pathology can pave the way for pathology departments to go “fully digital.” In this paper, we summarize our experiences so far in the process of implementing a fully digital workflow at our Pathology Department and the steps that are needed to complete this process. PMID:23858390

Enhancing and Customizing Laboratory Information Systems to Improve/Enhance Pathologist Workflow.

PubMed

Hartman, Douglas J

2015-06-01

Optimizing pathologist workflow can be difficult because it is affected by many variables. Surgical pathologists must complete many tasks that culminate in a final pathology report. Several software systems can be used to enhance/improve pathologist workflow. These include voice recognition software, pre-sign-out quality assurance, image utilization, and computerized provider order entry. Recent changes in the diagnostic coding and the more prominent role of centralized electronic health records represent potential areas for increased ways to enhance/improve the workflow for surgical pathologists. Additional unforeseen changes to the pathologist workflow may accompany the introduction of whole-slide imaging technology to the routine diagnostic work. Copyright © 2015 Elsevier Inc. All rights reserved.

Enhancing and Customizing Laboratory Information Systems to Improve/Enhance Pathologist Workflow.

PubMed

Hartman, Douglas J

2016-03-01

Optimizing pathologist workflow can be difficult because it is affected by many variables. Surgical pathologists must complete many tasks that culminate in a final pathology report. Several software systems can be used to enhance/improve pathologist workflow. These include voice recognition software, pre-sign-out quality assurance, image utilization, and computerized provider order entry. Recent changes in the diagnostic coding and the more prominent role of centralized electronic health records represent potential areas for increased ways to enhance/improve the workflow for surgical pathologists. Additional unforeseen changes to the pathologist workflow may accompany the introduction of whole-slide imaging technology to the routine diagnostic work. Copyright © 2016 Elsevier Inc. All rights reserved.

Taking advantage of HTML5 browsers to realize the concepts of session state and workflow sharing in web-tool applications

NASA Astrophysics Data System (ADS)

Suftin, I.; Read, J. S.; Walker, J.

2013-12-01

Scientists prefer not having to be tied down to a specific machine or operating system in order to analyze local and remote data sets or publish work. Increasingly, analysis has been migrating to decentralized web services and data sets, using web clients to provide the analysis interface. While simplifying workflow access, analysis, and publishing of data, the move does bring with it its own unique set of issues. Web clients used for analysis typically offer workflows geared towards a single user, with steps and results that are often difficult to recreate and share with others. Furthermore, workflow results often may not be easily used as input for further analysis. Older browsers further complicate things by having no way to maintain larger chunks of information, often offloading the job of storage to the back-end server or trying to squeeze it into a cookie. It has been difficult to provide a concept of "session storage" or "workflow sharing" without a complex orchestration of the back-end for storage depending on either a centralized file system or database. With the advent of HTML5, browsers gained the ability to store more information through the use of the Web Storage API (a browser-cookie holds a maximum of 4 kilobytes). Web Storage gives us the ability to store megabytes of arbitrary data in-browser either with an expiration date or just for a session. This allows scientists to create, update, persist and share their workflow without depending on the backend to store session information, providing the flexibility for new web-based workflows to emerge. In the DSASWeb portal ( http://cida.usgs.gov/DSASweb/ ), using these techniques, the representation of every step in the analyst's workflow is stored as plain-text serialized JSON, which we can generate as a text file and provide to the analyst as an upload. This file may then be shared with others and loaded back into the application, restoring the application to the state it was in when the session file was generated. A user may then view results produced during that session or go back and alter input parameters, creating new results and producing new, unique sessions which they can then again share. This technique not only provides independence for the user to manage their session as they like, but also allows much greater freedom for the application provider to scale out without having to worry about carrying over user information or maintaining it in a central location.

[Development and clinical evaluation of an anesthesia information management system].

PubMed

Feng, Jing-yi; Chen, Hua; Zhu, Sheng-mei

2010-09-21

To study the design, implementation and clinical evaluation of an anesthesia information management system. To record, process and store peri-operative patient data automatically, all kinds of bedside monitoring equipments are connected into the system based on information integrating technology; after a statistical analysis of those patient data by data mining technology, patient status can be evaluated automatically based on risk prediction standard and decision support system, and then anesthetist could perform reasonable and safe clinical processes; with clinical processes electronically recorded, standard record tables could be generated, and clinical workflow is optimized, as well. With the system, kinds of patient data could be collected, stored, analyzed and archived, kinds of anesthesia documents could be generated, and patient status could be evaluated to support clinic decision. The anesthesia information management system is useful for improving anesthesia quality, decreasing risk of patient and clinician, and aiding to provide clinical proof.

A laboratory information management system for DNA barcoding workflows.

PubMed

Vu, Thuy Duong; Eberhardt, Ursula; Szöke, Szániszló; Groenewald, Marizeth; Robert, Vincent

2012-07-01

This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.

A microseismic workflow for managing induced seismicity risk as CO 2 storage projects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matzel, E.; Morency, C.; Pyle, M.

2015-10-27

It is well established that fluid injection has the potential to induce earthquakes—from microseismicity to large, damaging events—by altering state-of-stress conditions in the subsurface. While induced seismicity has not been a major operational issue for carbon storage projects to date, a seismicity hazard exists and must be carefully addressed. Two essential components of effective seismic risk management are (1) sensitive microseismic monitoring and (2) robust data interpretation tools. This report describes a novel workflow, based on advanced processing algorithms applied to microseismic data, to help improve management of seismic risk. This workflow has three main goals: (1) to improve themore » resolution and reliability of passive seismic monitoring, (2) to extract additional, valuable information from continuous waveform data that is often ignored in standard processing, and (3) to minimize the turn-around time between data collection, interpretation, and decision-making. These three objectives can allow for a better-informed and rapid response to changing subsurface conditions.« less

Standards to support information systems integration in anatomic pathology.

PubMed

Daniel, Christel; García Rojo, Marcial; Bourquard, Karima; Henin, Dominique; Schrader, Thomas; Della Mea, Vincenzo; Gilbertson, John; Beckwith, Bruce A

2009-11-01

Integrating anatomic pathology information- text and images-into electronic health care records is a key challenge for enhancing clinical information exchange between anatomic pathologists and clinicians. The aim of the Integrating the Healthcare Enterprise (IHE) international initiative is precisely to ensure interoperability of clinical information systems by using existing widespread industry standards such as Digital Imaging and Communication in Medicine (DICOM) and Health Level Seven (HL7). To define standard-based informatics transactions to integrate anatomic pathology information to the Healthcare Enterprise. We used the methodology of the IHE initiative. Working groups from IHE, HL7, and DICOM, with special interest in anatomic pathology, defined consensual technical solutions to provide end-users with improved access to consistent information across multiple information systems. The IHE anatomic pathology technical framework describes a first integration profile, "Anatomic Pathology Workflow," dedicated to the diagnostic process including basic image acquisition and reporting solutions. This integration profile relies on 10 transactions based on HL7 or DICOM standards. A common specimen model was defined to consistently identify and describe specimens in both HL7 and DICOM transactions. The IHE anatomic pathology working group has defined standard-based informatics transactions to support the basic diagnostic workflow in anatomic pathology laboratories. In further stages, the technical framework will be completed to manage whole-slide images and semantically rich structured reports in the diagnostic workflow and to integrate systems used for patient care and those used for research activities (such as tissue bank databases or tissue microarrayers).

Developing Software to “Track and Catch” Missed Follow-up of Abnormal Test Results in a Complex Sociotechnical Environment

PubMed Central

Smith, M.; Murphy, D.; Laxmisan, A.; Sittig, D.; Reis, B.; Esquivel, A.; Singh, H.

2013-01-01

Summary Background Abnormal test results do not always receive timely follow-up, even when providers are notified through electronic health record (EHR)-based alerts. High workload, alert fatigue, and other demands on attention disrupt a provider’s prospective memory for tasks required to initiate follow-up. Thus, EHR-based tracking and reminding functionalities are needed to improve follow-up. Objectives The purpose of this study was to develop a decision-support software prototype enabling individual and system-wide tracking of abnormal test result alerts lacking follow-up, and to conduct formative evaluations, including usability testing. Methods We developed a working prototype software system, the Alert Watch And Response Engine (AWARE), to detect abnormal test result alerts lacking documented follow-up, and to present context-specific reminders to providers. Development and testing took place within the VA’s EHR and focused on four cancer-related abnormal test results. Design concepts emphasized mitigating the effects of high workload and alert fatigue while being minimally intrusive. We conducted a multifaceted formative evaluation of the software, addressing fit within the larger socio-technical system. Evaluations included usability testing with the prototype and interview questions about organizational and workflow factors. Participants included 23 physicians, 9 clinical information technology specialists, and 8 quality/safety managers. Results Evaluation results indicated that our software prototype fit within the technical environment and clinical workflow, and physicians were able to use it successfully. Quality/safety managers reported that the tool would be useful in future quality assurance activities to detect patients who lack documented follow-up. Additionally, we successfully installed the software on the local facility’s “test” EHR system, thus demonstrating technical compatibility. Conclusion To address the factors involved in missed test results, we developed a software prototype to account for technical, usability, organizational, and workflow needs. Our evaluation has shown the feasibility of the prototype as a means of facilitating better follow-up for cancer-related abnormal test results. PMID:24155789

Developing software to "track and catch" missed follow-up of abnormal test results in a complex sociotechnical environment.

PubMed

Smith, M; Murphy, D; Laxmisan, A; Sittig, D; Reis, B; Esquivel, A; Singh, H

2013-01-01

Abnormal test results do not always receive timely follow-up, even when providers are notified through electronic health record (EHR)-based alerts. High workload, alert fatigue, and other demands on attention disrupt a provider's prospective memory for tasks required to initiate follow-up. Thus, EHR-based tracking and reminding functionalities are needed to improve follow-up. The purpose of this study was to develop a decision-support software prototype enabling individual and system-wide tracking of abnormal test result alerts lacking follow-up, and to conduct formative evaluations, including usability testing. We developed a working prototype software system, the Alert Watch And Response Engine (AWARE), to detect abnormal test result alerts lacking documented follow-up, and to present context-specific reminders to providers. Development and testing took place within the VA's EHR and focused on four cancer-related abnormal test results. Design concepts emphasized mitigating the effects of high workload and alert fatigue while being minimally intrusive. We conducted a multifaceted formative evaluation of the software, addressing fit within the larger socio-technical system. Evaluations included usability testing with the prototype and interview questions about organizational and workflow factors. Participants included 23 physicians, 9 clinical information technology specialists, and 8 quality/safety managers. Evaluation results indicated that our software prototype fit within the technical environment and clinical workflow, and physicians were able to use it successfully. Quality/safety managers reported that the tool would be useful in future quality assurance activities to detect patients who lack documented follow-up. Additionally, we successfully installed the software on the local facility's "test" EHR system, thus demonstrating technical compatibility. To address the factors involved in missed test results, we developed a software prototype to account for technical, usability, organizational, and workflow needs. Our evaluation has shown the feasibility of the prototype as a means of facilitating better follow-up for cancer-related abnormal test results.

Technology in the OR: AORN Members' Perceptions of the Effects on Workflow Efficiency and Quality Patient Care.

PubMed

Sipes, Carolyn; Baker, Joy Don

2015-09-01

This collaborative study sought to describe technology used by AORN members at work, inclusive of radio-frequency identification or barcode scanning (RFID), data collection tools (DATA), workflow or dashboard management tools (DASHBOARD), and environmental services/room decontamination technologies (ENVIRON), and to identify the perceived effects of each technology on workflow efficiency (WFE) and quality patient care (QPC). The 462 respondents to the AORN Technology in the OR survey reported use of technology (USE) in all categories. Eleven of 17 RFID items had a strong positive correlation between the designated USE item and the perceived effect on WFE and QPC. Five of the most-used technology items were found in the DATA category. Two of the five related to Intraoperative Nursing Documentation and the use of the Perioperative Nursing Data Set. The other three related to Imaging Integration for Radiology Equipment, Video Camera Systems, and Fiber-optic Systems. All three elements explored in the DASHBOARD category (ie, Patient Update, OR Case, OR Efficiency) demonstrated approximately 50% or greater perceived effectiveness in WFE and QPC. There was a low reported use of ENVIRON technologies, resulting in limited WFE and QPC data for this category. Copyright © 2015 AORN, Inc. Published by Elsevier Inc. All rights reserved.

76 FR 71928 - Defense Federal Acquisition Regulation Supplement; Updates to Wide Area WorkFlow (DFARS Case 2011...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-21

... Defense Federal Acquisition Regulation Supplement; Updates to Wide Area WorkFlow (DFARS Case 2011-D027... Wide Area WorkFlow (WAWF) and TRICARE Encounter Data System (TEDS). WAWF, which electronically... civil emergencies, when access to Wide Area WorkFlow by those contractors is not feasible; (4) Purchases...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

This report contains papers on the following topics: NREN Security Issues: Policies and Technologies; Layer Wars: Protect the Internet with Network Layer Security; Electronic Commission Management; Workflow 2000 - Electronic Document Authorization in Practice; Security Issues of a UNIX PEM Implementation; Implementing Privacy Enhanced Mail on VMS; Distributed Public Key Certificate Management; Protecting the Integrity of Privacy-enhanced Electronic Mail; Practical Authorization in Large Heterogeneous Distributed Systems; Security Issues in the Truffles File System; Issues surrounding the use of Cryptographic Algorithms and Smart Card Applications; Smart Card Augmentation of Kerberos; and An Overview of the Advanced Smart Card Access Control System.more » Selected papers were processed separately for inclusion in the Energy Science and Technology Database.« less

Universal Payload Information Management

NASA Technical Reports Server (NTRS)

Elmore, Ralph B.

2003-01-01

As the overall manager and integrator of International Space Station (ISS) science payloads, the Payload Operations Integration Center (POIC) at Marshall Space Flight Center has a critical need to provide an information management system for exchange and control of ISS payload files as well as to coordinate ISS payload related operational changes. The POIC's information management system has a fundamental requirement to provide secure operational access not only to users physically located at the POIC, but also to remote experimenters and International Partners physically located in different parts of the world. The Payload Information Management System (PIMS) is a ground-based electronic document configuration management and collaborative workflow system that was built to service the POIC's information management needs. This paper discusses the application components that comprise the PIMS system, the challenges that influenced its design and architecture, and the selected technologies it employs. This paper will also touch on the advantages of the architecture, details of the user interface, and lessons learned along the way to a successful deployment. With PIMS, a sophisticated software solution has been built that is not only universally accessible for POIC customer s information management needs, but also universally adaptable in implementation and application as a generalized information management system.

The Symbiotic Relationship between Scientific Workflow and Provenance (Invited)

NASA Astrophysics Data System (ADS)

Stephan, E.

2010-12-01

The purpose of this presentation is to describe the symbiotic nature of scientific workflows and provenance. We will also discuss the current trends and real world challenges facing these two distinct research areas. Although motivated differently, the needs of the international science communities are the glue that binds this relationship together. Understanding and articulating the science drivers to these communities is paramount as these technologies evolve and mature. Originally conceived for managing business processes, workflows are now becoming invaluable assets in both computational and experimental sciences. These reconfigurable, automated systems provide essential technology to perform complex analyses by coupling together geographically distributed disparate data sources and applications. As a result, workflows are capable of higher throughput in a shorter amount of time than performing the steps manually. Today many different workflow products exist; these could include Kepler and Taverna or similar products like MeDICI, developed at PNNL, that are standardized on the Business Process Execution Language (BPEL). Provenance, originating from the French term Provenir “to come from”, is used to describe the curation process of artwork as art is passed from owner to owner. The concept of provenance was adopted by digital libraries as a means to track the lineage of documents while standards such as the DublinCore began to emerge. In recent years the systems science community has increasingly expressed the need to expand the concept of provenance to formally articulate the history of scientific data. Communities such as the International Provenance and Annotation Workshop (IPAW) have formalized a provenance data model. The Open Provenance Model, and the W3C is hosting a provenance incubator group featuring the Proof Markup Language. Although both workflows and provenance have risen from different communities and operate independently, their mutual success is tied together, forming a symbiotic relationship where research and development advances in one effort can provide tremendous benefits to the other. For example, automating provenance extraction within scientific applications is still a relatively new concept; the workflow engine provides the framework to capture application specific operations, inputs, and resulting data. It provides a description of the process history and data flow by wrapping workflow components around the applications and data sources. On the other hand, a lack of cooperation between workflows and provenance can inhibit usefulness of both to science. Blindly tracking the execution history without having a true understanding of what kinds of questions end users may have makes the provenance indecipherable to the target users. Over the past nine years PNNL has been actively involved in provenance research in support of computational chemistry, molecular dynamics, biology, hydrology, and climate. PNNL has also been actively involved in efforts by the international community to develop open standards for provenance and the development of architectures to support provenance capture, storage, and querying. This presentation will provide real world use cases of how provenance and workflow can be leveraged and implemented to meet different needs and the challenges that lie ahead.

Challenges in small screening laboratories: implementing an on-demand laboratory information management system.

PubMed

Lemmon, Vance P; Jia, Yuanyuan; Shi, Yan; Holbrook, S Douglas; Bixby, John L; Buchser, William

2011-11-01

The Miami Project to Cure Paralysis, part of the University of Miami Miller School of Medicine, includes a laboratory devoted to High Content Analysis (HCA) of neurons. The goal of the laboratory is to uncover signaling pathways, genes, compounds, or drugs that can be used to promote nerve growth. HCA permits the quantification of neuronal morphology, including the lengths and numbers of axons. HCA of various libraries on primary neurons requires a team-based approach, a variety of process steps and complex manipulations of cells and libraries to obtain meaningful results. HCA itself produces vast amounts of information including images, well-based data and cell-based phenotypic measures. Documenting and integrating the experimental workflows, library data and extensive experimental results is challenging. For academic laboratories generating large data sets from experiments involving thousands of perturbagens, a Laboratory Information Management System (LIMS) is the data tracking solution of choice. With both productivity and efficiency as driving rationales, the Miami Project has equipped its HCA laboratory with an On Demand or Software As A Service (SaaS) LIMS to ensure the quality of its experiments and workflows. The article discusses how the system was selected and integrated into the laboratory. The advantages of a SaaS based LIMS over a client-server based system are described. © 2011 Bentham Science Publishers

Acute pain management efficiency improves with point-of-care handheld electronic billing system.

