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.

Visualization and Analysis for Near-Real-Time Decision Making in Distributed Workflows

DOE PAGES

Pugmire, David; Kress, James; Choi, Jong; ...

2016-08-04

Data driven science is becoming increasingly more common, complex, and is placing tremendous stresses on visualization and analysis frameworks. Data sources producing 10GB per second (and more) are becoming increasingly commonplace in both simulation, sensor and experimental sciences. These data sources, which are often distributed around the world, must be analyzed by teams of scientists that are also distributed. Enabling scientists to view, query and interact with such large volumes of data in near-real-time requires a rich fusion of visualization and analysis techniques, middleware and workflow systems. Here, this paper discusses initial research into visualization and analysis of distributed datamore » workflows that enables scientists to make near-real-time decisions of large volumes of time varying data.« less

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.

Yadage and Packtivity - analysis preservation using parametrized workflows

NASA Astrophysics Data System (ADS)

Cranmer, Kyle; Heinrich, Lukas

2017-10-01

Preserving data analyses produced by the collaborations at LHC in a parametrized fashion is crucial in order to maintain reproducibility and re-usability. We argue for a declarative description in terms of individual processing steps - “packtivities” - linked through a dynamic directed acyclic graph (DAG) and present an initial set of JSON schemas for such a description and an implementation - “yadage” - capable of executing workflows of analysis preserved via Linux containers.

Agile parallel bioinformatics workflow management using Pwrake.

PubMed

Mishima, Hiroyuki; Sasaki, Kensaku; Tanaka, Masahiro; Tatebe, Osamu; Yoshiura, Koh-Ichiro

2011-09-08

In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles

Agile parallel bioinformatics workflow management using Pwrake

PubMed Central

2011-01-01

Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

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

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

Facilitating hydrological data analysis workflows in R: the RHydro package

NASA Astrophysics Data System (ADS)

Buytaert, Wouter; Moulds, Simon; Skoien, Jon; Pebesma, Edzer; Reusser, Dominik

2015-04-01

The advent of new technologies such as web-services and big data analytics holds great promise for hydrological data analysis and simulation. Driven by the need for better water management tools, it allows for the construction of much more complex workflows, that integrate more and potentially more heterogeneous data sources with longer tool chains of algorithms and models. With the scientific challenge of designing the most adequate processing workflow comes the technical challenge of implementing the workflow with a minimal risk for errors. A wide variety of new workbench technologies and other data handling systems are being developed. At the same time, the functionality of available data processing languages such as R and Python is increasing at an accelerating pace. Because of the large diversity of scientific questions and simulation needs in hydrology, it is unlikely that one single optimal method for constructing hydrological data analysis workflows will emerge. Nevertheless, languages such as R and Python are quickly gaining popularity because they combine a wide array of functionality with high flexibility and versatility. The object-oriented nature of high-level data processing languages makes them particularly suited for the handling of complex and potentially large datasets. In this paper, we explore how handling and processing of hydrological data in R can be facilitated further by designing and implementing a set of relevant classes and methods in the experimental R package RHydro. We build upon existing efforts such as the sp and raster packages for spatial data and the spacetime package for spatiotemporal data to define classes for hydrological data (HydroST). In order to handle simulation data from hydrological models conveniently, a HM class is defined. Relevant methods are implemented to allow for an optimal integration of the HM class with existing model fitting and simulation functionality in R. Lastly, we discuss some of the design challenges

A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology.

PubMed

Mirel, Barbara; Eichinger, Felix; Keller, Benjamin J; Kretzler, Matthias

2011-03-21

Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses. Tools need to accommodate the workflows that scientists actually perform for specific translational research questions. To understand and model one of these workflows, we conducted a case-based, cognitive task analysis of a biomedical specialist’s exploratory workflow for the question: What functional interactions among gene products of high throughput expression data suggest previously unknown mechanisms of a disease? From our cognitive task analysis four complementary representations of the targeted workflow were developed. They include: usage scenarios, flow diagrams, a cognitive task taxonomy, and a mapping between cognitive tasks and user-centered visualization requirements. The representations capture the flows of cognitive tasks that led a biomedical specialist to inferences critical to hypothesizing. We created representations at levels of detail that could strategically guide visualization development, and we confirmed this by making a trial prototype based on user requirements for a small portion of the workflow. Our results imply that visualizations should make available to scientific users “bundles of features” consonant with the compositional cognitive tasks purposefully enacted at specific points in the workflow. We also highlight certain aspects of visualizations that: (a) need more built-in flexibility; (b) are critical for negotiating meaning; and (c) are necessary for essential metacognitive support.

Next-Generation Climate Modeling Science Challenges for Simulation, Workflow and Analysis Systems

NASA Astrophysics Data System (ADS)

Koch, D. M.; Anantharaj, V. G.; Bader, D. C.; Krishnan, H.; Leung, L. R.; Ringler, T.; Taylor, M.; Wehner, M. F.; Williams, D. N.

2016-12-01

We will present two examples of current and future high-resolution climate-modeling research that are challenging existing simulation run-time I/O, model-data movement, storage and publishing, and analysis. In each case, we will consider lessons learned as current workflow systems are broken by these large-data science challenges, as well as strategies to repair or rebuild the systems. First we consider the science and workflow challenges to be posed by the CMIP6 multi-model HighResMIP, involving around a dozen modeling groups performing quarter-degree simulations, in 3-member ensembles for 100 years, with high-frequency (1-6 hourly) diagnostics, which is expected to generate over 4PB of data. An example of science derived from these experiments will be to study how resolution affects the ability of models to capture extreme-events such as hurricanes or atmospheric rivers. Expected methods to transfer (using parallel Globus) and analyze (using parallel "TECA" software tools) HighResMIP data for such feature-tracking by the DOE CASCADE project will be presented. A second example will be from the Accelerated Climate Modeling for Energy (ACME) project, which is currently addressing challenges involving multiple century-scale coupled high resolution (quarter-degree) climate simulations on DOE Leadership Class computers. ACME is anticipating production of over 5PB of data during the next 2 years of simulations, in order to investigate the drivers of water cycle changes, sea-level-rise, and carbon cycle evolution. The ACME workflow, from simulation to data transfer, storage, analysis and publication will be presented. Current and planned methods to accelerate the workflow, including implementing run-time diagnostics, and implementing server-side analysis to avoid moving large datasets will be presented.

BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

PubMed

Turewicz, Michael; Kohl, Michael; Ahrens, Maike; Mayer, Gerhard; Uszkoreit, Julian; Naboulsi, Wael; Bracht, Thilo; Megger, Dominik A; Sitek, Barbara; Marcus, Katrin; Eisenacher, Martin

2017-11-10

The analysis of high-throughput mass spectrometry-based proteomics data must address the specific challenges of this technology. To this end, the comprehensive proteomics workflow offered by the de.NBI service center BioInfra.Prot provides indispensable components for the computational and statistical analysis of this kind of data. These components include tools and methods for spectrum identification and protein inference, protein quantification, expression analysis as well as data standardization and data publication. All particular methods of the workflow which address these tasks are state-of-the-art or cutting edge. As has been shown in previous publications, each of these methods is adequate to solve its specific task and gives competitive results. However, the methods included in the workflow are continuously reviewed, updated and improved to adapt to new scientific developments. All of these particular components and methods are available as stand-alone BioInfra.Prot services or as a complete workflow. Since BioInfra.Prot provides manifold fast communication channels to get access to all components of the workflow (e.g., via the BioInfra.Prot ticket system: bioinfraprot@rub.de) users can easily benefit from this service and get support by experts. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

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

Focus: a robust workflow for one-dimensional NMR spectral analysis.