PubMed

Fahy, Brenda G

2009-02-01

Technology advances continue to impact patient care and physician workflow. To enable more efficient performance of billing activities, a point-of-care (POC) handheld computer technology replaced a paper-based system on an acute pain management service. Using a handheld personal digital assistant (PDA) and software from MDeverywhere (MDe, MDeverywhere, Long Island, NY), we performed a 1-yr prospective observational study of an anesthesiology acute pain management service billings and collections. Seventeen anesthesiologists providing billable acute pain services were trained and entered their charges on a PDA. Twelve months of data, just before electronic implementation (pre-elec), were compared to a 12-m period after implementation (post-elec). The total charges were 4883 for 890 patients pre-elec and 5368 for 1128 patients post-elec. With adoption of handheld billing, the charge lag days decreased from 29.3 to 7.0 (P < 0.001). The days in accounts receivable trended downward from 59.9 to 51.1 (P = 0.031). The average number of charge lag days decreased significantly with month (P = 0.0002). The net collection rate increased from 37.4% pre-elec to 40.3% post-elec (P < 0.001). The return on investment was 1.18 fold (118%). Implementation of POC electronic billing using PDAs to replace a paper-based billing system improved the collection rate and decreased the number of charge lag days with a positive return on investment. The handheld PDA billing system provided POC support for physicians during their daily clinical (e.g., patient locations, rounding lists) and billing activities, improving workflow.

Electronic Risk Assessment System as an Appropriate Tool for the Prevention of Cancer: a Qualitative Study.

PubMed

Javan Amoli, Amir Hossein; Maserat, Elham; Safdari, Reza; Zali, Mohammad Reza

2015-01-01

Decision making modalities for screening for many cancer conditions and different stages have become increasingly complex. Computer-based risk assessment systems facilitate scheduling and decision making and support the delivery of cancer screening services. The aim of this article was to survey electronic risk assessment system as an appropriate tool for the prevention of cancer. A qualitative design was used involving 21 face-to-face interviews. Interviewing involved asking questions and getting answers from exclusive managers of cancer screening. Of the participants 6 were female and 15 were male, and ages ranged from 32 to 78 years. The study was based on a grounded theory approach and the tool was a semi- structured interview. Researchers studied 5 dimensions, comprising electronic guideline standards of colorectal cancer screening, work flow of clinical and genetic activities, pathways of colorectal cancer screening and functionality of computer based guidelines and barriers. Electronic guideline standards of colorectal cancer screening were described in the s3 categories of content standard, telecommunications and technical standards and nomenclature and classification standards. According to the participations' views, workflow and genetic pathways of colorectal cancer screening were identified. The study demonstrated an effective role of computer-guided consultation for screening management. Electronic based systems facilitate real-time decision making during a clinical interaction. Electronic pathways have been applied for clinical and genetic decision support, workflow management, update recommendation and resource estimates. A suitable technical and clinical infrastructure is an integral part of clinical practice guidline of screening. As a conclusion, it is recommended to consider the necessity of architecture assessment and also integration standards.

Automatic Integration Testbeds validation on Open Science Grid

NASA Astrophysics Data System (ADS)

Caballero, J.; Thapa, S.; Gardner, R.; Potekhin, M.

2011-12-01

A recurring challenge in deploying high quality production middleware is the extent to which realistic testing occurs before release of the software into the production environment. We describe here an automated system for validating releases of the Open Science Grid software stack that leverages the (pilot-based) PanDA job management system developed and used by the ATLAS experiment. The system was motivated by a desire to subject the OSG Integration Testbed to more realistic validation tests. In particular those which resemble to every extent possible actual job workflows used by the experiments thus utilizing job scheduling at the compute element (CE), use of the worker node execution environment, transfer of data to/from the local storage element (SE), etc. The context is that candidate releases of OSG compute and storage elements can be tested by injecting large numbers of synthetic jobs varying in complexity and coverage of services tested. The native capabilities of the PanDA system can thus be used to define jobs, monitor their execution, and archive the resulting run statistics including success and failure modes. A repository of generic workflows and job types to measure various metrics of interest has been created. A command-line toolset has been developed so that testbed managers can quickly submit "VO-like" jobs into the system when newly deployed services are ready for testing. A system for automatic submission has been crafted to send jobs to integration testbed sites, collecting the results in a central service and generating regular reports for performance and reliability.

A Six‐Stage Workflow for Robust Application of Systems Pharmacology

PubMed Central

Gadkar, K; Kirouac, DC; Mager, DE; van der Graaf, PH

2016-01-01

Quantitative and systems pharmacology (QSP) is increasingly being applied in pharmaceutical research and development. One factor critical to the ultimate success of QSP is the establishment of commonly accepted language, technical criteria, and workflows. We propose an integrated workflow that bridges conceptual objectives with underlying technical detail to support the execution, communication, and evaluation of QSP projects. PMID:27299936

Proteomics data exchange and storage: the need for common standards and public repositories.

PubMed

Jiménez, Rafael C; Vizcaíno, Juan Antonio

2013-01-01

Both the existence of data standards and public databases or repositories have been key factors behind the development of the existing "omics" approaches. In this book chapter we first review the main existing mass spectrometry (MS)-based proteomics resources: PRIDE, PeptideAtlas, GPMDB, and Tranche. Second, we report on the current status of the different proteomics data standards developed by the Proteomics Standards Initiative (PSI): the formats mzML, mzIdentML, mzQuantML, TraML, and PSI-MI XML are then reviewed. Finally, we present an easy way to query and access MS proteomics data in the PRIDE database, as a representative of the existing repositories, using the workflow management system (WMS) tool Taverna. Two different publicly available workflows are explained and described.

Towards Exascale Seismic Imaging and Inversion

NASA Astrophysics Data System (ADS)

Tromp, J.; Bozdag, E.; Lefebvre, M. P.; Smith, J. A.; Lei, W.; Ruan, Y.

2015-12-01

Post-petascale supercomputers are now available to solve complex scientific problems that were thought unreachable a few decades ago. They also bring a cohort of concerns tied to obtaining optimum performance. Several issues are currently being investigated by the HPC community. These include energy consumption, fault resilience, scalability of the current parallel paradigms, workflow management, I/O performance and feature extraction with large datasets. In this presentation, we focus on the last three issues. In the context of seismic imaging and inversion, in particular for simulations based on adjoint methods, workflows are well defined.They consist of a few collective steps (e.g., mesh generation or model updates) and of a large number of independent steps (e.g., forward and adjoint simulations of each seismic event, pre- and postprocessing of seismic traces). The greater goal is to reduce the time to solution, that is, obtaining a more precise representation of the subsurface as fast as possible. This brings us to consider both the workflow in its entirety and the parts comprising it. The usual approach is to speedup the purely computational parts based on code optimization in order to reach higher FLOPS and better memory management. This still remains an important concern, but larger scale experiments show that the imaging workflow suffers from severe I/O bottlenecks. Such limitations occur both for purely computational data and seismic time series. The latter are dealt with by the introduction of a new Adaptable Seismic Data Format (ASDF). Parallel I/O libraries, namely HDF5 and ADIOS, are used to drastically reduce the cost of disk access. Parallel visualization tools, such as VisIt, are able to take advantage of ADIOS metadata to extract features and display massive datasets. Because large parts of the workflow are embarrassingly parallel, we are investigating the possibility of automating the imaging process with the integration of scientific workflow management tools, specifically Pegasus.

A WorkFlow Engine Oriented Modeling System for Hydrologic Sciences

NASA Astrophysics Data System (ADS)

Lu, B.; Piasecki, M.

2009-12-01

In recent years the use of workflow engines for carrying out modeling and data analyses tasks has gained increased attention in the science and engineering communities. Tasks like processing raw data coming from sensors and passing these raw data streams to filters for QA/QC procedures possibly require multiple and complicated steps that need to be repeated over and over again. A workflow sequence that carries out a number of steps of various complexity is an ideal approach to deal with these tasks because the sequence can be stored, called up and repeated over again and again. This has several advantages: for one it ensures repeatability of processing steps and with that provenance, an issue that is increasingly important in the science and engineering communities. It also permits the hand off of lengthy and time consuming tasks that can be error prone to a chain of processing actions that are carried out automatically thus reducing the chance for error on the one side and freeing up time to carry out other tasks on the other hand. This paper aims to present the development of a workflow engine embedded modeling system which allows to build up working sequences for carrying out numerical modeling tasks regarding to hydrologic science. Trident, which facilitates creating, running and sharing scientific data analysis workflows, is taken as the central working engine of the modeling system. Current existing functionalities of the modeling system involve digital watershed processing, online data retrieval, hydrologic simulation and post-event analysis. They are stored as sequences or modules respectively. The sequences can be invoked to implement their preset tasks in orders, for example, triangulating a watershed from raw DEM. Whereas the modules encapsulated certain functions can be selected and connected through a GUI workboard to form sequences. This modeling system is demonstrated by setting up a new sequence for simulating rainfall-runoff processes which involves embedded Penn State Integrated Hydrologic Model(PIHM) module for hydrologic simulation as a kernel, DEM processing sub-sequence which prepares geospatial data for PIHM, data retrieval module which access time series data from online data repository via web services or from local database, post- data management module which stores , visualizes and analyzes model outputs.

Function Model for Community Health Service Information

NASA Astrophysics Data System (ADS)

Yang, Peng; Pan, Feng; Liu, Danhong; Xu, Yongyong

In order to construct a function model of community health service (CHS) information for development of CHS information management system, Integration Definition for Function Modeling (IDEF0), an IEEE standard which is extended from Structured Analysis and Design(SADT) and now is a widely used function modeling method, was used to classifying its information from top to bottom. The contents of every level of the model were described and coded. Then function model for CHS information, which includes 4 super-classes, 15 classes and 28 sub-classed of business function, 43 business processes and 168 business activities, was established. This model can facilitate information management system development and workflow refinement.

Laboratory Information Systems.

PubMed

Henricks, Walter H

2015-06-01

Laboratory information systems (LISs) supply mission-critical capabilities for the vast array of information-processing needs of modern laboratories. LIS architectures include mainframe, client-server, and thin client configurations. The LIS database software manages a laboratory's data. LIS dictionaries are database tables that a laboratory uses to tailor an LIS to the unique needs of that laboratory. Anatomic pathology LIS (APLIS) functions play key roles throughout the pathology workflow, and laboratories rely on LIS management reports to monitor operations. This article describes the structure and functions of APLISs, with emphasis on their roles in laboratory operations and their relevance to pathologists. Copyright © 2015 Elsevier Inc. All rights reserved.

Analog to digital workflow improvement: a quantitative study.

PubMed

Wideman, Catherine; Gallet, Jacqueline

2006-01-01

This study tracked a radiology department's conversion from utilization of a Kodak Amber analog system to a Kodak DirectView DR 5100 digital system. Through the use of ProModel Optimization Suite, a workflow simulation software package, significant quantitative information was derived from workflow process data measured before and after the change to a digital system. Once the digital room was fully operational and the radiology staff comfortable with the new system, average patient examination time was reduced from 9.24 to 5.28 min, indicating that a higher patient throughput could be achieved. Compared to the analog system, chest examination time for modality specific activities was reduced by 43%. The percentage of repeat examinations experienced with the digital system also decreased to 8% vs. the level of 9.5% experienced with the analog system. The study indicated that it is possible to quantitatively study clinical workflow and productivity by using commercially available software.

Structured recording of intraoperative surgical workflows

NASA Astrophysics Data System (ADS)

Neumuth, T.; Durstewitz, N.; Fischer, M.; Strauss, G.; Dietz, A.; Meixensberger, J.; Jannin, P.; Cleary, K.; Lemke, H. U.; Burgert, O.

2006-03-01

Surgical Workflows are used for the methodical and scientific analysis of surgical interventions. The approach described here is a step towards developing surgical assist systems based on Surgical Workflows and integrated control systems for the operating room of the future. This paper describes concepts and technologies for the acquisition of Surgical Workflows by monitoring surgical interventions and their presentation. Establishing systems which support the Surgical Workflow in operating rooms requires a multi-staged development process beginning with the description of these workflows. A formalized description of surgical interventions is needed to create a Surgical Workflow. This description can be used to analyze and evaluate surgical interventions in detail. We discuss the subdivision of surgical interventions into work steps regarding different levels of granularity and propose a recording scheme for the acquisition of manual surgical work steps from running interventions. To support the recording process during the intervention, we introduce a new software architecture. Core of the architecture is our Surgical Workflow editor that is intended to deal with the manifold, complex and concurrent relations during an intervention. Furthermore, a method for an automatic generation of graphs is shown which is able to display the recorded surgical work steps of the interventions. Finally we conclude with considerations about extensions of our recording scheme to close the gap to S-PACS systems. The approach was used to record 83 surgical interventions from 6 intervention types from 3 different surgical disciplines: ENT surgery, neurosurgery and interventional radiology. The interventions were recorded at the University Hospital Leipzig, Germany and at the Georgetown University Hospital, Washington, D.C., USA.

Text mining meets workflow: linking U-Compare with Taverna

PubMed Central

Kano, Yoshinobu; Dobson, Paul; Nakanishi, Mio; Tsujii, Jun'ichi; Ananiadou, Sophia

2010-01-01

Summary: Text mining from the biomedical literature is of increasing importance, yet it is not easy for the bioinformatics community to create and run text mining workflows due to the lack of accessibility and interoperability of the text mining resources. The U-Compare system provides a wide range of bio text mining resources in a highly interoperable workflow environment where workflows can very easily be created, executed, evaluated and visualized without coding. We have linked U-Compare to Taverna, a generic workflow system, to expose text mining functionality to the bioinformatics community. Availability: http://u-compare.org/taverna.html, http://u-compare.org Contact: kano@is.s.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20709690

Integration of scanned document management with the anatomic pathology laboratory information system: analysis of benefits.

PubMed

Schmidt, Rodney A; Simmons, Kim; Grimm, Erin E; Middlebrooks, Michael; Changchien, Rosy

2006-11-01

Electronic document management systems (EDMSs) have the potential to improve the efficiency of anatomic pathology laboratories. We implemented a novel but simple EDMS for scanned documents as part of our laboratory information system (AP-LIS) and collected cost-benefit data with the intention of discerning the value of such a system in general and whether integration with the AP-LIS is advantageous. We found that the direct financial benefits are modest but the indirect and intangible benefits are large. Benefits of time savings and access to data particularly accrued to pathologists and residents (3.8 h/d saved for 26 pathologists and residents). Integrating the scanned document management system (SDMS) into the AP-LIS has major advantages in terms of workflow and overall simplicity. This simple, integrated SDMS is an excellent value in a practice like ours, and many of the benefits likely apply in other practice settings.

Agile Data Management with the Global Change Information System

NASA Astrophysics Data System (ADS)

Duggan, B.; Aulenbach, S.; Tilmes, C.; Goldstein, J.

2013-12-01

We describe experiences applying agile software development techniques to the realm of data management during the development of the Global Change Information System (GCIS), a web service and API for authoritative global change information under development by the US Global Change Research Program. Some of the challenges during system design and implementation have been : (1) balancing the need for a rigorous mechanism for ensuring information quality with the realities of large data sets whose contents are often in flux, (2) utilizing existing data to inform decisions about the scope and nature of new data, and (3) continuously incorporating new knowledge and concepts into a relational data model. The workflow for managing the content of the system has much in common with the development of the system itself. We examine various aspects of agile software development and discuss whether or how we have been able to use them for data curation as well as software development.

Modeling Business Processes in Public Administration

NASA Astrophysics Data System (ADS)

Repa, Vaclav

During more than 10 years of its existence business process modeling became a regular part of organization management practice. It is mostly regarded. as a part of information system development or even as a way to implement some supporting technology (for instance workflow system). Although I do not agree with such reduction of the real meaning of a business process, it is necessary to admit that information technologies play an essential role in business processes (see [1] for more information), Consequently, an information system is inseparable from a business process itself because it is a cornerstone of the general basic infrastructure of a business. This fact impacts on all dimensions of business process management. One of these dimensions is the methodology that postulates that the information systems development provide the business process management with exact methods and tools for modeling business processes. Also the methodology underlying the approach presented in this paper has its roots in the information systems development methodology.

Using location tracking data to assess efficiency in established clinical workflows.

PubMed

Meyer, Mark; Fairbrother, Pamela; Egan, Marie; Chueh, Henry; Sandberg, Warren S

2006-01-01

Location tracking systems are becoming more prevalent in clinical settings yet applications still are not common. We have designed a system to aid in the assessment of clinical workflow efficiency. Location data is captured from active RFID tags and processed into usable data. These data are stored and presented visually with trending capability over time. The system allows quick assessments of the impact of process changes on workflow, and isolates areas for improvement.

A New Nightly Build System for LHCb

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.

2014-06-01

The nightly build system used so far by LHCb has been implemented as an extension of the system developed by CERN PH/SFT group (as presented at CHEP2010). Although this version has been working for many years, it has several limitations in terms of extensibility, management and ease of use, so that it was decided to develop a new version based on a continuous integration system. In this paper we describe a new implementation of the LHCb Nightly Build System based on the open source continuous integration system Jenkins and report on the experience of configuring a complex build workflow in Jenkins.

Scheduling Operational Operational-Level Courses of Action

DTIC Science & Technology

2003-10-01

Process modelling and analysis – process synchronisation techniques Information and knowledge management – Collaborative planning systems – Workflow...logistics – Some tasks may consume resources The military user may wish to impose synchronisation constraints among tasks A military end state can be...effects, – constrained with resource and synchronisation considerations, and – lead to the achievement of conditions set in the end state. The COA is

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-11-28

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-03-01

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Data Integration Tool: From Permafrost Data Translation Research Tool to A Robust Research Application

NASA Astrophysics Data System (ADS)

Wilcox, H.; Schaefer, K. M.; Jafarov, E. E.; Strawhacker, C.; Pulsifer, P. L.; Thurmes, N.

2016-12-01

The United States National Science Foundation funded PermaData project led by the National Snow and Ice Data Center (NSIDC) with a team from the Global Terrestrial Network for Permafrost (GTN-P) aimed to improve permafrost data access and discovery. We developed a Data Integration Tool (DIT) to significantly speed up the time of manual processing needed to translate inconsistent, scattered historical permafrost data into files ready to ingest directly into the GTN-P. We leverage this data to support science research and policy decisions. DIT is a workflow manager that divides data preparation and analysis into a series of steps or operations called widgets. Each widget does a specific operation, such as read, multiply by a constant, sort, plot, and write data. DIT allows the user to select and order the widgets as desired to meet their specific needs. Originally it was written to capture a scientist's personal, iterative, data manipulation and quality control process of visually and programmatically iterating through inconsistent input data, examining it to find problems, adding operations to address the problems, and rerunning until the data could be translated into the GTN-P standard format. Iterative development of this tool led to a Fortran/Python hybrid then, with consideration of users, licensing, version control, packaging, and workflow, to a publically available, robust, usable application. Transitioning to Python allowed the use of open source frameworks for the workflow core and integration with a javascript graphical workflow interface. DIT is targeted to automatically handle 90% of the data processing for field scientists, modelers, and non-discipline scientists. It is available as an open source tool in GitHub packaged for a subset of Mac, Windows, and UNIX systems as a desktop application with a graphical workflow manager. DIT was used to completely translate one dataset (133 sites) that was successfully added to GTN-P, nearly translate three datasets (270 sites), and is scheduled to translate 10 more datasets ( 1000 sites) from the legacy inactive site data holdings of the Frozen Ground Data Center (FGDC). Iterative development has provided the permafrost and wider scientific community with an extendable tool designed specifically for the iterative process of translating unruly data.

Big Data Architectures for Operationalized Seismic and Subsurface Monitoring and Decision Support Workflows

NASA Astrophysics Data System (ADS)

Irving, D. H.; Rasheed, M.; Hillman, C.; O'Doherty, N.

2012-12-01

Oilfield management is moving to a more operational footing with near-realtime seismic and sensor monitoring governing drilling, fluid injection and hydrocarbon extraction workflows within safety, productivity and profitability constraints. To date, the geoscientific analytical architectures employed are configured for large volumes of data, computational power or analytical latency and compromises in system design must be made to achieve all three aspects. These challenges are encapsulated by the phrase 'Big Data' which has been employed for over a decade in the IT industry to describe the challenges presented by data sets that are too large, volatile and diverse for existing computational architectures and paradigms. We present a data-centric architecture developed to support a geoscientific and geotechnical workflow whereby: ●scientific insight is continuously applied to fresh data ●insights and derived information are incorporated into engineering and operational decisions ●data governance and provenance are routine within a broader data management framework Strategic decision support systems in large infrastructure projects such as oilfields are typically relational data environments; data modelling is pervasive across analytical functions. However, subsurface data and models are typically non-relational (i.e. file-based) in the form of large volumes of seismic imaging data or rapid streams of sensor feeds and are analysed and interpreted using niche applications. The key architectural challenge is to move data and insight from a non-relational to a relational, or structured, data environment for faster and more integrated analytics. We describe how a blend of MapReduce and relational database technologies can be applied in geoscientific decision support, and the strengths and weaknesses of each in such an analytical ecosystem. In addition we discuss hybrid technologies that use aspects of both and translational technologies for moving data and analytics across these platforms. Moving to a data-centric architecture requires data management methodologies to be overhauled by default and we show how end-to-end data provenancing and dependency management is implicit in such an environment and how it benefits system administration as well as the user community. Whilst the architectural experiences are drawn from the oil industry, we believe that they are more broadly applicable in academic and government settings where large volumes of data are added to incrementally and require revisiting with low analytical latency and we suggest application to earthquake monitoring and remote sensing networks.

Workflows for microarray data processing in the Kepler environment.

PubMed

Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

2012-05-17

Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R/BioConductor scripting approaches to pipeline design. Finally, we suggest that microarray data processing task workflows may provide a basis for future example-based comparison of different workflow systems. We provide a set of tools and complete workflows for microarray data analysis in the Kepler environment, which has the advantages of offering graphical, clear display of conceptual steps and parameters and the ability to easily integrate other resources such as remote data and web services.

Applying operations research to optimize a novel population management system for cancer screening.

PubMed

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-02-01

To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management.

Server-based enterprise collaboration software improves safety and quality in high-volume PET/CT practice.

PubMed

McDonald, James E; Kessler, Marcus M; Hightower, Jeremy L; Henry, Susan D; Deloney, Linda A

2013-12-01

With increasing volumes of complex imaging cases and rising economic pressure on physician staffing, timely reporting will become progressively challenging. Current and planned iterations of PACS and electronic medical record systems do not offer workflow management tools to coordinate delivery of imaging interpretations with the needs of the patient and ordering physician. The adoption of a server-based enterprise collaboration software system by our Division of Nuclear Medicine has significantly improved our efficiency and quality of service.

Optimizing insulin pump therapy: the potential advantages of using a structured diabetes management program.

PubMed

Lange, Karin; Ziegler, Ralph; Neu, Andreas; Reinehr, Thomas; Daab, Iris; Walz, Marion; Maraun, Michael; Schnell, Oliver; Kulzer, Bernhard; Reichel, Andreas; Heinemann, Lutz; Parkin, Christopher G; Haak, Thomas

2015-03-01

Use of continuous subcutaneous insulin infusion (CSII) therapy improves glycemic control, reduces hypoglycemia and increases treatment satisfaction in individuals with diabetes. As a number of patient- and clinician-related factors can hinder the effectiveness and optimal usage of CSII therapy, new approaches are needed to address these obstacles. Ceriello and colleagues recently proposed a model of care that incorporates the collaborative use of structured SMBG into a formal approach to personalized diabetes management within all diabetes populations. We adapted this model for use in CSII-treated patients in order to enable the implementation of a workflow structure that enhances patient-physician communication and supports patients' diabetes self-management skills. We recognize that time constraints and current reimbursement policies pose significant challenges to healthcare providers integrating the Personalised Diabetes Management (PDM) process into clinical practice. We believe, however, that the time invested in modifying practice workflow and learning to apply the various steps of the PDM process will be offset by improved workflow and more effective patient consultations. This article describes how to implement PDM into clinical practice as a systematic, standardized process that can optimize CSII therapy.

Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics

PubMed Central

Astakhov, V.; Bandrowski, A.; Gupta, A.; Kulungowski, A.W.; Grethe, J.S.; Bouwer, J.; Molina, T.; Rowley, V.; Penticoff, S.; Terada, M.; Wong, W.; Hakozaki, H.; Kwon, O.; Martone, M.E.; Ellisman, M.

2016-01-01

We report on progress of employing the Kepler workflow engine to prototype “end-to-end” application integration workflows that concern data coming from microscopes deployed at the National Center for Microscopy Imaging Research (NCMIR). This system is built upon the mature code base of the Cell Centered Database (CCDB) and integrated rule-oriented data system (IRODS) for distributed storage. It provides integration with external projects such as the Whole Brain Catalog (WBC) and Neuroscience Information Framework (NIF), which benefit from NCMIR data. We also report on specific workflows which spawn from main workflows and perform data fusion and orchestration of Web services specific for the NIF project. This “Brain data flow” presents a user with categorized information about sources that have information on various brain regions. PMID:28479932

Studies of Big Data metadata segmentation between relational and non-relational databases

NASA Astrophysics Data System (ADS)

Golosova, M. V.; Grigorieva, M. A.; Klimentov, A. A.; Ryabinkin, E. A.; Dimitrov, G.; Potekhin, M.

2015-12-01

In recent years the concepts of Big Data became well established in IT. Systems managing large data volumes produce metadata that describe data and workflows. These metadata are used to obtain information about current system state and for statistical and trend analysis of the processes these systems drive. Over the time the amount of the stored metadata can grow dramatically. In this article we present our studies to demonstrate how metadata storage scalability and performance can be improved by using hybrid RDBMS/NoSQL architecture.

An ontology-based framework for bioinformatics workflows.

PubMed

Digiampietri, Luciano A; Perez-Alcazar, Jose de J; Medeiros, Claudia Bauzer

2007-01-01

The proliferation of bioinformatics activities brings new challenges - how to understand and organise these resources, how to exchange and reuse successful experimental procedures, and to provide interoperability among data and tools. This paper describes an effort toward these directions. It is based on combining research on ontology management, AI and scientific workflows to design, reuse and annotate bioinformatics experiments. The resulting framework supports automatic or interactive composition of tasks based on AI planning techniques and takes advantage of ontologies to support the specification and annotation of bioinformatics workflows. We validate our proposal with a prototype running on real data.

Designing healthcare information technology to catalyse change in clinical care.

PubMed

Lester, William T; Zai, Adrian H; Grant, Richard W; Chueh, Henry C

2008-01-01

The gap between best practice and actual patient care continues to be a pervasive problem in our healthcare system. Efforts to improve on this knowledge-performance gap have included computerised disease management programs designed to improve guideline adherence. However, current computerised reminder and decision support interventions directed at changing physician behaviour have had only a limited and variable effect on clinical outcomes. Further, immediate pay-for-performance financial pressures on institutions have created an environment where disease management systems are often created under duress, appended to existing clinical systems and poorly integrated into the existing workflow, potentially limiting their real-world effectiveness. The authors present a review of disease management as well as a conceptual framework to guide the development of more effective health information technology (HIT) tools for translating clinical information into clinical action.

A Mobile Computerized Decision Support System to Prevent Hypoglycemia in Hospitalized Patients With Type 2 Diabetes Mellitus

PubMed Central

Spat, Stephan; Donsa, Klaus; Beck, Peter; Höll, Bernhard; Mader, Julia K.; Schaupp, Lukas; Augustin, Thomas; Chiarugi, Franco; Lichtenegger, Katharina M.; Plank, Johannes; Pieber, Thomas R.

2016-01-01

Background: Diabetes management requires complex and interdisciplinary cooperation of health care professionals (HCPs). To support this complex process, IT-support is recommended by clinical guidelines. The aim of this article is to report on results from a clinical feasibility study testing the prototype of a mobile, tablet-based client-server system for computerized decision and workflow support (GlucoTab®) and to discuss its impact on hypoglycemia prevention. Methods: The system was tested in a monocentric, open, noncontrolled intervention study in 30 patients with type 2 diabetes mellitus (T2DM). The system supports HCPs in performing a basal-bolus insulin therapy. Diabetes therapy, adverse events, software errors and user feedback were documented. Safety, efficacy and user acceptance of the system were investigated. Results: Only 1.3% of blood glucose (BG) measurements were <70 mg/dl and only 2.6% were >300 mg/dl. The availability of the system (97.3%) and the rate of treatment activities documented with the system (>93.5%) were high. Only few suggestions from the system were overruled by the users (>95.7% adherence). Evaluation of the 3 anonymous questionnaires showed that confidence in the system increased over time. The majority of users believed that treatment errors could be prevented by using this system. Conclusions: Data from our feasibility study show a significant reduction of hypoglycemia by implementing a computerized system for workflow and decision support for diabetes management, compared to a paper-based process. The system was well accepted by HCPs, which is shown in the user acceptance analysis and that users adhered to the insulin dose suggestions made by the system. PMID:27810995

Teaching Workflow Analysis and Lean Thinking via Simulation: A Formative Evaluation

PubMed Central

Campbell, Robert James; Gantt, Laura; Congdon, Tamara

2009-01-01

This article presents the rationale for the design and development of a video simulation used to teach lean thinking and workflow analysis to health services and health information management students enrolled in a course on the management of health information. The discussion includes a description of the design process, a brief history of the use of simulation in healthcare, and an explanation of how video simulation can be used to generate experiential learning environments. Based on the results of a survey given to 75 students as part of a formative evaluation, the video simulation was judged effective because it allowed students to visualize a real-world process (concrete experience), contemplate the scenes depicted in the video along with the concepts presented in class in a risk-free environment (reflection), develop hypotheses about why problems occurred in the workflow process (abstract conceptualization), and develop solutions to redesign a selected process (active experimentation). PMID:19412533

Virtual Sensor Web Architecture

NASA Astrophysics Data System (ADS)

Bose, P.; Zimdars, A.; Hurlburt, N.; Doug, S.

2006-12-01

NASA envisions the development of smart sensor webs, intelligent and integrated observation network that harness distributed sensing assets, their associated continuous and complex data sets, and predictive observation processing mechanisms for timely, collaborative hazard mitigation and enhanced science productivity and reliability. This paper presents Virtual Sensor Web Infrastructure for Collaborative Science (VSICS) Architecture for sustained coordination of (numerical and distributed) model-based processing, closed-loop resource allocation, and observation planning. VSICS's key ideas include i) rich descriptions of sensors as services based on semantic markup languages like OWL and SensorML; ii) service-oriented workflow composition and repair for simple and ensemble models; event-driven workflow execution based on event-based and distributed workflow management mechanisms; and iii) development of autonomous model interaction management capabilities providing closed-loop control of collection resources driven by competing targeted observation needs. We present results from initial work on collaborative science processing involving distributed services (COSEC framework) that is being extended to create VSICS.

Bridging the guideline implementation gap: a systematic, document-centered approach to guideline implementation.

PubMed

Shiffman, Richard N; Michel, George; Essaihi, Abdelwaheb; Thornquist, Elizabeth

2004-01-01

A gap exists between the information contained in published clinical practice guidelines and the knowledge and information that are necessary to implement them. This work describes a process to systematize and make explicit the translation of document-based knowledge into workflow-integrated clinical decision support systems. This approach uses the Guideline Elements Model (GEM) to represent the guideline knowledge. Implementation requires a number of steps to translate the knowledge contained in guideline text into a computable format and to integrate the information into clinical workflow. The steps include: (1) selection of a guideline and specific recommendations for implementation, (2) markup of the guideline text, (3) atomization, (4) deabstraction and (5) disambiguation of recommendation concepts, (6) verification of rule set completeness, (7) addition of explanations, (8) building executable statements, (9) specification of origins of decision variables and insertions of recommended actions, (10) definition of action types and selection of associated beneficial services, (11) choice of interface components, and (12) creation of requirement specification. The authors illustrate these component processes using examples drawn from recent experience translating recommendations from the National Heart, Lung, and Blood Institute's guideline on management of chronic asthma into a workflow-integrated decision support system that operates within the Logician electronic health record system. Using the guideline document as a knowledge source promotes authentic translation of domain knowledge and reduces the overall complexity of the implementation task. From this framework, we believe that a better understanding of activities involved in guideline implementation will emerge.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

PubMed

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-11-23

Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.

Anima: Modular Workflow System for Comprehensive Image Data Analysis

PubMed Central

Rantanen, Ville; Valori, Miko; Hautaniemi, Sampsa

2014-01-01

Modern microscopes produce vast amounts of image data, and computational methods are needed to analyze and interpret these data. Furthermore, a single image analysis project may require tens or hundreds of analysis steps starting from data import and pre-processing to segmentation and statistical analysis; and ending with visualization and reporting. To manage such large-scale image data analysis projects, we present here a modular workflow system called Anima. Anima is designed for comprehensive and efficient image data analysis development, and it contains several features that are crucial in high-throughput image data analysis: programing language independence, batch processing, easily customized data processing, interoperability with other software via application programing interfaces, and advanced multivariate statistical analysis. The utility of Anima is shown with two case studies focusing on testing different algorithms developed in different imaging platforms and an automated prediction of alive/dead C. elegans worms by integrating several analysis environments. Anima is a fully open source and available with documentation at www.anduril.org/anima. PMID:25126541

Implementation of workflow engine technology to deliver basic clinical decision support functionality.

PubMed

Huser, Vojtech; Rasmussen, Luke V; Oberg, Ryan; Starren, Justin B

2011-04-10

Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. We describe an implementation of a free workflow technology software suite (available at http://code.google.com/p/healthflow) and its application in the domain of clinical decision support. Our implementation seamlessly supports clinical logic testing on retrospective data and offers a user-friendly knowledge representation paradigm. With the presented software implementation, we demonstrate that workflow engine technology can provide a decision support platform which evaluates well against an established clinical decision support architecture evaluation framework. Due to cross-industry usage of workflow engine technology, we can expect significant future functionality enhancements that will further improve the technology's capacity to serve as a clinical decision support platform.

Using ERP and WfM Systems for Implementing Business Processes: An Empirical Study

NASA Astrophysics Data System (ADS)

Aversano, Lerina; Tortorella, Maria

Software systems mainly considered from enterprises for dealing with a business process automation belong to the following two categories: Workflow Management Systems (WfMS) and Enterprise Resource Planning (ERP) systems. The wider diffusion of ERP systems tends to favourite this solution, but there are several limitations of most ERP systems for automating business processes. This paper reports an empirical study aiming at comparing the ability of implementing business processes of ERP systems and WfMSs. Two different case studies have been considered in the empirical study. It evaluates and analyses the correctness and completeness of the process models implemented by using ERP and WfM systems.

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.

PubMed

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System

PubMed Central

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C.; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI). PMID:28381997

Information Issues and Contexts that Impair Team Based Communication Workflow: A Palliative Sedation Case Study.

PubMed

Cornett, Alex; Kuziemsky, Craig

2015-01-01

Implementing team based workflows can be complex because of the scope of providers involved and the extent of information exchange and communication that needs to occur. While a workflow may represent the ideal structure of communication that needs to occur, information issues and contextual factors may impact how the workflow is implemented in practice. Understanding these issues will help us better design systems to support team based workflows. In this paper we use a case study of palliative sedation therapy (PST) to model a PST workflow and then use it to identify purposes of communication, information issues and contextual factors that impact them. We then suggest how our findings could inform health information technology (HIT) design to support team based communication workflows.

Ctrl "C"-Ctrl "V"; Using Gaming Peripherals to Improve Library Workflows and Enhance Staff Efficiency

ERIC Educational Resources Information Center

Litsey, Ryan; Harris, Rea; London, Jessie

2018-01-01

Library workflows are an area where repetitive stress can potentially reduce staff efficiency. Day to day activities that require a repetitive motion can bring about physical and psychological fatigue. For library managers, it is important to seek ways in which this type of repetitive stress can be alleviated while having the added benefit of…

A case study of polypharmacy management in nine European countries: Implications for change management and implementation.

PubMed

McIntosh, Jennifer; Alonso, Albert; MacLure, Katie; Stewart, Derek; Kempen, Thomas; Mair, Alpana; Castel-Branco, Margarida; Codina, Carles; Fernandez-Llimos, Fernando; Fleming, Glenda; Gennimata, Dimitra; Gillespie, Ulrika; Harrison, Cathy; Illario, Maddalena; Junius-Walker, Ulrike; Kampolis, Christos F; Kardas, Przemyslaw; Lewek, Pawel; Malva, João; Menditto, Enrica; Scullin, Claire; Wiese, Birgitt

2018-01-01

Multimorbidity and its associated polypharmacy contribute to an increase in adverse drug events, hospitalizations, and healthcare spending. This study aimed to address: what exists regarding polypharmacy management in the European Union (EU); why programs were, or were not, developed; and, how identified initiatives were developed, implemented, and sustained. Change management principles (Kotter) and normalization process theory (NPT) informed data collection and analysis. Nine case studies were conducted in eight EU countries: Germany (Lower Saxony), Greece, Italy (Campania), Poland, Portugal, Spain (Catalonia), Sweden (Uppsala), and the United Kingdom (Northern Ireland and Scotland). The workflow included a review of country/region specific polypharmacy policies, key informant interviews with stakeholders involved in policy development and implementation and, focus groups of clinicians and managers. Data were analyzed using thematic analysis of individual cases and framework analysis across cases. Polypharmacy initiatives were identified in five regions (Catalonia, Lower Saxony, Northern Ireland, Scotland, and Uppsala) and included all care settings. There was agreement, even in cases without initiatives, that polypharmacy is a significant issue to address. Common themes regarding the development and implementation of polypharmacy management initiatives were: locally adapted solutions, organizational culture supporting innovation and teamwork, adequate workforce training, multidisciplinary teams, changes in workflow, redefinition of roles and responsibilities of professionals, policies and legislation supporting the initiative, and data management and information and communication systems to assist development and implementation. Depending on the setting, these were considered either facilitators or barriers to implementation. Within the studied EU countries, polypharmacy management was not widely addressed. These results highlight the importance of change management and theory-based implementation strategies, and provide examples of polypharmacy management initiatives that can assist managers and policymakers in developing new programs or scaling up existing ones, particularly in places currently lacking such initiatives.