PubMed

Alonso, Arnald; Rodríguez, Miguel A; Vinaixa, Maria; Tortosa, Raül; Correig, Xavier; Julià, Antonio; Marsal, Sara

2014-01-21

One-dimensional (1)H NMR represents one of the most commonly used analytical techniques in metabolomic studies. The increase in the number of samples analyzed as well as the technical improvements involving instrumentation and spectral acquisition demand increasingly accurate and efficient high-throughput data processing workflows. We present FOCUS, an integrated and innovative methodology that provides a complete data analysis workflow for one-dimensional NMR-based metabolomics. This tool will allow users to easily obtain a NMR peak feature matrix ready for chemometric analysis as well as metabolite identification scores for each peak that greatly simplify the biological interpretation of the results. The algorithm development has been focused on solving the critical difficulties that appear at each data processing step and that can dramatically affect the quality of the results. As well as method integration, simplicity has been one of the main objectives in FOCUS development, requiring very little user input to perform accurate peak alignment, peak picking, and metabolite identification. The new spectral alignment algorithm, RUNAS, allows peak alignment with no need of a reference spectrum, and therefore, it reduces the bias introduced by other alignment approaches. Spectral alignment has been tested against previous methodologies obtaining substantial improvements in the case of moderate or highly unaligned spectra. Metabolite identification has also been significantly improved, using the positional and correlation peak patterns in contrast to a reference metabolite panel. Furthermore, the complete workflow has been tested using NMR data sets from 60 human urine samples and 120 aqueous liver extracts, reaching a successful identification of 42 metabolites from the two data sets. The open-source software implementation of this methodology is available at http://www.urr.cat/FOCUS.

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.

The equivalency between logic Petri workflow nets and workflow nets.

PubMed

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented.

The Equivalency between Logic Petri Workflow Nets and Workflow Nets

PubMed Central

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented. PMID:25821845

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

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

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.

Structuring Clinical Workflows for Diabetes Care

PubMed Central

Lasierra, N.; Oberbichler, S.; Toma, I.; Fensel, A.; Hoerbst, A.

2014-01-01

Summary Background Electronic health records (EHRs) play an important role in the treatment of chronic diseases such as diabetes mellitus. Although the interoperability and selected functionality of EHRs are already addressed by a number of standards and best practices, such as IHE or HL7, the majority of these systems are still monolithic from a user-functionality perspective. The purpose of the OntoHealth project is to foster a functionally flexible, standards-based use of EHRs to support clinical routine task execution by means of workflow patterns and to shift the present EHR usage to a more comprehensive integration concerning complete clinical workflows. Objectives The goal of this paper is, first, to introduce the basic architecture of the proposed OntoHealth project and, second, to present selected functional needs and a functional categorization regarding workflow-based interactions with EHRs in the domain of diabetes. Methods A systematic literature review regarding attributes of workflows in the domain of diabetes was conducted. Eligible references were gathered and analyzed using a qualitative content analysis. Subsequently, a functional workflow categorization was derived from diabetes-specific raw data together with existing general workflow patterns. Results This paper presents the design of the architecture as well as a categorization model which makes it possible to describe the components or building blocks within clinical workflows. The results of our study lead us to identify basic building blocks, named as actions, decisions, and data elements, which allow the composition of clinical workflows within five identified contexts. Conclusions The categorization model allows for a description of the components or building blocks of clinical workflows from a functional view. PMID:25024765

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

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

Radiology Workflow Dynamics: How Workflow Patterns Impact Radiologist Perceptions of Workplace Satisfaction.