A clinical perspective on electronically collecting patient-reported outcomes at the point-of-care for overactive bladder

PubMed Central

Desantis, Darren; Baverstock, Richard J.; Civitarese, Andrea; Crump, R. Trafford; Carlson, Kevin V.

2016-01-01

Introduction Collecting patient-reported outcomes (PROs) can inform the treatment and management of overactive bladder (OAB). However, collecting these data at the point-of-care can be time-consuming and have a negative impact on a clinic’s workflow. The purpose of this study was to pilot a digital system for collecting PROs at the point-of-care and qualitatively assess clinicians’ perspectives in terms of the system’s impact on the delivery of care for OAB. Methods Patients visiting a urology clinic for OAB completed several PRO instruments using a tablet while awaiting assessment. Clinicians reviewed their responses using a digital dashboard during clinical encounters. Qualitative interviews were conducted with the clinicians, to assess the collection system’s impact in terms of: 1) logistics, 2) workflow; 3) patient communication; 4) influence on clinical decisions; 5) user experiences; and 6) the care model. Results Six interviews were conducted and thematic saturation was met, with several themes emerging. All participants were generally positive regarding the use of the digital collecting system. Participants felt that the dashboard improved workflow and enhanced communication with patients, but it was not thought to be any more influential on clinical decision-making than conventional collection methods. Several aspects of the digital PRO collection system were identified as needing improvement. Conclusions The digital PRO collection system used at the point-of-care had a positive impact on the delivery of care for OAB. The results from this study could provide insight to other urologists who are interested in collecting PROs in their clinic. PMID:27942273

Managing a Multisite Academic-Private Radiology Practice Reading Environment: Impact of IT Downtimes on Enterprise Efficiency.

PubMed

Becker, Murray; Goldszal, Alberto; Detal, Julie; Gronlund-Jacob, Judith; Epstein, Robert

2015-06-01

The aim of this study was to assess whether the complex radiology IT infrastructures needed for large, geographically diversified, radiology practices are inherently stable with respect to system downtimes, and to characterize the nature of the downtimes to better understand their impact on radiology department workflow. All radiology IT unplanned downtimes over a 12-month period in a hybrid academic-private practice that performs all interpretations in-house (no commercial "nighthawk" services) for approximately 900,000 studies per year, originating at 6 hospitals, 10 outpatient imaging centers, and multiple low-volume off-hours sites, were logged and characterized using 5 downtime metrics: duration, etiology, failure type, extent, and severity. In 12 consecutive months, 117 unplanned downtimes occurred with the following characteristics: duration: median time = 3.5 hours with 34% <1.5 hours and 30% >12 hours; etiology: 87% were due to software malfunctions, and 13% to hardware malfunctions; failure type: 88% were transient component failures, 12% were complete component failures; extent: all sites experienced downtimes, but downtimes were always localized to a subset of sites, and no system-wide downtimes occurred; severity (impact on radiologist workflow): 47% had minimal impact, 50% moderate impact, and 3% severe impact. In the complex radiology IT system that was studied, downtimes were common; they were usually a result of transient software malfunctions; the geographic extent was always localized rather than system wide; and most often, the impacts on radiologist workflow were modest. Copyright © 2015 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Adaptive Workflows for Diabetes Management: Self-Management Assistant and Remote Treatment for Diabetes.

PubMed

Contreras, Iván; Kiefer, Stephan; Vehi, Josep

2017-01-01

Diabetes self-management is a crucial element for all people with diabetes and those at risk for developing the disease. Diabetic patients should be empowered to increase their self-management skills in order to prevent or delay the complications of diabetes. This work presents the proposal and first development stages of a smartphone application focused on the empowerment of the patients with diabetes. The concept of this interventional tool is based on the personalization of the user experience from an adaptive and dynamic perspective. The segmentation of the population and the dynamical treatment of user profiles among the different experience levels is the main challenge of the implementation. The self-management assistant and remote treatment for diabetes aims to develop a platform to integrate a series of innovative models and tools rigorously tested and supported by the research literature in diabetes together the use of a proved engine to manage workflows for healthcare.

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.

PubMed

Garcia Castro, Alexander; Thoraval, Samuel; Garcia, Leyla J; Ragan, Mark A

2005-04-07

Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive), ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download). From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools.

[Integration of the radiotherapy irradiation planning in the digital workflow].

PubMed

Röhner, F; Schmucker, M; Henne, K; Momm, F; Bruggmoser, G; Grosu, A-L; Frommhold, H; Heinemann, F E

2013-02-01

At the Clinic of Radiotherapy at the University Hospital Freiburg, all relevant workflow is paperless. After implementing the Operating Schedule System (OSS) as a framework, all processes are being implemented into the departmental system MOSAIQ. Designing a digital workflow for radiotherapy irradiation planning is a large challenge, it requires interdisciplinary expertise and therefore the interfaces between the professions also have to be interdisciplinary. For every single step of radiotherapy irradiation planning, distinct responsibilities have to be defined and documented. All aspects of digital storage, backup and long-term availability of data were considered and have already been realized during the OSS project. After an analysis of the complete workflow and the statutory requirements, a detailed project plan was designed. In an interdisciplinary workgroup, problems were discussed and a detailed flowchart was developed. The new functionalities were implemented in a testing environment by the Clinical and Administrative IT Department (CAI). After extensive tests they were integrated into the new modular department system. The Clinic of Radiotherapy succeeded in realizing a completely digital workflow for radiotherapy irradiation planning. During the testing phase, our digital workflow was examined and afterwards was approved by the responsible authority.

Data management and data enrichment for systems biology projects.

PubMed

Wittig, Ulrike; Rey, Maja; Weidemann, Andreas; Müller, Wolfgang

2017-11-10

Collecting, curating, interlinking, and sharing high quality data are central to de.NBI-SysBio, the systems biology data management service center within the de.NBI network (German Network for Bioinformatics Infrastructure). The work of the center is guided by the FAIR principles for scientific data management and stewardship. FAIR stands for the four foundational principles Findability, Accessibility, Interoperability, and Reusability which were established to enhance the ability of machines to automatically find, access, exchange and use data. Within this overview paper we describe three tools (SABIO-RK, Excemplify, SEEK) that exemplify the contribution of de.NBI-SysBio services to FAIR data, models, and experimental methods storage and exchange. The interconnectivity of the tools and the data workflow within systems biology projects will be explained. For many years we are the German partner in the FAIRDOM initiative (http://fair-dom.org) to establish a European data and model management service facility for systems biology. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Challenges in Small Screening Laboratories: SaaS to the rescue

PubMed Central

Lemmon, Vance P.; Jia, Yuanyuan; Shi, Yan; Holbrook, S. Douglas; Bixby, John L; Buchser, William

2012-01-01

The Miami Project to Cure Paralysis, part of the University of Miami Miller School of Medicine, includes a laboratory devoted to High Content Analysis (HCA) of neurons. The goal of the laboratory is to uncover signalling pathways, genes, compounds, or drugs that can be used to promote nerve growth. HCA permits the quantification of neuronal morphology, including the lengths and numbers of axons. HCA screening of various libraries on primary neurons requires a team-based approach, a variety of process steps and complex manipulations of cells and libraries to obtain meaningful results. HCA itself produces vast amounts of information including images, well-based data and cell-based phenotypic measures. Managing experimental workflow and library data, along with the extensive amount of experimental results is challenging. For academic laboratories generating large data sets from experiments using thousands of perturbagens, a laboratory information management system (LIMS) is the data tracking solution of choice. With both productivity and efficiency as driving rationales, the Miami Project has equipped its HCA laboratory with a Software As A Service (SAAS) LIMS to ensure the quality of its experiments and workflows. The article discusses this application in detail, and how the system was selected and integrated into the laboratory. The advantages of SaaS are described. PMID:21631415

Low Latency Workflow Scheduling and an Application of Hyperspectral Brightness Temperatures

NASA Astrophysics Data System (ADS)

Nguyen, P. T.; Chapman, D. R.; Halem, M.

2012-12-01

New system analytics for Big Data computing holds the promise of major scientific breakthroughs and discoveries from the exploration and mining of the massive data sets becoming available to the science community. However, such data intensive scientific applications face severe challenges in accessing, managing and analyzing petabytes of data. While the Hadoop MapReduce environment has been successfully applied to data intensive problems arising in business, there are still many scientific problem domains where limitations in the functionality of MapReduce systems prevent its wide adoption by those communities. This is mainly because MapReduce does not readily support the unique science discipline needs such as special science data formats, graphic and computational data analysis tools, maintaining high degrees of computational accuracies, and interfacing with application's existing components across heterogeneous computing processors. We address some of these limitations by exploiting the MapReduce programming model for satellite data intensive scientific problems and address scalability, reliability, scheduling, and data management issues when dealing with climate data records and their complex observational challenges. In addition, we will present techniques to support the unique Earth science discipline needs such as dealing with special science data formats (HDF and NetCDF). We have developed a Hadoop task scheduling algorithm that improves latency by 2x for a scientific workflow including the gridding of the EOS AIRS hyperspectral Brightness Temperatures (BT). This workflow processing algorithm has been tested at the Multicore Computing Center private Hadoop based Intel Nehalem cluster, as well as in a virtual mode under the Open Source Eucalyptus cloud. The 55TB AIRS hyperspectral L1b Brightness Temperature record has been gridded at the resolution of 0.5x1.0 degrees, and we have computed a 0.9 annual anti-correlation to the El Nino Southern oscillation in the Nino 4 region, as well as a 1.9 Kelvin decadal Arctic warming in the 4u and 12u spectral regions. Additionally, we will present the frequency of extreme global warming events by the use of a normalized maximum BT in a grid cell relative to its local standard deviation. A low-latency Hadoop scheduling environment maintains data integrity and fault tolerance in a MapReduce data intensive Cloud environment while improving the "time to solution" metric by 35% when compared to a more traditional parallel processing system for the same dataset. Our next step will be to improve the usability of our Hadoop task scheduling system, to enable rapid prototyping of data intensive experiments by means of processing "kernels". We will report on the performance and experience of implementing these experiments on the NEX testbed, and propose the use of a graphical directed acyclic graph (DAG) interface to help us develop on-demand scientific experiments. Our workflow system works within Hadoop infrastructure as a replacement for the FIFO or FairScheduler, thus the use of Apache "Pig" latin or other Apache tools may also be worth investigating on the NEX system to improve the usability of our workflow scheduling infrastructure for rapid experimentation.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

PubMed

Misirli, Göksel; Nguyen, Tramy; McLaughlin, James Alastair; Vaidyanathan, Prashant; Jones, Timothy S; Densmore, Douglas; Myers, Chris; Wipat, Anil

2018-06-05

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the complexity of building computational models. This approach can further be incorporated into other computational workflows for design automation.

Hospital Management Between The Modern Image And Aging

NASA Astrophysics Data System (ADS)

Dadulescu, Ana-Maria

2015-09-01

Hospital management has experienced significant progress with the evolution of the Romanian health system reform, it has made strides in terms of resource allocation and cost control, new systems for classification, evaluation and monitoring (DRGs, SIUI, CaPeSaRo) were implemented, some taken from other countries and adapted to local conditions, but not always integrated with the other components and sometimes incompletely implemented and developed. This material does not offer definite solutions to current problems. It only briefly addresses the main aspects of hospital activity, and points out some failures with whom hospital managers are presently faced. Once the problems are identified it creates prerequisites for solving them, it opens channels of research and development of new methodologies or correlation of the existing deficient workflows that can be corrected.

An automated analysis workflow for optimization of force-field parameters using neutron scattering data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lynch, Vickie E.; Borreguero, Jose M.; Bhowmik, Debsindhu

Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parametersmore » which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.« less

Clinical Decision Support Systems (CDSS) for preventive management of COPD patients.

PubMed

Velickovski, Filip; Ceccaroni, Luigi; Roca, Josep; Burgos, Felip; Galdiz, Juan B; Marina, Nuria; Lluch-Ariet, Magí

2014-11-28

The use of information and communication technologies to manage chronic diseases allows the application of integrated care pathways, and the optimization and standardization of care processes. Decision support tools can assist in the adherence to best-practice medicine in critical decision points during the execution of a care pathway. The objectives are to design, develop, and assess a clinical decision support system (CDSS) offering a suite of services for the early detection and assessment of chronic obstructive pulmonary disease (COPD), which can be easily integrated into a healthcare providers' work-flow. The software architecture model for the CDSS, interoperable clinical-knowledge representation, and inference engine were designed and implemented to form a base CDSS framework. The CDSS functionalities were iteratively developed through requirement-adjustment/development/validation cycles using enterprise-grade software-engineering methodologies and technologies. Within each cycle, clinical-knowledge acquisition was performed by a health-informatics engineer and a clinical-expert team. A suite of decision-support web services for (i) COPD early detection and diagnosis, (ii) spirometry quality-control support, (iii) patient stratification, was deployed in a secured environment on-line. The CDSS diagnostic performance was assessed using a validation set of 323 cases with 90% specificity, and 96% sensitivity. Web services were integrated in existing health information system platforms. Specialized decision support can be offered as a complementary service to existing policies of integrated care for chronic-disease management. The CDSS was able to issue recommendations that have a high degree of accuracy to support COPD case-finding. Integration into healthcare providers' work-flow can be achieved seamlessly through the use of a modular design and service-oriented architecture that connect to existing health information systems.

Clinical Decision Support Systems (CDSS) for preventive management of COPD patients

PubMed Central

2014-01-01

Background The use of information and communication technologies to manage chronic diseases allows the application of integrated care pathways, and the optimization and standardization of care processes. Decision support tools can assist in the adherence to best-practice medicine in critical decision points during the execution of a care pathway. Objectives The objectives are to design, develop, and assess a clinical decision support system (CDSS) offering a suite of services for the early detection and assessment of chronic obstructive pulmonary disease (COPD), which can be easily integrated into a healthcare providers' work-flow. Methods The software architecture model for the CDSS, interoperable clinical-knowledge representation, and inference engine were designed and implemented to form a base CDSS framework. The CDSS functionalities were iteratively developed through requirement-adjustment/development/validation cycles using enterprise-grade software-engineering methodologies and technologies. Within each cycle, clinical-knowledge acquisition was performed by a health-informatics engineer and a clinical-expert team. Results A suite of decision-support web services for (i) COPD early detection and diagnosis, (ii) spirometry quality-control support, (iii) patient stratification, was deployed in a secured environment on-line. The CDSS diagnostic performance was assessed using a validation set of 323 cases with 90% specificity, and 96% sensitivity. Web services were integrated in existing health information system platforms. Conclusions Specialized decision support can be offered as a complementary service to existing policies of integrated care for chronic-disease management. The CDSS was able to issue recommendations that have a high degree of accuracy to support COPD case-finding. Integration into healthcare providers' work-flow can be achieved seamlessly through the use of a modular design and service-oriented architecture that connect to existing health information systems. PMID:25471545

VisTrails SAHM: visualization and workflow management for species habitat modeling

USGS Publications Warehouse

Morisette, Jeffrey T.; Jarnevich, Catherine S.; Holcombe, Tracy R.; Talbert, Colin B.; Ignizio, Drew A.; Talbert, Marian; Silva, Claudio; Koop, David; Swanson, Alan; Young, Nicholas E.

2013-01-01

The Software for Assisted Habitat Modeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre- and post-processing steps and modeling options incorporated in the construction of a species distribution model through the established workflow management and visualization VisTrails software. This paper provides an overview of the VisTrails:SAHM software including a link to the open source code, a table detailing the current SAHM modules, and a simple example modeling an invasive weed species in Rocky Mountain National Park, USA.

Realising the Uncertainty Enabled Model Web

NASA Astrophysics Data System (ADS)

Cornford, D.; Bastin, L.; Pebesma, E. J.; Williams, M.; Stasch, C.; Jones, R.; Gerharz, L.

2012-12-01

The FP7 funded UncertWeb project aims to create the "uncertainty enabled model web". The central concept here is that geospatial models and data resources are exposed via standard web service interfaces, such as the Open Geospatial Consortium (OGC) suite of encodings and interface standards, allowing the creation of complex workflows combining both data and models. The focus of UncertWeb is on the issue of managing uncertainty in such workflows, and providing the standards, architecture, tools and software support necessary to realise the "uncertainty enabled model web". In this paper we summarise the developments in the first two years of UncertWeb, illustrating several key points with examples taken from the use case requirements that motivate the project. Firstly we address the issue of encoding specifications. We explain the usage of UncertML 2.0, a flexible encoding for representing uncertainty based on a probabilistic approach. This is designed to be used within existing standards such as Observations and Measurements (O&M) and data quality elements of ISO19115 / 19139 (geographic information metadata and encoding specifications) as well as more broadly outside the OGC domain. We show profiles of O&M that have been developed within UncertWeb and how UncertML 2.0 is used within these. We also show encodings based on NetCDF and discuss possible future directions for encodings in JSON. We then discuss the issues of workflow construction, considering discovery of resources (both data and models). We discuss why a brokering approach to service composition is necessary in a world where the web service interfaces remain relatively heterogeneous, including many non-OGC approaches, in particular the more mainstream SOAP and WSDL approaches. We discuss the trade-offs between delegating uncertainty management functions to the service interfaces themselves and integrating the functions in the workflow management system. We describe two utility services to address conversion between uncertainty types, and between the spatial / temporal support of service inputs / outputs. Finally we describe the tools being generated within the UncertWeb project, considering three main aspects: i) Elicitation of uncertainties on model inputs. We are developing tools to enable domain experts to provide judgements about input uncertainties from UncertWeb model components (e.g. parameters in meteorological models) which allow panels of experts to engage in the process and reach a consensus view on the current knowledge / beliefs about that parameter or variable. We are developing systems for continuous and categorical variables as well as stationary spatial fields. ii) Visualisation of the resulting uncertain outputs from the end of the workflow, but also at intermediate steps. At this point we have prototype implementations driven by the requirements from the use cases that motivate UncertWeb. iii) Sensitivity and uncertainty analysis on model outputs. Here we show the design of the overall system we are developing, including the deployment of an emulator framework to allow computationally efficient approaches. We conclude with a summary of the open issues and remaining challenges we are facing in UncertWeb, and provide a brief overview of how we plan to tackle these.

Dawn: A Simulation Model for Evaluating Costs and Tradeoffs of Big Data Science Architectures

NASA Astrophysics Data System (ADS)

Cinquini, L.; Crichton, D. J.; Braverman, A. J.; Kyo, L.; Fuchs, T.; Turmon, M.