PubMed

Lee, Matthew H; Schemmel, Andrew J; Pooler, B Dustin; Hanley, Taylor; Kennedy, Tabassum; Field, Aaron; Wiegmann, Douglas; Yu, John-Paul J

2017-04-01

The study aimed to assess perceptions of reading room workflow and the impact separating image-interpretive and nonimage-interpretive task workflows can have on radiologist perceptions of workplace disruptions, workload, and overall satisfaction. A 14-question survey instrument was developed to measure radiologist perceptions of workplace interruptions, satisfaction, and workload prior to and following implementation of separate image-interpretive and nonimage-interpretive reading room workflows. The results were collected over 2 weeks preceding the intervention and 2 weeks following the end of the intervention. The results were anonymized and analyzed using univariate analysis. A total of 18 people responded to the preintervention survey: 6 neuroradiology fellows and 12 attending neuroradiologists. Fifteen people who were then present for the 1-month intervention period responded to the postintervention survey. Perceptions of workplace disruptions, image interpretation, quality of trainee education, ability to perform nonimage-interpretive tasks, and quality of consultations (P < 0.0001) all improved following the intervention. Mental effort and workload also improved across all assessment domains, as did satisfaction with quality of image interpretation and consultative work. Implementation of parallel dedicated image-interpretive and nonimage-interpretive workflows may improve markers of radiologist perceptions of workplace satisfaction. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

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

Integrated workflows for spiking neuronal network simulations

PubMed Central

Antolík, Ján; Davison, Andrew P.

2013-01-01

The increasing availability of computational resources is enabling more detailed, realistic modeling in computational neuroscience, resulting in a shift toward more heterogeneous models of neuronal circuits, and employment of complex experimental protocols. This poses a challenge for existing tool chains, as the set of tools involved in a typical modeler's workflow is expanding concomitantly, with growing complexity in the metadata flowing between them. For many parts of the workflow, a range of tools is available; however, numerous areas lack dedicated tools, while integration of existing tools is limited. This forces modelers to either handle the workflow manually, leading to errors, or to write substantial amounts of code to automate parts of the workflow, in both cases reducing their productivity. To address these issues, we have developed Mozaik: a workflow system for spiking neuronal network simulations written in Python. Mozaik integrates model, experiment and stimulation specification, simulation execution, data storage, data analysis and visualization into a single automated workflow, ensuring that all relevant metadata are available to all workflow components. It is based on several existing tools, including PyNN, Neo, and Matplotlib. It offers a declarative way to specify models and recording configurations using hierarchically organized configuration files. Mozaik automatically records all data together with all relevant metadata about the experimental context, allowing automation of the analysis and visualization stages. Mozaik has a modular architecture, and the existing modules are designed to be extensible with minimal programming effort. Mozaik increases the productivity of running virtual experiments on highly structured neuronal networks by automating the entire experimental cycle, while increasing the reliability of modeling studies by relieving the user from manual handling of the flow of metadata between the individual workflow stages. PMID

Integrated workflows for spiking neuronal network simulations.

PubMed

Antolík, Ján; Davison, Andrew P

2013-01-01

The increasing availability of computational resources is enabling more detailed, realistic modeling in computational neuroscience, resulting in a shift toward more heterogeneous models of neuronal circuits, and employment of complex experimental protocols. This poses a challenge for existing tool chains, as the set of tools involved in a typical modeler's workflow is expanding concomitantly, with growing complexity in the metadata flowing between them. For many parts of the workflow, a range of tools is available; however, numerous areas lack dedicated tools, while integration of existing tools is limited. This forces modelers to either handle the workflow manually, leading to errors, or to write substantial amounts of code to automate parts of the workflow, in both cases reducing their productivity. To address these issues, we have developed Mozaik: a workflow system for spiking neuronal network simulations written in Python. Mozaik integrates model, experiment and stimulation specification, simulation execution, data storage, data analysis and visualization into a single automated workflow, ensuring that all relevant metadata are available to all workflow components. It is based on several existing tools, including PyNN, Neo, and Matplotlib. It offers a declarative way to specify models and recording configurations using hierarchically organized configuration files. Mozaik automatically records all data together with all relevant metadata about the experimental context, allowing automation of the analysis and visualization stages. Mozaik has a modular architecture, and the existing modules are designed to be extensible with minimal programming effort. Mozaik increases the productivity of running virtual experiments on highly structured neuronal networks by automating the entire experimental cycle, while increasing the reliability of modeling studies by relieving the user from manual handling of the flow of metadata between the individual workflow stages.