2014-12-01

In many scientific disciplines, scientists and data managers are bracing for an upcoming deluge of big data volumes, which will increase the size of current data archives by a factor of 10-100 times. For example, the next Climate Model Inter-comparison Project (CMIP6) will generate a global archive of model output of approximately 10-20 Peta-bytes, while the upcoming next generation of NASA decadal Earth Observing instruments are expected to collect tens of Giga-bytes/day. In radio-astronomy, the Square Kilometre Array (SKA) will collect data in the Exa-bytes/day range, of which (after reduction and processing) around 1.5 Exa-bytes/year will be stored. The effective and timely processing of these enormous data streams will require the design of new data reduction and processing algorithms, new system architectures, and new techniques for evaluating computation uncertainty. Yet at present no general software tool or framework exists that will allow system architects to model their expected data processing workflow, and determine the network, computational and storage resources needed to prepare their data for scientific analysis. In order to fill this gap, at NASA/JPL we have been developing a preliminary model named DAWN (Distributed Analytics, Workflows and Numerics) for simulating arbitrary complex workflows composed of any number of data processing and movement tasks. The model can be configured with a representation of the problem at hand (the data volumes, the processing algorithms, the available computing and network resources), and is able to evaluate tradeoffs between different possible workflows based on several estimators: overall elapsed time, separate computation and transfer times, resulting uncertainty, and others. So far, we have been applying DAWN to analyze architectural solutions for 4 different use cases from distinct science disciplines: climate science, astronomy, hydrology and a generic cloud computing use case. This talk will present preliminary results and discuss how DAWN can be evolved into a powerful tool for designing system architectures for data intensive science.

Collection to Archival: A Data Management Strategy for the Ocean Acidification Community

NASA Astrophysics Data System (ADS)

Burger, E. F.; Smith, K. M.; Parsons, A. R.; Wanninkhof, R. H.; O'Brien, K.; Barbero, L.; Schweitzer, R.; Manke, A.

2014-12-01

Recently new data collection platforms, many of them autonomous mobile platforms, have added immensely to the data volume the Ocean Acidification community is dealing with. This is no exception with NOAA's Pacific Marine Environmental Laboratory (PMEL) Ocean Acidification (OA) effort. Collaboration between the PMEL Carbon group and the PMEL Science Data Integration group to manage local data has spawned the development of a data management strategy that covers the data lifecycle from collection to analysis to quality control to archival. The proposed software and workflow will leverage the successful data management framework pioneered by the Surface Ocean CO2 Atlas (SOCAT) project, but customized for Ocean Acidification requirements. This presentation will give a brief overview of the data management framework that will be implemented for Ocean Acidification data that are collected by PMEL scientists. We will also be discussing our plans to leverage this system to build an east coast ocean acidification management system at NOAA's Atlantic Oceanographic and Meteorological Laboratory (AOML), as well as a national OA management system at NOAA's National Oceanographic Data Center (NODC).

Using EHR audit trail logs to analyze clinical workflow: A case study from community-based ambulatory clinics.

PubMed

Wu, Danny T Y; Smart, Nikolas; Ciemins, Elizabeth L; Lanham, Holly J; Lindberg, Curt; Zheng, Kai

2017-01-01

To develop a workflow-supported clinical documentation system, it is a critical first step to understand clinical workflow. While Time and Motion studies has been regarded as the gold standard of workflow analysis, this method can be resource consuming and its data may be biased due to the cognitive limitation of human observers. In this study, we aimed to evaluate the feasibility and validity of using EHR audit trail logs to analyze clinical workflow. Specifically, we compared three known workflow changes from our previous study with the corresponding EHR audit trail logs of the study participants. The results showed that EHR audit trail logs can be a valid source for clinical workflow analysis, and can provide an objective view of clinicians' behaviors, multi-dimensional comparisons, and a highly extensible analysis framework.

The ATLAS Production System Evolution: New Data Processing and Analysis Paradigm for the LHC Run2 and High-Luminosity

NASA Astrophysics Data System (ADS)

Barreiro, F. H.; Borodin, M.; De, K.; Golubkov, D.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Padolski, S.; Wenaus, T.; ATLAS Collaboration

2017-10-01

The second generation of the ATLAS Production System called ProdSys2 is a distributed workload manager that runs daily hundreds of thousands of jobs, from dozens of different ATLAS specific workflows, across more than hundred heterogeneous sites. It achieves high utilization by combining dynamic job definition based on many criteria, such as input and output size, memory requirements and CPU consumption, with manageable scheduling policies and by supporting different kind of computational resources, such as GRID, clouds, supercomputers and volunteer-computers. The system dynamically assigns a group of jobs (task) to a group of geographically distributed computing resources. Dynamic assignment and resources utilization is one of the major features of the system, it didn’t exist in the earliest versions of the production system where Grid resources topology was predefined using national or/and geographical pattern. Production System has a sophisticated job fault-recovery mechanism, which efficiently allows to run multi-Terabyte tasks without human intervention. We have implemented “train” model and open-ended production which allow to submit tasks automatically as soon as new set of data is available and to chain physics groups data processing and analysis with central production by the experiment. We present an overview of the ATLAS Production System and its major components features and architecture: task definition, web user interface and monitoring. We describe the important design decisions and lessons learned from an operational experience during the first year of LHC Run2. We also report the performance of the designed system and how various workflows, such as data (re)processing, Monte-Carlo and physics group production, users analysis, are scheduled and executed within one production system on heterogeneous computing resources.

Chang'E-3 data pre-processing system based on scientific workflow

NASA Astrophysics Data System (ADS)

tan, xu; liu, jianjun; wang, yuanyuan; yan, wei; zhang, xiaoxia; li, chunlai

2016-04-01

The Chang'E-3(CE3) mission have obtained a huge amount of lunar scientific data. Data pre-processing is an important segment of CE3 ground research and application system. With a dramatic increase in the demand of data research and application, Chang'E-3 data pre-processing system(CEDPS) based on scientific workflow is proposed for the purpose of making scientists more flexible and productive by automating data-driven. The system should allow the planning, conduct and control of the data processing procedure with the following possibilities: • describe a data processing task, include:1)define input data/output data, 2)define the data relationship, 3)define the sequence of tasks,4)define the communication between tasks,5)define mathematical formula, 6)define the relationship between task and data. • automatic processing of tasks. Accordingly, Describing a task is the key point whether the system is flexible. We design a workflow designer which is a visual environment for capturing processes as workflows, the three-level model for the workflow designer is discussed:1) The data relationship is established through product tree.2)The process model is constructed based on directed acyclic graph(DAG). Especially, a set of process workflow constructs, including Sequence, Loop, Merge, Fork are compositional one with another.3)To reduce the modeling complexity of the mathematical formulas using DAG, semantic modeling based on MathML is approached. On top of that, we will present how processed the CE3 data with CEDPS.

Challenges and issues of geolocation in clinical environment.

PubMed

Issom, David-Zacharie; Hagry, Claire; Wodia Mendo, Laetitia; Seng, Henry; Ehrler, Frederic; Lovis, Christian

2012-01-01

Reaching a good indoor geolocation without deploying extensive and expensive infrastructure is a challenge, because satellite positioning system is not available indoors. Geolocation could be of major use in healthcare facilities; to help care providers, visitors and patients to navigate, to improve movements and flows efficiency or to implement location-awareness systems. A system able to provide the location of a person in a hospital requires precision, multi-floors and obstacles management and should also perform in basements and outdoors. Such system needs also to be insensitive to environmental variations occurring in a hospital. These changes may be various kinds of obstacles. These can be the displacement of metallic objects, metallic machines, strong magnetic fields or simply human displacement. A system conforming to the above requirements can also answer various security questions, operational workflow management but also assist movement of people.

A Scalable, Open Source Platform for Data Processing, Archiving and Dissemination

DTIC Science & Technology

2016-01-01

Object Oriented Data Technology (OODT) big data toolkit developed by NASA and the Work-flow INstance Generation and Selection (WINGS) scientific work...to several challenge big data problems and demonstrated the utility of OODT-WINGS in addressing them. Specific demonstrated analyses address i...source software, Apache, Object Oriented Data Technology, OODT, semantic work-flows, WINGS, big data , work- flow management 16. SECURITY CLASSIFICATION OF

Metaworkflows and Workflow Interoperability for Heliophysics

NASA Astrophysics Data System (ADS)

Pierantoni, Gabriele; Carley, Eoin P.

2014-06-01

Heliophysics is a relatively new branch of physics that investigates the relationship between the Sun and the other bodies of the solar system. To investigate such relationships, heliophysicists can rely on various tools developed by the community. Some of these tools are on-line catalogues that list events (such as Coronal Mass Ejections, CMEs) and their characteristics as they were observed on the surface of the Sun or on the other bodies of the Solar System. Other tools offer on-line data analysis and access to images and data catalogues. During their research, heliophysicists often perform investigations that need to coordinate several of these services and to repeat these complex operations until the phenomena under investigation are fully analyzed. Heliophysicists combine the results of these services; this service orchestration is best suited for workflows. This approach has been investigated in the HELIO project. The HELIO project developed an infrastructure for a Virtual Observatory for Heliophysics and implemented service orchestration using TAVERNA workflows. HELIO developed a set of workflows that proved to be useful but lacked flexibility and re-usability. The TAVERNA workflows also needed to be executed directly in TAVERNA workbench, and this forced all users to learn how to use the workbench. Within the SCI-BUS and ER-FLOW projects, we have started an effort to re-think and re-design the heliophysics workflows with the aim of fostering re-usability and ease of use. We base our approach on two key concepts, that of meta-workflows and that of workflow interoperability. We have divided the produced workflows in three different layers. The first layer is Basic Workflows, developed both in the TAVERNA and WS-PGRADE languages. They are building blocks that users compose to address their scientific challenges. They implement well-defined Use Cases that usually involve only one service. The second layer is Science Workflows usually developed in TAVERNA. They- implement Science Cases (the definition of a scientific challenge) by composing different Basic Workflows. The third and last layer,Iterative Science Workflows, is developed in WSPGRADE. It executes sub-workflows (either Basic or Science Workflows) as parameter sweep jobs to investigate Science Cases on large multiple data sets. So far, this approach has proven fruitful for three Science Cases of which one has been completed and two are still being tested.

Cloud-based opportunities in scientific computing: insights from processing Suomi National Polar-Orbiting Partnership (S-NPP) Direct Broadcast data

NASA Astrophysics Data System (ADS)

Evans, J. D.; Hao, W.; Chettri, S.

2013-12-01

The cloud is proving to be a uniquely promising platform for scientific computing. Our experience with processing satellite data using Amazon Web Services highlights several opportunities for enhanced performance, flexibility, and cost effectiveness in the cloud relative to traditional computing -- for example: - Direct readout from a polar-orbiting satellite such as the Suomi National Polar-Orbiting Partnership (S-NPP) requires bursts of processing a few times a day, separated by quiet periods when the satellite is out of receiving range. In the cloud, by starting and stopping virtual machines in minutes, we can marshal significant computing resources quickly when needed, but not pay for them when not needed. To take advantage of this capability, we are automating a data-driven approach to the management of cloud computing resources, in which new data availability triggers the creation of new virtual machines (of variable size and processing power) which last only until the processing workflow is complete. - 'Spot instances' are virtual machines that run as long as one's asking price is higher than the provider's variable spot price. Spot instances can greatly reduce the cost of computing -- for software systems that are engineered to withstand unpredictable interruptions in service (as occurs when a spot price exceeds the asking price). We are implementing an approach to workflow management that allows data processing workflows to resume with minimal delays after temporary spot price spikes. This will allow systems to take full advantage of variably-priced 'utility computing.' - Thanks to virtual machine images, we can easily launch multiple, identical machines differentiated only by 'user data' containing individualized instructions (e.g., to fetch particular datasets or to perform certain workflows or algorithms) This is particularly useful when (as is the case with S-NPP data) we need to launch many very similar machines to process an unpredictable number of data files concurrently. Our experience shows the viability and flexibility of this approach to workflow management for scientific data processing. - Finally, cloud computing is a promising platform for distributed volunteer ('interstitial') computing, via mechanisms such as the Berkeley Open Infrastructure for Network Computing (BOINC) popularized with the SETI@Home project and others such as ClimatePrediction.net and NASA's Climate@Home. Interstitial computing faces significant challenges as commodity computing shifts from (always on) desktop computers towards smartphones and tablets (untethered and running on scarce battery power); but cloud computing offers significant slack capacity. This capacity includes virtual machines with unused RAM or underused CPUs; virtual storage volumes allocated (& paid for) but not full; and virtual machines that are paid up for the current hour but whose work is complete. We are devising ways to facilitate the reuse of these resources (i.e., cloud-based interstitial computing) for satellite data processing and related analyses. We will present our findings and research directions on these and related topics.

Processing, Cataloguing and Distribution of Uas Images in Near Real Time

NASA Astrophysics Data System (ADS)

Runkel, I.

2013-08-01

Why are UAS such a hype? UAS make the data capture flexible, fast and easy. For many applications this is more important than a perfect photogrammetric aerial image block. To ensure, that the advantage of a fast data capturing will be valid up to the end of the processing chain, all intermediate steps like data processing and data dissemination to the customer need to be flexible and fast as well. GEOSYSTEMS has established the whole processing workflow as server/client solution. This is the focus of the presentation. Depending on the image acquisition system the image data can be down linked during the flight to the data processing computer or it is stored on a mobile device and hooked up to the data processing computer after the flight campaign. The image project manager reads the data from the device and georeferences the images according to the position data. The meta data is converted into an ISO conform format and subsequently all georeferenced images are catalogued in the raster data management System ERDAS APOLLO. APOLLO provides the data, respectively the images as an OGC-conform services to the customer. Within seconds the UAV-images are ready to use for GIS application, image processing or direct interpretation via web applications - where ever you want. The whole processing chain is built in a generic manner. It can be adapted to a magnitude of applications. The UAV imageries can be processed and catalogued as single ortho imges or as image mosaic. Furthermore, image data of various cameras can be fusioned. By using WPS (web processing services) image enhancement, image analysis workflows like change detection layers can be calculated and provided to the image analysts. The processing of the WPS runs direct on the raster data management server. The image analyst has no data and no software on his local computer. This workflow is proven to be fast, stable and accurate. It is designed to support time critical applications for security demands - the images can be checked and interpreted in near real-time. For sensible areas it gives you the possibility to inform remote decision makers or interpretation experts in order to provide them situations awareness, wherever they are. For monitoring and inspection tasks it speeds up the process of data capture and data interpretation. The fully automated workflow of data pre-processing, data georeferencing, data cataloguing and data dissemination in near real time was developed based on the Intergraph products ERDAS IMAGINE, ERDAS APOLLO and GEOSYSTEMS METAmorph!IT. It is offered as adaptable solution by GEOSYSTEMS GmbH.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow

PubMed Central

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-01-01

Background Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. Results In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. Conclusion JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from or . PMID:17123449

A mobile phone based remote patient monitoring system for chronic disease management.

PubMed

Trudel, Mathieu; Cafazzo, Joseph A; Hamill, Melinda; Igharas, Walter; Tallevi, Kevin; Picton, Peter; Lam, Jack; Rossos, Peter G; Easty, Anthony C; Logan, Alexander

2007-01-01

Rising concern over the poor state of chronic disease management led to the user-informed design and development of a home tele-monitoring system. Focus groups with patients and primary care providers guided the research team towards a design that would accommodate the workflow and concerns of the healthcare providers and the low use and comfort with technology found among the patient population. The system was trialed in a before-and-after pilot study of 34 patients with diabetes and hypertension. Findings demonstrate a significant improvement in systolic and diastolic blood pressure. An RCT beginning in 2007 is being conducted to confirm these findings. It is hypothesized that this user-centred approach, utilizing focus groups, iterative design and human factors methods of evaluation, will lead to the next-generation of home tele-monitoring applications that are more intuitive, less cumbersome, and ultimately bring about greater patient compliance and better physician management.

Standardization and quality management in next-generation sequencing.

PubMed

Endrullat, Christoph; Glökler, Jörn; Franke, Philipp; Frohme, Marcus

2016-09-01

DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.

Next Generation Workload Management System For Big Data on Heterogeneous Distributed Computing

NASA Astrophysics Data System (ADS)

Klimentov, A.; Buncic, P.; De, K.; Jha, S.; Maeno, T.; Mount, R.; Nilsson, P.; Oleynik, D.; Panitkin, S.; Petrosyan, A.; Porter, R. J.; Read, K. F.; Vaniachine, A.; Wells, J. C.; Wenaus, T.

2015-05-01

The Large Hadron Collider (LHC), operating at the international CERN Laboratory in Geneva, Switzerland, is leading Big Data driven scientific explorations. Experiments at the LHC explore the fundamental nature of matter and the basic forces that shape our universe, and were recently credited for the discovery of a Higgs boson. ATLAS and ALICE are the largest collaborations ever assembled in the sciences and are at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, both experiments rely on a heterogeneous distributed computational infrastructure. The ATLAS experiment uses PanDA (Production and Data Analysis) Workload Management System (WMS) for managing the workflow for all data processing on hundreds of data centers. Through PanDA, ATLAS physicists see a single computing facility that enables rapid scientific breakthroughs for the experiment, even though the data centers are physically scattered all over the world. The scale is demonstrated by the following numbers: PanDA manages O(102) sites, O(105) cores, O(108) jobs per year, O(103) users, and ATLAS data volume is O(1017) bytes. In 2013 we started an ambitious program to expand PanDA to all available computing resources, including opportunistic use of commercial and academic clouds and Leadership Computing Facilities (LCF). The project titled ‘Next Generation Workload Management and Analysis System for Big Data’ (BigPanDA) is funded by DOE ASCR and HEP. Extending PanDA to clouds and LCF presents new challenges in managing heterogeneity and supporting workflow. The BigPanDA project is underway to setup and tailor PanDA at the Oak Ridge Leadership Computing Facility (OLCF) and at the National Research Center "Kurchatov Institute" together with ALICE distributed computing and ORNL computing professionals. Our approach to integration of HPC platforms at the OLCF and elsewhere is to reuse, as much as possible, existing components of the PanDA system. We will present our current accomplishments with running the PanDA WMS at OLCF and other supercomputers and demonstrate our ability to use PanDA as a portal independent of the computing facilities infrastructure for High Energy and Nuclear Physics as well as other data-intensive science applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Edward J., Jr.; Henry, Karen Lynne

Sandia National Laboratories develops technologies to: (1) sustain, modernize, and protect our nuclear arsenal (2) Prevent the spread of weapons of mass destruction; (3) Provide new capabilities to our armed forces; (4) Protect our national infrastructure; (5) Ensure the stability of our nation's energy and water supplies; and (6) Defend our nation against terrorist threats. We identified the need for a single overarching Integrated Workplace Management System (IWMS) that would enable us to focus on customer missions and improve FMOC processes. Our team selected highly configurable commercial-off-the-shelf (COTS) software with out-of-the-box workflow processes that integrate strategic planning, project management, facilitymore » assessments, and space management, and can interface with existing systems, such as Oracle, PeopleSoft, Maximo, Bentley, and FileNet. We selected the Integrated Workplace Management System (IWMS) from Tririga, Inc. Facility Management System (FMS) Benefits are: (1) Create a single reliable source for facility data; (2) Improve transparency with oversight organizations; (3) Streamline FMOC business processes with a single, integrated facility-management tool; (4) Give customers simple tools and real-time information; (5) Reduce indirect costs; (6) Replace approximately 30 FMOC systems and 60 homegrown tools (such as Microsoft Access databases); and (7) Integrate with FIMS.« less

Experiences with Deriva: An Asset Management Platform for Accelerating eScience.