RNA-Seq workflow: gene-level exploratory analysis and differential expression

PubMed Central

Love, Michael I.; Anders, Simon; Kim, Vladislav; Huber, Wolfgang

2015-01-01

Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results. PMID:26674615

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

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

PubMed

Cock, Peter J A; Grüning, Björn A; Paszkiewicz, Konrad; Pritchard, Leighton

2013-01-01

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).

An integrated workflow for analysis of ChIP-chip data.

PubMed

Weigelt, Karin; Moehle, Christoph; Stempfl, Thomas; Weber, Bernhard; Langmann, Thomas

2008-08-01

Although ChIP-chip is a powerful tool for genome-wide discovery of transcription factor target genes, the steps involving raw data analysis, identification of promoters, and correlation with binding sites are still laborious processes. Therefore, we report an integrated workflow for the analysis of promoter tiling arrays with the Genomatix ChipInspector system. We compare this tool with open-source software packages to identify PU.1 regulated genes in mouse macrophages. Our results suggest that ChipInspector data analysis, comparative genomics for binding site prediction, and pathway/network modeling significantly facilitate and enhance whole-genome promoter profiling to reveal in vivo sites of transcription factor-DNA interactions.

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.

Metagenomics workflow analysis of endophytic bacteria from oil palm fruits

NASA Astrophysics Data System (ADS)

Tanjung, Z. A.; Aditama, R.; Sudania, W. M.; Utomo, C.; Liwang, T.

2017-05-01

Next-Generation Sequencing (NGS) has become a powerful sequencing tool for microbial study especially to lead the establishment of the field area of metagenomics. This study described a workflow to analyze metagenomics data of a Sequence Read Archive (SRA) file under accession ERP004286 deposited by University of Sao Paulo. It was a direct sequencing data generated by 454 pyrosequencing platform originated from oil palm fruits endophytic bacteria which were cultured using oil-palm enriched medium. This workflow used SortMeRNA to split ribosomal reads sequence, Newbler (GS Assembler and GS Mapper) to assemble and map reads into genome reference, BLAST package to identify and annotate contigs sequence, and QualiMap for statistical analysis. Eight bacterial species were identified in this study. Enterobacter cloacae was the most abundant species followed by Citrobacter koseri, Seratia marcescens, Latococcus lactis subsp. lactis, Klebsiella pneumoniae, Citrobacter amalonaticus, Achromobacter xylosoxidans, and Pseudomonas sp. respectively. All of these species have been reported as endophyte bacteria in various plant species and each has potential as plant growth promoting bacteria or another application in agricultural industries.

Bioinformatics workflows and web services in systems biology made easy for experimentalists.

PubMed

Jimenez, Rafael C; Corpas, Manuel

2013-01-01

Workflows are useful to perform data analysis and integration in systems biology. Workflow management systems can help users create workflows without any previous knowledge in programming and web services. However the computational skills required to build such workflows are usually above the level most biological experimentalists are comfortable with. In this chapter we introduce workflow management systems that reuse existing workflows instead of creating them, making it easier for experimentalists to perform computational tasks.