PubMed

Bugacov, Alejandro; Czajkowski, Karl; Kesselman, Carl; Kumar, Anoop; Schuler, Robert E; Tangmunarunkit, Hongsuda

2017-10-01

The pace of discovery in eScience is increasingly dependent on a scientist's ability to acquire, curate, integrate, analyze, and share large and diverse collections of data. It is all too common for investigators to spend inordinate amounts of time developing ad hoc procedures to manage their data. In previous work, we presented Deriva, a Scientific Asset Management System, designed to accelerate data driven discovery. In this paper, we report on the use of Deriva in a number of substantial and diverse eScience applications. We describe the lessons we have learned, both from the perspective of the Deriva technology, as well as the ability and willingness of scientists to incorporate Scientific Asset Management into their daily workflows.

Grid infrastructure for automatic processing of SAR data for flood applications

NASA Astrophysics Data System (ADS)

Kussul, Natalia; Skakun, Serhiy; Shelestov, Andrii

2010-05-01

More and more geosciences applications are being put on to the Grids. Due to the complexity of geosciences applications that is caused by complex workflow, the use of computationally intensive environmental models, the need of management and integration of heterogeneous data sets, Grid offers solutions to tackle these problems. Many geosciences applications, especially those related to the disaster management and mitigations require the geospatial services to be delivered in proper time. For example, information on flooded areas should be provided to corresponding organizations (local authorities, civil protection agencies, UN agencies etc.) no more than in 24 h to be able to effectively allocate resources required to mitigate the disaster. Therefore, providing infrastructure and services that will enable automatic generation of products based on the integration of heterogeneous data represents the tasks of great importance. In this paper we present Grid infrastructure for automatic processing of synthetic-aperture radar (SAR) satellite images to derive flood products. In particular, we use SAR data acquired by ESA's ENVSAT satellite, and neural networks to derive flood extent. The data are provided in operational mode from ESA rolling archive (within ESA Category-1 grant). We developed a portal that is based on OpenLayers frameworks and provides access point to the developed services. Through the portal the user can define geographical region and search for the required data. Upon selection of data sets a workflow is automatically generated and executed on the resources of Grid infrastructure. For workflow execution and management we use Karajan language. The workflow of SAR data processing consists of the following steps: image calibration, image orthorectification, image processing with neural networks, topographic effects removal, geocoding and transformation to lat/long projection, and visualisation. These steps are executed by different software, and can be executed by different resources of the Grid system. The resulting geospatial services are available in various OGC standards such as KML and WMS. Currently, the Grid infrastructure integrates the resources of several geographically distributed organizations, in particular: Space Research Institute NASU-NSAU (Ukraine) with deployed computational and storage nodes based on Globus Toolkit 4 (htpp://www.globus.org) and gLite 3 (http://glite.web.cern.ch) middleware, access to geospatial data and a Grid portal; Institute of Cybernetics of NASU (Ukraine) with deployed computational and storage nodes (SCIT-1/2/3 clusters) based on Globus Toolkit 4 middleware and access to computational resources (approximately 500 processors); Center of Earth Observation and Digital Earth Chinese Academy of Sciences (CEODE-CAS, China) with deployed computational nodes based on Globus Toolkit 4 middleware and access to geospatial data (approximately 16 processors). We are currently adding new geospatial services based on optical satellite data, namely MODIS. This work is carried out jointly with the CEODE-CAS. Using workflow patterns that were developed for SAR data processing we are building new workflows for optical data processing.

Empowering file-based radio production through media asset management systems

NASA Astrophysics Data System (ADS)

Muylaert, Bjorn; Beckers, Tom

2006-10-01

In recent years, IT-based production and archiving of media has matured to a level which enables broadcasters to switch over from tape- or CD-based to file-based workflows for the production of their radio and television programs. This technology is essential for the future of broadcasters as it provides the flexibility and speed of execution the customer demands by enabling, among others, concurrent access and production, faster than real-time ingest, edit during ingest, centrally managed annotation and quality preservation of media. In terms of automation of program production, the radio department is the most advanced within the VRT, the Flemish broadcaster. Since a couple of years ago, the radio department has been working with digital equipment and producing its programs mainly on standard IT equipment. Historically, the shift from analogue to digital based production has been a step by step process initiated and coordinated by each radio station separately, resulting in a multitude of tools and metadata collections, some of them developed in-house, lacking integration. To make matters worse, each of those stations adopted a slightly different production methodology. The planned introduction of a company-wide Media Asset Management System allows a coordinated overhaul to a unified production architecture. Benefits include the centralized ingest and annotation of audio material and the uniform, integrated (in terms of IT infrastructure) workflow model. Needless to say, the ingest strategy, metadata management and integration with radio production systems play a major role in the level of success of any improvement effort. This paper presents a data model for audio-specific concepts relevant to radio production. It includes an investigation of ingest techniques and strategies. Cooperation with external, professional production tools is demonstrated through a use-case scenario: the integration of an existing, multi-track editing tool with a commercially available Media Asset Management System. This will enable an uncomplicated production chain, with a recognizable look and feel for all system users, regardless of their affiliated radio station, as well as central retrieval and storage of information and metadata.

A Chaotic Particle Swarm Optimization-Based Heuristic for Market-Oriented Task-Level Scheduling in Cloud Workflow Systems.

PubMed

Li, Xuejun; Xu, Jia; Yang, Yun

2015-01-01

Cloud workflow system is a kind of platform service based on cloud computing. It facilitates the automation of workflow applications. Between cloud workflow system and its counterparts, market-oriented business model is one of the most prominent factors. The optimization of task-level scheduling in cloud workflow system is a hot topic. As the scheduling is a NP problem, Ant Colony Optimization (ACO) and Particle Swarm Optimization (PSO) have been proposed to optimize the cost. However, they have the characteristic of premature convergence in optimization process and therefore cannot effectively reduce the cost. To solve these problems, Chaotic Particle Swarm Optimization (CPSO) algorithm with chaotic sequence and adaptive inertia weight factor is applied to present the task-level scheduling. Chaotic sequence with high randomness improves the diversity of solutions, and its regularity assures a good global convergence. Adaptive inertia weight factor depends on the estimate value of cost. It makes the scheduling avoid premature convergence by properly balancing between global and local exploration. The experimental simulation shows that the cost obtained by our scheduling is always lower than the other two representative counterparts.

A Chaotic Particle Swarm Optimization-Based Heuristic for Market-Oriented Task-Level Scheduling in Cloud Workflow Systems

PubMed Central

Li, Xuejun; Xu, Jia; Yang, Yun

2015-01-01

Cloud workflow system is a kind of platform service based on cloud computing. It facilitates the automation of workflow applications. Between cloud workflow system and its counterparts, market-oriented business model is one of the most prominent factors. The optimization of task-level scheduling in cloud workflow system is a hot topic. As the scheduling is a NP problem, Ant Colony Optimization (ACO) and Particle Swarm Optimization (PSO) have been proposed to optimize the cost. However, they have the characteristic of premature convergence in optimization process and therefore cannot effectively reduce the cost. To solve these problems, Chaotic Particle Swarm Optimization (CPSO) algorithm with chaotic sequence and adaptive inertia weight factor is applied to present the task-level scheduling. Chaotic sequence with high randomness improves the diversity of solutions, and its regularity assures a good global convergence. Adaptive inertia weight factor depends on the estimate value of cost. It makes the scheduling avoid premature convergence by properly balancing between global and local exploration. The experimental simulation shows that the cost obtained by our scheduling is always lower than the other two representative counterparts. PMID:26357510

High-Performance Compute Infrastructure in Astronomy: 2020 Is Only Months Away

NASA Astrophysics Data System (ADS)

Berriman, B.; Deelman, E.; Juve, G.; Rynge, M.; Vöckler, J. S.

2012-09-01

By 2020, astronomy will be awash with as much as 60 PB of public data. Full scientific exploitation of such massive volumes of data will require high-performance computing on server farms co-located with the data. Development of this computing model will be a community-wide enterprise that has profound cultural and technical implications. Astronomers must be prepared to develop environment-agnostic applications that support parallel processing. The community must investigate the applicability and cost-benefit of emerging technologies such as cloud computing to astronomy, and must engage the Computer Science community to develop science-driven cyberinfrastructure such as workflow schedulers and optimizers. We report here the results of collaborations between a science center, IPAC, and a Computer Science research institute, ISI. These collaborations may be considered pathfinders in developing a high-performance compute infrastructure in astronomy. These collaborations investigated two exemplar large-scale science-driver workflow applications: 1) Calculation of an infrared atlas of the Galactic Plane at 18 different wavelengths by placing data from multiple surveys on a common plate scale and co-registering all the pixels; 2) Calculation of an atlas of periodicities present in the public Kepler data sets, which currently contain 380,000 light curves. These products have been generated with two workflow applications, written in C for performance and designed to support parallel processing on multiple environments and platforms, but with different compute resource needs: the Montage image mosaic engine is I/O-bound, and the NASA Star and Exoplanet Database periodogram code is CPU-bound. Our presentation will report cost and performance metrics and lessons-learned for continuing development. Applicability of Cloud Computing: Commercial Cloud providers generally charge for all operations, including processing, transfer of input and output data, and for storage of data, and so the costs of running applications vary widely according to how they use resources. The cloud is well suited to processing CPU-bound (and memory bound) workflows such as the periodogram code, given the relatively low cost of processing in comparison with I/O operations. I/O-bound applications such as Montage perform best on high-performance clusters with fast networks and parallel file-systems. Science-driven Cyberinfrastructure: Montage has been widely used as a driver application to develop workflow management services, such as task scheduling in distributed environments, designing fault tolerance techniques for job schedulers, and developing workflow orchestration techniques. Running Parallel Applications Across Distributed Cloud Environments: Data processing will eventually take place in parallel distributed across cyber infrastructure environments having different architectures. We have used the Pegasus Work Management System (WMS) to successfully run applications across three very different environments: TeraGrid, OSG (Open Science Grid), and FutureGrid. Provisioning resources across different grids and clouds (also referred to as Sky Computing), involves establishing a distributed environment, where issues of, e.g, remote job submission, data management, and security need to be addressed. This environment also requires building virtual machine images that can run in different environments. Usually, each cloud provides basic images that can be customized with additional software and services. In most of our work, we provisioned compute resources using a custom application, called Wrangler. Pegasus WMS abstracts the architectures of the compute environments away from the end-user, and can be considered a first-generation tool suitable for scientists to run their applications on disparate environments.

Implementation of workflow engine technology to deliver basic clinical decision support functionality

PubMed Central

2011-01-01

Background Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. Results We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. Conclusions We describe an implementation of a free workflow technology software suite (available at http://code.google.com/p/healthflow) and its application in the domain of clinical decision support. Our implementation seamlessly supports clinical logic testing on retrospective data and offers a user-friendly knowledge representation paradigm. With the presented software implementation, we demonstrate that workflow engine technology can provide a decision support platform which evaluates well against an established clinical decision support architecture evaluation framework. Due to cross-industry usage of workflow engine technology, we can expect significant future functionality enhancements that will further improve the technology's capacity to serve as a clinical decision support platform. PMID:21477364

Web-video-mining-supported workflow modeling for laparoscopic surgeries.

PubMed

Liu, Rui; Zhang, Xiaoli; Zhang, Hao

2016-11-01

As quality assurance is of strong concern in advanced surgeries, intelligent surgical systems are expected to have knowledge such as the knowledge of the surgical workflow model (SWM) to support their intuitive cooperation with surgeons. For generating a robust and reliable SWM, a large amount of training data is required. However, training data collected by physically recording surgery operations is often limited and data collection is time-consuming and labor-intensive, severely influencing knowledge scalability of the surgical systems. The objective of this research is to solve the knowledge scalability problem in surgical workflow modeling with a low cost and labor efficient way. A novel web-video-mining-supported surgical workflow modeling (webSWM) method is developed. A novel video quality analysis method based on topic analysis and sentiment analysis techniques is developed to select high-quality videos from abundant and noisy web videos. A statistical learning method is then used to build the workflow model based on the selected videos. To test the effectiveness of the webSWM method, 250 web videos were mined to generate a surgical workflow for the robotic cholecystectomy surgery. The generated workflow was evaluated by 4 web-retrieved videos and 4 operation-room-recorded videos, respectively. The evaluation results (video selection consistency n-index ≥0.60; surgical workflow matching degree ≥0.84) proved the effectiveness of the webSWM method in generating robust and reliable SWM knowledge by mining web videos. With the webSWM method, abundant web videos were selected and a reliable SWM was modeled in a short time with low labor cost. Satisfied performances in mining web videos and learning surgery-related knowledge show that the webSWM method is promising in scaling knowledge for intelligent surgical systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Modernizing Earth and Space Science Modeling Workflows in the Big Data Era

NASA Astrophysics Data System (ADS)

Kinter, J. L.; Feigelson, E.; Walker, R. J.; Tino, C.

2017-12-01

Modeling is a major aspect of the Earth and space science research. The development of numerical models of the Earth system, planetary systems or astrophysical systems is essential to linking theory with observations. Optimal use of observations that are quite expensive to obtain and maintain typically requires data assimilation that involves numerical models. In the Earth sciences, models of the physical climate system are typically used for data assimilation, climate projection, and inter-disciplinary research, spanning applications from analysis of multi-sensor data sets to decision-making in climate-sensitive sectors with applications to ecosystems, hazards, and various biogeochemical processes. In space physics, most models are from first principles, require considerable expertise to run and are frequently modified significantly for each case study. The volume and variety of model output data from modeling Earth and space systems are rapidly increasing and have reached a scale where human interaction with data is prohibitively inefficient. A major barrier to progress is that modeling workflows isn't deemed by practitioners to be a design problem. Existing workflows have been created by a slow accretion of software, typically based on undocumented, inflexible scripts haphazardly modified by a succession of scientists and students not trained in modern software engineering methods. As a result, existing modeling workflows suffer from an inability to onboard new datasets into models; an inability to keep pace with accelerating data production rates; and irreproducibility, among other problems. These factors are creating an untenable situation for those conducting and supporting Earth system and space science. Improving modeling workflows requires investments in hardware, software and human resources. This paper describes the critical path issues that must be targeted to accelerate modeling workflows, including script modularization, parallelization, and automation in the near term, and longer term investments in virtualized environments for improved scalability, tolerance for lossy data compression, novel data-centric memory and storage technologies, and tools for peer reviewing, preserving and sharing workflows, as well as fundamental statistical and machine learning algorithms.

Applying operations research to optimize a novel population management system for cancer screening

PubMed Central

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-01-01

Objective To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. Materials and methods TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. Results TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Conclusions Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management. PMID:24043318

Build and Execute Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guan, Qiang

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows willmore » compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.« less

A conceptual framework for managing clinical processes.

PubMed

Buffone, G J; Moreau, D

1997-01-01

Reengineering of the health care delivery system is underway, as is the transformation of the processes and methods used for recording information describing patient care (i.e., the development of a computer-based record). This report describes the use of object-oriented analysis and design to develop and implement clinical process reengineering as well as the organization of clinical data. In addition, the facility of the proposed framework for implementing workflow computing is discussed.

Active Provenance in Data-intensive Research

NASA Astrophysics Data System (ADS)

Spinuso, Alessandro; Mihajlovski, Andrej; Filgueira, Rosa; Atkinson, Malcolm

2017-04-01

Scientific communities are building platforms where the usage of data-intensive workflows is crucial to conduct their research campaigns. However managing and effectively support the understanding of the 'live' processes, fostering computational steering, sharing and re-use of data and methods, present several bottlenecks. These are often caused by the poor level of documentation on the methods and the data and how users interact with it. This work wants to explore how in such systems, flexibility in the management of the provenance and its adaptation to the different users and application contexts can lead to new opportunities for its exploitation, improving productivity. In particular, this work illustrates a conceptual and technical framework enabling tunable and actionable provenance in data-intensive workflow systems in support of reproducible science. It introduces the concept of Agile data-intensive systems to define the characteristic of our target platform. It shows a novel approach to the integration of provenance mechanisms, offering flexibility in the scale and in the precision of the provenance data collected, ensuring its relevance to the domain of the data-intensive task, fostering its rapid exploitation. The contributions address aspects of the scale of the provenance records, their usability and active role in the research life-cycle. We will discuss the use of dynamically generated provenance types as the approach for the integration of provenance mechanisms into a data-intensive workflow system. Enabling provenance can be transparent to the workflow user and developer, as well as fully controllable and customisable, depending from their expertise and the application's reproducibility, monitoring and validation requirements. The API that allows the realisation and adoption of a provenance type is presented, especially for what concerns the support of provenance profiling, contextualisation and precision. An actionable approach to provenance management will be also discussed, enabling provenance-driven operations at runtime, regardless of the enactment technologies and connectivity impediments. We proposes a framework based on concepts such as provenance clusters and provenance sensors, envisaging new potential for exploiting large quantities of provenance traces at runtime. Finally the work will also introduce how the underlying provenance model can be explored with big-data visualization techniques, aiming at producing comprehensive and interactive views on top of large and heterogeneous provenance data. We will demonstrate the adoption of alternative visualisation methods, from detailed and localised interactive graphs to radial-views, serving different purposes and expertise. Combining provenance types, selective rules, extensible metadata with reactive clustering opens a new and more versatile role of the lineage information in the research life-cycle, thanks to its improved usability. The flexible profiling of the proposed framework offers aid to the human analysis of the process, with the support of advanced and intuitive interactive graphical tools. The Active provenance methods are discussed in the context of a real implementation for a data-intensive library (dispel4py) and its adoption within use cases for computational seismology, climate studies and generic correlation analysis.