Workflow management systems in radiology

NASA Astrophysics Data System (ADS)

Wendler, Thomas; Meetz, Kirsten; Schmidt, Joachim

1998-07-01

In a situation of shrinking health care budgets, increasing cost pressure and growing demands to increase the efficiency and the quality of medical services, health care enterprises are forced to optimize or complete re-design their processes. Although information technology is agreed to potentially contribute to cost reduction and efficiency improvement, the real success factors are the re-definition and automation of processes: Business Process Re-engineering and Workflow Management. In this paper we discuss architectures for the use of workflow management systems in radiology. We propose to move forward from information systems in radiology (RIS, PACS) to Radiology Management Systems, in which workflow functionality (process definitions and process automation) is implemented through autonomous workflow management systems (WfMS). In a workflow oriented architecture, an autonomous workflow enactment service communicates with workflow client applications via standardized interfaces. In this paper, we discuss the need for and the benefits of such an approach. The separation of workflow management system and application systems is emphasized, and the consequences that arise for the architecture of workflow oriented information systems. This includes an appropriate workflow terminology, and the definition of standard interfaces for workflow aware application systems. Workflow studies in various institutions have shown that most of the processes in radiology are well structured and suited for a workflow management approach. Numerous commercially available Workflow Management Systems (WfMS) were investigated, and some of them, which are process- oriented and application independent, appear suitable for use in radiology.

Integrative analysis workflow for the structural and functional classification of C-type lectins

PubMed Central

2011-01-01

Background It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles. Results Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner. Conclusions The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments. PMID:22372988

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

PubMed Central

Grüning, Björn A.; Paszkiewicz, Konrad; Pritchard, Leighton

2013-01-01

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu). PMID:24109552

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

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

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow.

PubMed

Suryawanshi, Gajendra W; Xu, Song; Xie, Yiming; Chou, Tom; Kim, Namshin; Chen, Irvin S Y; Kim, Sanggu

2017-06-14

Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities. This work provides a detailed protocol and data analysis workflow for bidirectional IS analysis. The bidirectional assay can simultaneously sequence both upstream and downstream vector-host junctions. Compared to conventional unidirectional IS sequencing approaches, the bidirectional approach significantly improves IS detection rates and the characterization of integration events at both ends of the target DNA. The data analysis pipeline described here accurately identifies and enumerates identical IS sequences through multiple steps of comparison that map IS sequences onto the reference genome and determine sequencing errors. Using an optimized assay procedure, we have recently published the detailed repopulation patterns of thousands of Hematopoietic Stem Cell (HSC) clones following transplant in rhesus macaques, demonstrating for the first time the precise time point of HSC repopulation and the functional heterogeneity of HSCs in the primate system. The following protocol describes the step-by-step experimental procedure and data analysis workflow that accurately identifies and quantifies identical IS sequences.

Comparison of peak-picking workflows for untargeted liquid chromatography/high-resolution mass spectrometry metabolomics data analysis.

PubMed

Rafiei, Atefeh; Sleno, Lekha

2015-01-15

Data analysis is a key step in mass spectrometry based untargeted metabolomics, starting with the generation of generic peak lists from raw liquid chromatography/mass spectrometry (LC/MS) data. Due to the use of various algorithms by different workflows, the results of different peak-picking strategies often differ widely. Raw LC/HRMS data from two types of biological samples (bile and urine), as well as a standard mixture of 84 metabolites, were processed with four peak-picking softwares: Peakview®, Markerview™, MetabolitePilot™ and XCMS Online. The overlaps between the results of each peak-generating method were then investigated. To gauge the relevance of peak lists, a database search using the METLIN online database was performed to determine which features had accurate masses matching known metabolites as well as a secondary filtering based on MS/MS spectral matching. In this study, only a small proportion of all peaks (less than 10%) were common to all four software programs. Comparison of database searching results showed peaks found uniquely by one workflow have less chance of being found in the METLIN metabolomics database and are even less likely to be confirmed by MS/MS. It was shown that the performance of peak-generating workflows has a direct impact on untargeted metabolomics results. As it was demonstrated that the peaks found in more than one peak detection workflow have higher potential to be identified by accurate mass as well as MS/MS spectrum matching, it is suggested to use the overlap of different peak-picking workflows as preliminary peak lists for more rugged statistical analysis in global metabolomics investigations. Copyright © 2014 John Wiley & Sons, Ltd.

Integrative workflows for metagenomic analysis

PubMed Central

Ladoukakis, Efthymios; Kolisis, Fragiskos N.; Chatziioannou, Aristotelis A.

2014-01-01

The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS), have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e., Sanger). From a bioinformatic perspective, this boils down to many GB of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control, and annotation of metagenomic data, embracing various, major sequencing technologies and applications. PMID:25478562

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.

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

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.

Standardizing clinical trials workflow representation in UML for international site comparison.

PubMed

de Carvalho, Elias Cesar Araujo; Jayanti, Madhav Kishore; Batilana, Adelia Portero; Kozan, Andreia M O; Rodrigues, Maria J; Shah, Jatin; Loures, Marco R; Patil, Sunita; Payne, Philip; Pietrobon, Ricardo

2010-11-09

With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative analysis of international clinical trials

Standardizing Clinical Trials Workflow Representation in UML for International Site Comparison

PubMed Central

de Carvalho, Elias Cesar Araujo; Jayanti, Madhav Kishore; Batilana, Adelia Portero; Kozan, Andreia M. O.; Rodrigues, Maria J.; Shah, Jatin; Loures, Marco R.; Patil, Sunita; Payne, Philip; Pietrobon, Ricardo

2010-01-01

Background With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. Methods Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. Results Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. Conclusions This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative

An Integrated Framework for Parameter-based Optimization of Scientific Workflows.

PubMed

Kumar, Vijay S; Sadayappan, P; Mehta, Gaurang; Vahi, Karan; Deelman, Ewa; Ratnakar, Varun; Kim, Jihie; Gil, Yolanda; Hall, Mary; Kurc, Tahsin; Saltz, Joel

2009-01-01

Data analysis processes in scientific applications can be expressed as coarse-grain workflows of complex data processing operations with data flow dependencies between them. Performance optimization of these workflows can be viewed as a search for a set of optimal values in a multi-dimensional parameter space. While some performance parameters such as grouping of workflow components and their mapping to machines do not a ect the accuracy of the output, others may dictate trading the output quality of individual components (and of the whole workflow) for performance. This paper describes an integrated framework which is capable of supporting performance optimizations along multiple dimensions of the parameter space. Using two real-world applications in the spatial data analysis domain, we present an experimental evaluation of the proposed framework.

Flexible workflow sharing and execution services for e-scientists

NASA Astrophysics Data System (ADS)

Kacsuk, Péter; Terstyanszky, Gábor; Kiss, Tamas; Sipos, Gergely

2013-04-01

The sequence of computational and data manipulation steps required to perform a specific scientific analysis is called a workflow. Workflows that orchestrate data and/or compute intensive applications on Distributed Computing Infrastructures (DCIs) recently became standard tools in e-science. At the same time the broad and fragmented landscape of workflows and DCIs slows down the uptake of workflow-based work. The development, sharing, integration and execution of workflows is still a challenge for many scientists. The FP7 "Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs" (SHIWA) project significantly improved the situation, with a simulation platform that connects different workflow systems, different workflow languages, different DCIs and workflows into a single, interoperable unit. The SHIWA Simulation Platform is a service package, already used by various scientific communities, and used as a tool by the recently started ER-flow FP7 project to expand the use of workflows among European scientists. The presentation will introduce the SHIWA Simulation Platform and the services that ER-flow provides based on the platform to space and earth science researchers. The SHIWA Simulation Platform includes: 1. SHIWA Repository: A database where workflows and meta-data about workflows can be stored. The database is a central repository to discover and share workflows within and among communities . 2. SHIWA Portal: A web portal that is integrated with the SHIWA Repository and includes a workflow executor engine that can orchestrate various types of workflows on various grid and cloud platforms. 3. SHIWA Desktop: A desktop environment that provides similar access capabilities than the SHIWA Portal, however it runs on the users' desktops/laptops instead of a portal server. 4. Workflow engines: the ASKALON, Galaxy, GWES, Kepler, LONI Pipeline, MOTEUR, Pegasus, P-GRADE, ProActive, Triana, Taverna and WS-PGRADE workflow engines are already

Laboratory Workflow Analysis of Culture of Periprosthetic Tissues in Blood Culture Bottles.