Observing System Simulation Experiment (OSSE) for the HyspIRI Spectrometer Mission

NASA Technical Reports Server (NTRS)

Turmon, Michael J.; Block, Gary L.; Green, Robert O.; Hua, Hook; Jacob, Joseph C.; Sobel, Harold R.; Springer, Paul L.; Zhang, Qingyuan

2010-01-01

The OSSE software provides an integrated end-to-end environment to simulate an Earth observing system by iteratively running a distributed modeling workflow based on the HyspIRI Mission, including atmospheric radiative transfer, surface albedo effects, detection, and retrieval for agile exploration of the mission design space. The software enables an Observing System Simulation Experiment (OSSE) and can be used for design trade space exploration of science return for proposed instruments by modeling the whole ground truth, sensing, and retrieval chain and to assess retrieval accuracy for a particular instrument and algorithm design. The OSSE in fra struc ture is extensible to future National Research Council (NRC) Decadal Survey concept missions where integrated modeling can improve the fidelity of coupled science and engineering analyses for systematic analysis and science return studies. This software has a distributed architecture that gives it a distinct advantage over other similar efforts. The workflow modeling components are typically legacy computer programs implemented in a variety of programming languages, including MATLAB, Excel, and FORTRAN. Integration of these diverse components is difficult and time-consuming. In order to hide this complexity, each modeling component is wrapped as a Web Service, and each component is able to pass analysis parameterizations, such as reflectance or radiance spectra, on to the next component downstream in the service workflow chain. In this way, the interface to each modeling component becomes uniform and the entire end-to-end workflow can be run using any existing or custom workflow processing engine. The architecture lets users extend workflows as new modeling components become available, chain together the components using any existing or custom workflow processing engine, and distribute them across any Internet-accessible Web Service endpoints. The workflow components can be hosted on any Internet-accessible machine. This has the advantages that the computations can be distributed to make best use of the available computing resources, and each workflow component can be hosted and maintained by their respective domain experts.

Electronic Derivative Classifier/Reviewing Official

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, Joshua C; McDuffie, Gregory P; Light, Ken L

2017-02-17

The electronic Derivative Classifier, Reviewing Official (eDC/RO) is a web based document management and routing system that reduces security risks and increases workflow efficiencies. The system automates the upload, notification review request, and document status tracking of documents for classification review on a secure server. It supports a variety of document formats (i.e., pdf, doc, docx, xls, xlsx, xlsm, ppt, pptx, vsd, vsdx and txt), and allows for the dynamic placement of classification markings such as the classification level, category and caveats on the document, in addition to a document footer and digital signature.

Digital transformation in home care. A case study.

PubMed

Bennis, Sandy; Costanzo, Diane; Flynn, Ann Marie; Reidy, Agatha; Tronni, Catherine

2007-01-01

Simply implementing software and technology does not assure that an organization's targeted clinical and financial goals will be realized. No longer is it possible to roll out a new system--by solely providing end user training and overlaying it on top of already inefficient workflows and outdated roles--and know with certainty that targets will be met. At Virtua Health's Home Care, based in south New Jersey, implementation of their electronic system initially followed this more traditional approach. Unable to completely attain their earlier identified return on investment, they enlisted the help of a new role within their health system, that of the nurse informaticist. Knowledgeable in complex clinical processes and not bound by the technology at hand, the informaticist analyzed physical workflow, digital workflow, roles and physical layout. Leveraging specific tools such as change acceleration, workouts and LEAN, the informaticist was able to redesign workflow and support new levels of functionality. This article provides a view from the "finish line", recounting how this role worked with home care to assimilate information delivery into more efficient processes and align resources to support the new workflow, ultimately achieving real tangible returns.

Dynamic reusable workflows for ocean science

USGS Publications Warehouse

Signell, Richard; Fernandez, Filipe; Wilcox, Kyle

2016-01-01

Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog search and data access make it now possible to create catalog-driven workflows that automate — end-to-end — data search, analysis and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill-assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enters the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic notebooks across the geoscience domains.

Parametric Workflow (BIM) for the Repair Construction of Traditional Historic Architecture in Taiwan

NASA Astrophysics Data System (ADS)

Ma, Y.-P.; Hsu, C. C.; Lin, M.-C.; Tsai, Z.-W.; Chen, J.-Y.

2015-08-01

In Taiwan, numerous existing traditional buildings are constructed with wooden structures, brick structures, and stone structures. This paper will focus on the Taiwan traditional historic architecture and target the traditional wooden structure buildings as the design proposition and process the BIM workflow for modeling complex wooden combination geometry, integrating with more traditional 2D documents and for visualizing repair construction assumptions within the 3D model representation. The goal of this article is to explore the current problems to overcome in wooden historic building conservation, and introduce the BIM technology in the case of conserving, documenting, managing, and creating full engineering drawings and information for effectively support historic conservation. Although BIM is mostly oriented to current construction praxis, there have been some attempts to investigate its applicability in historic conservation projects. This article also illustrates the importance and advantages of using BIM workflow in repair construction process, when comparing with generic workflow.

Bridging the Guideline Implementation Gap: A Systematic, Document-Centered Approach to Guideline Implementation

PubMed Central

Shiffman, Richard N.; Michel, George; Essaihi, Abdelwaheb; Thornquist, Elizabeth

2004-01-01

Objective: A gap exists between the information contained in published clinical practice guidelines and the knowledge and information that are necessary to implement them. This work describes a process to systematize and make explicit the translation of document-based knowledge into workflow-integrated clinical decision support systems. Design: This approach uses the Guideline Elements Model (GEM) to represent the guideline knowledge. Implementation requires a number of steps to translate the knowledge contained in guideline text into a computable format and to integrate the information into clinical workflow. The steps include: (1) selection of a guideline and specific recommendations for implementation, (2) markup of the guideline text, (3) atomization, (4) deabstraction and (5) disambiguation of recommendation concepts, (6) verification of rule set completeness, (7) addition of explanations, (8) building executable statements, (9) specification of origins of decision variables and insertions of recommended actions, (10) definition of action types and selection of associated beneficial services, (11) choice of interface components, and (12) creation of requirement specification. Results: The authors illustrate these component processes using examples drawn from recent experience translating recommendations from the National Heart, Lung, and Blood Institute's guideline on management of chronic asthma into a workflow-integrated decision support system that operates within the Logician electronic health record system. Conclusion: Using the guideline document as a knowledge source promotes authentic translation of domain knowledge and reduces the overall complexity of the implementation task. From this framework, we believe that a better understanding of activities involved in guideline implementation will emerge. PMID:15187061

Anti-Runaway Prevention System with Wireless Sensors for Intelligent Track Skates at Railway Stations.

PubMed

Jiang, Chaozhe; Xu, Yibo; Wen, Chao; Chen, Dilin

2017-12-19

Anti-runaway prevention of rolling stocks at a railway station is essential in railway safety management. The traditional track skates for anti-runaway prevention of rolling stocks have some disadvantages since they are operated and monitored completely manually. This paper describes an anti-runaway prevention system (ARPS) based on intelligent track skates equipped with sensors and real-time monitoring and management system. This system, which has been updated from the traditional track skates, comprises four parts: intelligent track skates, a signal reader, a database station, and a monitoring system. This system can monitor the real-time situation of track skates without changing their workflow for anti-runaway prevention, and thus realize the integration of anti-runaway prevention information management. This system was successfully tested and practiced at Sunjia station in Harbin Railway Bureau in 2014, and the results confirmed that the system showed 100% accuracy in reflecting the usage status of the track skates. The system could meet practical demands, as it is highly reliable and supports long-distance communication.

Anti-Runaway Prevention System with Wireless Sensors for Intelligent Track Skates at Railway Stations

PubMed Central

Jiang, Chaozhe; Xu, Yibo; Chen, Dilin

2017-01-01

Anti-runaway prevention of rolling stocks at a railway station is essential in railway safety management. The traditional track skates for anti-runaway prevention of rolling stocks have some disadvantages since they are operated and monitored completely manually. This paper describes an anti-runaway prevention system (ARPS) based on intelligent track skates equipped with sensors and real-time monitoring and management system. This system, which has been updated from the traditional track skates, comprises four parts: intelligent track skates, a signal reader, a database station, and a monitoring system. This system can monitor the real-time situation of track skates without changing their workflow for anti-runaway prevention, and thus realize the integration of anti-runaway prevention information management. This system was successfully tested and practiced at Sunjia station in Harbin Railway Bureau in 2014, and the results confirmed that the system showed 100% accuracy in reflecting the usage status of the track skates. The system could meet practical demands, as it is highly reliable and supports long-distance communication. PMID:29257108

[Multimodal document management in radiotherapy].

PubMed

Fahrner, H; Kirrmann, S; Röhner, F; Schmucker, M; Hall, M; Heinemann, F

2013-12-01

After incorporating treatment planning and the organisational model of treatment planning in the operating schedule system (BAS, "Betriebsablaufsystem"), complete document qualities were embedded in the digital environment. The aim of this project was to integrate all documents independent of their source (paper-bound or digital) and to make content from the BAS available in a structured manner. As many workflow steps as possible should be automated, e.g. assigning a document to a patient in the BAS. Additionally it must be guaranteed that at all times it could be traced who, when, how and from which source documents were imported into the departmental system. Furthermore work procedures should be changed that the documentation conducted either directly in the departmental system or from external systems can be incorporated digitally and paper document can be completely avoided (e.g. documents such as treatment certificate, treatment plans or documentation). It was a further aim, if possible, to automate the removal of paper documents from the departmental work flow, or even to make such paper documents superfluous. In this way patient letters for follow-up appointments should automatically generated from the BAS. Similarly patient record extracts in the form of PDF files should be enabled, e.g. for controlling purposes. The available document qualities were analysed in detail by a multidisciplinary working group (BAS-AG) and after this examination and assessment of the possibility of modelling in our departmental workflow (BAS) they were transcribed into a flow diagram. The gathered specifications were implemented in a test environment by the clinical and administrative IT group of the department of radiation oncology and subsequent to a detailed analysis introduced into clinical routine. The department has succeeded under the conditions of the aforementioned criteria to embed all relevant documents in the departmental workflow via continuous processes. Since the completion of the concepts and the implementation in our test environment 15,000 documents were introduced into the departmental workflow following routine approval. Furthermore approximately 5000 appointment letters for patient aftercare per year were automatically generated by the BAS. In addition patient record extracts in the form of PDF files for the medical services of the healthcare insurer can be generated.

Improving adherence to the Epic Beacon ambulatory workflow.

PubMed

Chackunkal, Ellen; Dhanapal Vogel, Vishnuprabha; Grycki, Meredith; Kostoff, Diana

2017-06-01

Computerized physician order entry has been shown to significantly improve chemotherapy safety by reducing the number of prescribing errors. Epic's Beacon Oncology Information System of computerized physician order entry and electronic medication administration was implemented in Henry Ford Health System's ambulatory oncology infusion centers on 9 November 2013. Since that time, compliance to the infusion workflow had not been assessed. The objective of this study was to optimize the current workflow and improve the compliance to this workflow in the ambulatory oncology setting. This study was a retrospective, quasi-experimental study which analyzed the composite workflow compliance rate of patient encounters from 9 to 23 November 2014. Based on this analysis, an intervention was identified and implemented in February 2015 to improve workflow compliance. The primary endpoint was to compare the composite compliance rate to the Beacon workflow before and after a pharmacy-initiated intervention. The intervention, which was education of infusion center staff, was initiated by ambulatory-based, oncology pharmacists and implemented by a multi-disciplinary team of pharmacists and nurses. The composite compliance rate was then reassessed for patient encounters from 2 to 13 March 2015 in order to analyze the effects of the determined intervention on compliance. The initial analysis in November 2014 revealed a composite compliance rate of 38%, and data analysis after the intervention revealed a statistically significant increase in the composite compliance rate to 83% ( p < 0.001). This study supports a pharmacist-initiated educational intervention can improve compliance to an ambulatory, oncology infusion workflow.

Guest editorial. Integrated healthcare information systems.

PubMed

Li, Ling; Ge, Ri-Li; Zhou, Shang-Ming; Valerdi, Ricardo

2012-07-01

The use of integrated information systems for healthcare has been started more than a decade ago. In recent years, rapid advances in information integration methods have spurred tremendous growth in the use of integrated information systems in healthcare delivery. Various techniques have been used for probing such integrated systems. These techniques include service-oriented architecture (SOA), EAI, workflow management, grid computing, and others. Many applications require a combination of these techniques, which gives rise to the emergence of enterprise systems in healthcare. Development of the techniques originated from different disciplines has the potential to significantly improve the performance of enterprise systems in healthcare. This editorial paper briefly introduces the enterprise systems in the perspective of healthcare informatics.

Health information systems.

PubMed

Hovenga, Evelyn J S; Grain, Heather

2013-01-01

Health information provides the foundation for all decision making in healthcare whether clinical at the bed side, or at a national government level. This information is generally collected as part of systems which support administrative or clinical workflow and practice. This chapter describes the many and varied features of systems such as electronic health records (EHRs), how they fit with health information systems and how they collectively manage information flow. Systems engineering methods and tools are described together with their use to suit the health industry. This focuses on the need for suitable system architectures and semantic interoperability. These concepts and their relevance to the health industry are explained. The relationship and requirements for appropriate data governance in these systems is also considered.

Scaling Critical Zone analysis tasks from desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study for project based learning of Cyberinfrastructure concepts

NASA Astrophysics Data System (ADS)

Swetnam, T. L.; Pelletier, J. D.; Merchant, N.; Callahan, N.; Lyons, E.

2015-12-01

Earth science is making rapid advances through effective utilization of large-scale data repositories such as aerial LiDAR and access to NSF-funded cyberinfrastructures (e.g. the OpenTopography.org data portal, iPlant Collaborative, and XSEDE). Scaling analysis tasks that are traditionally developed using desktops, laptops or computing clusters to effectively leverage national and regional scale cyberinfrastructure pose unique challenges and barriers to adoption. To address some of these challenges in Fall 2014 an 'Applied Cyberinfrastructure Concepts' a project-based learning course (ISTA 420/520) at the University of Arizona focused on developing scalable models of 'Effective Energy and Mass Transfer' (EEMT, MJ m-2 yr-1) for use by the NSF Critical Zone Observatories (CZO) project. EEMT is a quantitative measure of the flux of available energy to the critical zone, and its computation involves inputs that have broad applicability (e.g. solar insolation). The course comprised of 25 students with varying level of computational skills and with no prior domain background in the geosciences, collaborated with domain experts to develop the scalable workflow. The original workflow relying on open-source QGIS platform on a laptop was scaled to effectively utilize cloud environments (Openstack), UA Campus HPC systems, iRODS, and other XSEDE and OSG resources. The project utilizes public data, e.g. DEMs produced by OpenTopography.org and climate data from Daymet, which are processed using GDAL, GRASS and SAGA and the Makeflow and Work-queue task management software packages. Students were placed into collaborative groups to develop the separate aspects of the project. They were allowed to change teams, alter workflows, and design and develop novel code. The students were able to identify all necessary dependencies, recompile source onto the target execution platforms, and demonstrate a functional workflow, which was further improved upon by one of the group leaders over Spring 2015. All of the code, documentation and workflow description are currently available on GitHub and a public data portal is in development. We present a case study of how students reacted to the challenge of a real science problem, their interactions with end-users, what went right, and what could be done better in the future.

From the desktop to the grid: scalable bioinformatics via workflow conversion.

PubMed

de la Garza, Luis; Veit, Johannes; Szolek, Andras; Röttig, Marc; Aiche, Stephan; Gesing, Sandra; Reinert, Knut; Kohlbacher, Oliver

2016-03-12

Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization, among others. Workflows rest upon the notion of splitting complex work into the joint effort of several manageable tasks. There are several engines that give users the ability to design and execute workflows. Each engine was created to address certain problems of a specific community, therefore each one has its advantages and shortcomings. Furthermore, not all features of all workflow engines are royalty-free -an aspect that could potentially drive away members of the scientific community. We have developed a set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor documents. We have also overcome the shortcomings and combined the features of two royalty-free workflow engines with a substantial user community: the Konstanz Information Miner, an engine which we see as a formidable workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources. We have thus created a free and highly accessible way to design workflows on a desktop computer and execute them on high-performance computing resources. Our work will not only reduce time spent on designing scientific workflows, but also make executing workflows on remote high-performance computing resources more accessible to technically inexperienced users. We strongly believe that our efforts not only decrease the turnaround time to obtain scientific results but also have a positive impact on reproducibility, thus elevating the quality of obtained scientific results.

The Open Data Repositorys Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Downs, R. T.; Blake, D.; Bristow, T.; Fonda, M.; Pires, A.

2015-01-01

Data management and data publication are becoming increasingly important components of researcher's workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity.

The implementation of an integrated information system for substance use screening in general medical settings.

PubMed

Shanahan, C W; Sorensen-Alawad, A; Carney, B L; Persand, I; Cruz, A; Botticelli, M; Pressman, K; Adams, W G; Brolin, M; Alford, D P

2014-01-01

The Massachusetts Screening, Brief Intervention and Referral to Treatment (MASBIRT) Program, a substance use screening program in general medical settings, created a web-based, point-of-care (POC), application--the MASBIRT Portal (the "Portal") to meet program goals. We report on development and implementation of the Portal. Five year program process outcomes recorded by an independent evaluator and an anonymous survey of Health Educator's (HEs) adoption, perceptions and Portal use with a modified version of the Technology Readiness Index are described. [8] Specific management team members, selected based on their roles in program leadership, development and implementation of the Portal and supervision of HEs, participated in semi-structured, qualitative interviews. At the conclusion of the program 73% (24/33) of the HEs completed a survey on their experience using the Portal. HEs reported that the Portal made recording screening information easy (96%); improved planning their workday (83%); facilitated POC data collection (84%); decreased time dedicated to data entry (100%); and improved job satisfaction (59%). The top two barriers to use were "no or limited wireless connectivity" (46%) and "the tablet was too heavy/bulky to carry" (29%). Qualitative management team interviews identified strategies for successful HIT implementation: importance of engaging HEs in outlining specifications and workflow needs, collaborative testing prior to implementation and clear agreement on data collection purpose, quality requirements and staff roles. Overall, HEs perceived the Portal favorably with regard to time saving ability and improved workflow. Lessons learned included identifying core requirements early during system development and need for managers to institute and enforce consistent behavioral work norms. Barriers and HEs' views of technology impacted the utilization of the MASBIRT Portal. Further research is needed to determine best approaches for HIT system implementation in general medical settings.

An Architecture for Automated Fire Detection Early Warning System Based on Geoprocessing Service Composition

NASA Astrophysics Data System (ADS)

Samadzadegan, F.; Saber, M.; Zahmatkesh, H.; Joze Ghazi Khanlou, H.

2013-09-01

Rapidly discovering, sharing, integrating and applying geospatial information are key issues in the domain of emergency response and disaster management. Due to the distributed nature of data and processing resources in disaster management, utilizing a Service Oriented Architecture (SOA) to take advantages of workflow of services provides an efficient, flexible and reliable implementations to encounter different hazardous situation. The implementation specification of the Web Processing Service (WPS) has guided geospatial data processing in a Service Oriented Architecture (SOA) platform to become a widely accepted solution for processing remotely sensed data on the web. This paper presents an architecture design based on OGC web services for automated workflow for acquisition, processing remotely sensed data, detecting fire and sending notifications to the authorities. A basic architecture and its building blocks for an automated fire detection early warning system are represented using web-based processing of remote sensing imageries utilizing MODIS data. A composition of WPS processes is proposed as a WPS service to extract fire events from MODIS data. Subsequently, the paper highlights the role of WPS as a middleware interface in the domain of geospatial web service technology that can be used to invoke a large variety of geoprocessing operations and chaining of other web services as an engine of composition. The applicability of proposed architecture by a real world fire event detection and notification use case is evaluated. A GeoPortal client with open-source software was developed to manage data, metadata, processes, and authorities. Investigating feasibility and benefits of proposed framework shows that this framework can be used for wide area of geospatial applications specially disaster management and environmental monitoring.

SAHM:VisTrails (Software for Assisted Habitat Modeling for VisTrails): training course

USGS Publications Warehouse

Holcombe, Tracy

2014-01-01

VisTrails is an open-source management and scientific workflow system designed to integrate the best of both scientific workflow and scientific visualization systems. Developers can extend the functionality of the VisTrails system by creating custom modules for bundled VisTrails packages. The Invasive Species Science Branch of the U.S. Geological Survey (USGS) Fort Collins Science Center (FORT) and the U.S. Department of the Interior’s North Central Climate Science Center have teamed up to develop and implement such a module—the Software for Assisted Habitat Modeling (SAHM). SAHM expedites habitat modeling and helps maintain a record of the various input data, the steps before and after processing, and the modeling options incorporated in the construction of an ecological response model. There are four main advantages to using the SAHM:VisTrails combined package for species distribution modeling: (1) formalization and tractable recording of the entire modeling process; (2) easier collaboration through a common modeling framework; (3) a user-friendly graphical interface to manage file input, model runs, and output; and (4) extensibility to incorporate future and additional modeling routines and tools. In order to meet increased interest in the SAHM:VisTrails package, the FORT offers a training course twice a year. The course includes a combination of lecture, hands-on work, and discussion. Please join us and other ecological modelers to learn the capabilities of the SAHM:VisTrails package.

Architectures Toward Reusable Science Data Systems

NASA Astrophysics Data System (ADS)

Moses, J. F.

2014-12-01

Science Data Systems (SDS) comprise an important class of data processing systems that support product generation from remote sensors and in-situ observations. These systems enable research into new science data products, replication of experiments and verification of results. NASA has been building ground systems for satellite data processing since the first Earth observing satellites launched and is continuing development of systems to support NASA science research, NOAA's weather satellites and USGS's Earth observing satellite operations. The basic data processing workflows and scenarios continue to be valid for remote sensor observations research as well as for the complex multi-instrument operational satellite data systems being built today. System functions such as ingest, product generation and distribution need to be configured and performed in a consistent and repeatable way with an emphasis on scalability. This paper will examine the key architectural elements of several NASA satellite data processing systems currently in operation and under development that make them suitable for scaling and reuse. Examples of architectural elements that have become attractive include virtual machine environments, standard data product formats, metadata content and file naming, workflow and job management frameworks, data acquisition, search, and distribution protocols. By highlighting key elements and implementation experience the goal is to recognize architectures that will outlast their original application and be readily adaptable for new applications. Concepts and principles are explored that lead to sound guidance for SDS developers and strategists.

Architectures Toward Reusable Science Data Systems

NASA Technical Reports Server (NTRS)

Moses, John

2015-01-01

Science Data Systems (SDS) comprise an important class of data processing systems that support product generation from remote sensors and in-situ observations. These systems enable research into new science data products, replication of experiments and verification of results. NASA has been building systems for satellite data processing since the first Earth observing satellites launched and is continuing development of systems to support NASA science research and NOAAs Earth observing satellite operations. The basic data processing workflows and scenarios continue to be valid for remote sensor observations research as well as for the complex multi-instrument operational satellite data systems being built today. System functions such as ingest, product generation and distribution need to be configured and performed in a consistent and repeatable way with an emphasis on scalability. This paper will examine the key architectural elements of several NASA satellite data processing systems currently in operation and under development that make them suitable for scaling and reuse. Examples of architectural elements that have become attractive include virtual machine environments, standard data product formats, metadata content and file naming, workflow and job management frameworks, data acquisition, search, and distribution protocols. By highlighting key elements and implementation experience we expect to find architectures that will outlast their original application and be readily adaptable for new applications. Concepts and principles are explored that lead to sound guidance for SDS developers and strategists.

Computer imaging and workflow systems in the business office.

PubMed

Adams, W T; Veale, F H; Helmick, P M

1999-05-01

Computer imaging and workflow technology automates many business processes that currently are performed using paper processes. Documents are scanned into the imaging system and placed in electronic patient account folders. Authorized users throughout the organization, including preadmission, verification, admission, billing, cash posting, customer service, and financial counseling staff, have online access to the information they need when they need it. Such streamlining of business functions can increase collections and customer satisfaction while reducing labor, supply, and storage costs. Because the costs of a comprehensive computer imaging and workflow system can be considerable, healthcare organizations should consider implementing parts of such systems that can be cost-justified or include implementation as part of a larger strategic technology initiative.

Impact of digital radiography on clinical workflow.

PubMed

May, G A; Deer, D D; Dackiewicz, D

2000-05-01

It is commonly accepted that digital radiography (DR) improves workflow and patient throughput compared with traditional film radiography or computed radiography (CR). DR eliminates the film development step and the time to acquire the image from a CR reader. In addition, the wide dynamic range of DR is such that the technologist can perform the quality-control (QC) step directly at the modality in a few seconds, rather than having to transport the newly acquired image to a centralized QC station for review. Furthermore, additional workflow efficiencies can be achieved with DR by employing tight radiology information system (RIS) integration. In the DR imaging environment, this provides for patient demographic information to be automatically downloaded from the RIS to populate the DR Digital Imaging and Communications in Medicine (DICOM) image header. To learn more about this workflow efficiency improvement, we performed a comparative study of workflow steps under three different conditions: traditional film/screen x-ray, DR without RIS integration (ie, manual entry of patient demographics), and DR with RIS integration. This study was performed at the Cleveland Clinic Foundation (Cleveland, OH) using a newly acquired amorphous silicon flat-panel DR system from Canon Medical Systems (Irvine, CA). Our data show that DR without RIS results in substantial workflow savings over traditional film/screen practice. There is an additional 30% reduction in total examination time using DR with RIS integration.

A Portable Regional Weather and Climate Downscaling System Using GEOS-5, LIS-6, WRF, and the NASA Workflow Tool

NASA Astrophysics Data System (ADS)

Kemp, E. M.; Putman, W. M.; Gurganus, J.; Burns, R. W.; Damon, M. R.; McConaughy, G. R.; Seablom, M. S.; Wojcik, G. S.

2009-12-01

We present a regional downscaling system (RDS) suitable for high-resolution weather and climate simulations in multiple supercomputing environments. The RDS is built on the NASA Workflow Tool, a software framework for configuring, running, and managing computer models on multiple platforms with a graphical user interface. The Workflow Tool is used to run the NASA Goddard Earth Observing System Model Version 5 (GEOS-5), a global atmospheric-ocean model for weather and climate simulations down to 1/4 degree resolution; the NASA Land Information System Version 6 (LIS-6), a land surface modeling system that can simulate soil temperature and moisture profiles; and the Weather Research and Forecasting (WRF) community model, a limited-area atmospheric model for weather and climate simulations down to 1-km resolution. The Workflow Tool allows users to customize model settings to user needs; saves and organizes simulation experiments; distributes model runs across different computer clusters (e.g., the DISCOVER cluster at Goddard Space Flight Center, the Cray CX-1 Desktop Supercomputer, etc.); and handles all file transfers and network communications (e.g., scp connections). Together, the RDS is intended to aid researchers by making simulations as easy as possible to generate on the computer resources available. Initial conditions for LIS-6 and GEOS-5 are provided by Modern Era Retrospective-Analysis for Research and Applications (MERRA) reanalysis data stored on DISCOVER. The LIS-6 is first run for 2-4 years forced by MERRA atmospheric analyses, generating initial conditions for the WRF soil physics. GEOS-5 is then initialized from MERRA data and run for the period of interest. Large-scale atmospheric data, sea-surface temperatures, and sea ice coverage from GEOS-5 are used as boundary conditions for WRF, which is run for the same period of interest. Multiply nested grids are used for both LIS-6 and WRF, with the innermost grid run at a resolution sufficient for typical local weather features (terrain, convection, etc.) All model runs, restarts, and file transfers are coordinated by the Workflow Tool. Two use cases are being pursued. First, the RDS generates regional climate simulations down to 4-km for the Chesapeake Bay region, with WRF output provided as input to more specialized models (e.g., ocean/lake, hydrological, marine biology, and air pollution). This will allow assessment of climate impact on local interests (e.g., changes in Bay water levels and temperatures, innundation, fish kills, etc.) Second, the RDS generates high-resolution hurricane simulations in the tropical North Atlantic. This use case will support Observing System Simulation Experiments (OSSEs) of dynamically-targeted lidar observations as part of the NASA Sensor Web Simulator project. Sample results will be presented at the AGU Fall Meeting.

Inventory-based landscape-scale simulation of management effectiveness and economic feasibility with BioSum

Treesearch

Jeremy S. Fried; Larry D. Potts; Sara M. Loreno; Glenn A. Christensen; R. Jamie Barbour

2017-01-01

The Forest Inventory and Analysis (FIA)-based BioSum (Bioregional Inventory Originated Simulation Under Management) is a free policy analysis framework and workflow management software solution. It addresses complex management questions concerning forest health and vulnerability for large, multimillion acre, multiowner landscapes using FIA plot data as the initial...

A standard-enabled workflow for synthetic biology.

PubMed

Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

2017-06-15

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Supporting Community Pharmacies with Implementation of a Web-Based Medication Management Application.

PubMed

Turner, Kea; Renfro, Chelsea; Ferreri, Stefanie; Roberts, Kim; Pfeiffenberger, Trista; Shea, Christopher M

2018-04-01

 Community pharmacists' role in clinical care is expanding in the United States and information systems are needed that extend beyond a dispensing workflow. As pharmacies adopt new systems, implementation support will be needed. This study identifies the barriers and facilitators experienced by community pharmacies in implementing a Web-based medication management application and describes the implementation strategies used to support these pharmacies.  Semistructured interviews were conducted with 28 program and research staff that provides support to community pharmacies participating in a statewide pharmacy network. Interviews were recorded, transcribed verbatim, and analyzed for themes using the Expert Recommendations for Implementing Change (ERIC).  Findings suggest that leadership support, clinical training, and computer literacy facilitated implementation, while lack of system integration, staff resistance to change, and provider reluctance to share data served as barriers. To overcome the barriers, implementation support was provided, such as assessing readiness for implementation, developing a standardized and interoperable care plan, and audit and feedback of documentation quality.  Participants used a wide array of strategies to support community pharmacies with implementation and tailored approaches to accommodate pharmacy-specific preferences. Most of the support was delivered preimplementation or in the early phase of implementation and by program or research staff rather than peer-to-peer. Implementing new pharmacy information system requires a significant amount of implementation support to help end-users learn about program features, how to integrate the software into workflow, and how to optimize the software to improve patient care. Future research should identify which implementation strategies are associated with program performance. Schattauer.

SU-E-J-73: Extension of a Clinical OIS/EMR/R&V System to Deliver Safe and Efficient Adaptive Plan-Of-The-Day Treatments Using a Fully Customizable Plan-Library-Based Workflow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akhiat, A.; Elekta, Sunnyvale, CA; Kanis, A.P.

Purpose: To extend a clinical Record and Verify (R&V) system to enable a safe and fast workflow for Plan-of-the-Day (PotD) adaptive treatments based on patient-specific plan libraries. Methods: Plan libraries for PotD adaptive treatments contain for each patient several pre-treatment generated treatment plans. They may be generated for various patient anatomies or CTV-PTV margins. For each fraction, a Cone Beam CT scan is acquired to support the selection of the plan that best fits the patient’s anatomy-of-the-day. To date, there are no commercial R&V systems that support PotD delivery strategies. Consequently, the clinical workflow requires many manual interventions. Moreover, multiplemore » scheduled plans have a high risk of excessive dose delivery. In this work we extended a commercial R&V system (MOSAIQ) to support PotD workflows using IQ-scripting. The PotD workflow was designed after extensive risk analysis of the manual procedure, and all identified risks were incorporated as logical checks. Results: All manual PotD activities were automated. The workflow first identifies if the patient is scheduled for PotD, then performs safety checks, and continues to treatment plan selection only if no issues were found. The user selects the plan to deliver from a list of candidate plans. After plan selection, the workflow makes the treatment fields of the selected plan available for delivery by adding them to the treatment calendar. Finally, control is returned to the R&V system to commence treatment. Additional logic was added to incorporate off-line changes such as updating the plan library. After extensive testing including treatment fraction interrupts and plan-library updates during the treatment course, the workflow is running successfully in a clinical pilot, in which 35 patients have been treated since October 2014. Conclusion: We have extended a commercial R&V system for improved safety and efficiency in library-based adaptive strategies enabling a wide-spread implementation of those strategies. This work was in part funded by a research grant of Elekta AB, Stockholm, Sweden.« less

Approach to implementing a DICOM network: incorporate both economics and workflow adaptation

NASA Astrophysics Data System (ADS)

Beaver, S. Merritt; Sippel-Schmidt, Teresa M.

1995-05-01

This paper describes an approach to aide in the decision-making process for the justification and design of a digital image and information management system. It identifies key technical and clinical issues that need to be addressed by a healthcare institution during this process. Some issues identified here are very controversial and may take months or years for a department to determine solutions which meet their specific staffing, financial, and technical needs.

Resilient workflows for computational mechanics platforms

NASA Astrophysics Data System (ADS)

Nguyên, Toàn; Trifan, Laurentiu; Désidéri, Jean-Antoine

2010-06-01

Workflow management systems have recently been the focus of much interest and many research and deployment for scientific applications worldwide [26, 27]. Their ability to abstract the applications by wrapping application codes have also stressed the usefulness of such systems for multidiscipline applications [23, 24]. When complex applications need to provide seamless interfaces hiding the technicalities of the computing infrastructures, their high-level modeling, monitoring and execution functionalities help giving production teams seamless and effective facilities [25, 31, 33]. Software integration infrastructures based on programming paradigms such as Python, Mathlab and Scilab have also provided evidence of the usefulness of such approaches for the tight coupling of multidisciplne application codes [22, 24]. Also high-performance computing based on multi-core multi-cluster infrastructures open new opportunities for more accurate, more extensive and effective robust multi-discipline simulations for the decades to come [28]. This supports the goal of full flight dynamics simulation for 3D aircraft models within the next decade, opening the way to virtual flight-tests and certification of aircraft in the future [23, 24, 29].

Designing the safety of healthcare. Participation of ergonomics to the design of cooperative systems in radiotherapy.

PubMed

Munoz, Maria Isabel; Bouldi, Nadia; Barcellini, Flore; Nascimento, Adelaide

2012-01-01

This communication deals with the involvement of ergonomists in a research-action design process of a software platform in radiotherapy. The goal of the design project is to enhance patient safety by designing a workflow software that supports cooperation between professionals producing treatment in radiotherapy. The general framework of our approach is the ergonomics management of a design process, which is based in activity analysis and grounded in participatory design. Two fields are concerned by the present action: a design environment which is a participatory design process that involves software designers, caregivers as future users and ergonomists; and a reference real work setting in radiotherapy. Observations, semi-structured interviews and participatory workshops allow the characterization of activity in radiotherapy dealing with uses of cooperative tools, sources of variability and non-ruled strategies to manage the variability of the situations. This production of knowledge about work searches to enhance the articulation between technocentric and anthropocentric approaches, and helps in clarifying design requirements. An issue of this research-action is to develop a framework to define the parameters of the workflow tool, and the conditions of its deployment.

Use of mechanistic simulations as a quantitative risk-ranking tool within the quality by design framework.

PubMed

Stocker, Elena; Toschkoff, Gregor; Sacher, Stephan; Khinast, Johannes G

2014-11-20

The purpose of this study is to evaluate the use of computer simulations for generating quantitative knowledge as a basis for risk ranking and mechanistic process understanding, as required by ICH Q9 on quality risk management systems. In this specific publication, the main focus is the demonstration of a risk assessment workflow, including a computer simulation for the generation of mechanistic understanding of active tablet coating in a pan coater. Process parameter screening studies are statistically planned under consideration of impacts on a potentially critical quality attribute, i.e., coating mass uniformity. Based on computer simulation data the process failure mode and effects analysis of the risk factors is performed. This results in a quantitative criticality assessment of process parameters and the risk priority evaluation of failure modes. The factor for a quantitative reassessment of the criticality and risk priority is the coefficient of variation, which represents the coating mass uniformity. The major conclusion drawn from this work is a successful demonstration of the integration of computer simulation in the risk management workflow leading to an objective and quantitative risk assessment. Copyright © 2014. Published by Elsevier B.V.

Design and implementation of an automated compound management system in support of lead optimization.

PubMed

Quintero, Catherine; Kariv, Ilona

2009-06-01

To meet the needs of the increasingly rapid and parallelized lead optimization process, a fully integrated local compound storage and liquid handling system was designed and implemented to automate the generation of assay-ready plates directly from newly submitted and cherry-picked compounds. A key feature of the system is the ability to create project- or assay-specific compound-handling methods, which provide flexibility for any combination of plate types, layouts, and plate bar-codes. Project-specific workflows can be created by linking methods for processing new and cherry-picked compounds and control additions to produce a complete compound set for both biological testing and local storage in one uninterrupted workflow. A flexible cherry-pick approach allows for multiple, user-defined strategies to select the most appropriate replicate of a compound for retesting. Examples of custom selection parameters include available volume, compound batch, and number of freeze/thaw cycles. This adaptable and integrated combination of software and hardware provides a basis for reducing cycle time, fully automating compound processing, and ultimately increasing the rate at which accurate, biologically relevant results can be produced for compounds of interest in the lead optimization process.

Digital pathology: DICOM-conform draft, testbed, and first results.

PubMed

Zwönitzer, Ralf; Kalinski, Thomas; Hofmann, Harald; Roessner, Albert; Bernarding, Johannes

2007-09-01

Hospital information systems are state of the art nowadays. Therefore, Digital Pathology, also labelled as Virtual Microscopy, has gained increased attention. Triggered by radiology, standardized information models and workflows were world-wide defined based on DICOM. However, DICOM-conform integration of Digital Pathology into existing clinical information systems imposes new problems requiring specific solutions concerning the huge amount of data as well as the special structure of the data to be managed, transferred, and stored. We implemented a testbed to realize and evaluate the workflow of digitized slides from acquisition to archiving. The experiences led to the draft of a DICOM-conform information model that accounted for extensions, definitions, and technical requirements necessary to integrate digital pathology in a hospital-wide DICOM environment. Slides were digitized, compressed, and could be viewed remotely. Real-time transfer of the huge amount of data was optimized using streaming techniques. Compared to a recent discussion in the DICOM Working Group for Digital Pathology (WG26) our experiences led to a preference of a JPEG2000/JPIP-based streaming of the whole slide image. The results showed that digital pathology is feasible but strong efforts by users and vendors are still necessary to integrate Digital Pathology into existing information systems.