PubMed

Peel, Trisha N; Sedarski, John A; Dylla, Brenda L; Shannon, Samantha K; Amirahmadi, Fazlollaah; Hughes, John G; Cheng, Allen C; Patel, Robin

2017-09-01

Culture of periprosthetic tissue specimens in blood culture bottles is more sensitive than conventional techniques, but the impact on laboratory workflow has yet to be addressed. Herein, we examined the impact of culture of periprosthetic tissues in blood culture bottles on laboratory workflow and cost. The workflow was process mapped, decision tree models were constructed using probabilities of positive and negative cultures drawn from our published study (T. N. Peel, B. L. Dylla, J. G. Hughes, D. T. Lynch, K. E. Greenwood-Quaintance, A. C. Cheng, J. N. Mandrekar, and R. Patel, mBio 7:e01776-15, 2016, https://doi.org/10.1128/mBio.01776-15), and the processing times and resource costs from the laboratory staff time viewpoint were used to compare periprosthetic tissues culture processes using conventional techniques with culture in blood culture bottles. Sensitivity analysis was performed using various rates of positive cultures. Annualized labor savings were estimated based on salary costs from the U.S. Labor Bureau for Laboratory staff. The model demonstrated a 60.1% reduction in mean total staff time with the adoption of tissue inoculation into blood culture bottles compared to conventional techniques (mean ± standard deviation, 30.7 ± 27.6 versus 77.0 ± 35.3 h per month, respectively; P < 0.001). The estimated annualized labor cost savings of culture using blood culture bottles was $10,876.83 (±$337.16). Sensitivity analysis was performed using various rates of culture positivity (5 to 50%). Culture in blood culture bottles was cost-effective, based on the estimated labor cost savings of $2,132.71 for each percent increase in test accuracy. In conclusion, culture of periprosthetic tissue in blood culture bottles is not only more accurate than but is also cost-saving compared to conventional culture methods. Copyright © 2017 American Society for Microbiology.

Progress in digital color workflow understanding in the International Color Consortium (ICC) Workflow WG

NASA Astrophysics Data System (ADS)

McCarthy, Ann

2006-01-01

The ICC Workflow WG serves as the bridge between ICC color management technologies and use of those technologies in real world color production applications. ICC color management is applicable to and is used in a wide range of color systems, from highly specialized digital cinema color special effects to high volume publications printing to home photography. The ICC Workflow WG works to align ICC technologies so that the color management needs of these diverse use case systems are addressed in an open, platform independent manner. This report provides a high level summary of the ICC Workflow WG objectives and work to date, focusing on the ways in which workflow can impact image quality and color systems performance. The 'ICC Workflow Primitives' and 'ICC Workflow Patterns and Dimensions' workflow models are covered in some detail. Consider the questions, "How much of dissatisfaction with color management today is the result of 'the wrong color transformation at the wrong time' and 'I can't get to the right conversion at the right point in my work process'?" Put another way, consider how image quality through a workflow can be negatively affected when the coordination and control level of the color management system is not sufficient.

Time-Efficiency Analysis Comparing Digital and Conventional Workflows for Implant Crowns: A Prospective Clinical Crossover Trial.

PubMed

Joda, Tim; Brägger, Urs

2015-01-01

To compare time-efficiency in the production of implant crowns using a digital workflow versus the conventional pathway. This prospective clinical study used a crossover design that included 20 study participants receiving single-tooth replacements in posterior sites. Each patient received a customized titanium abutment plus a computer-aided design/computer-assisted manufacture (CAD/CAM) zirconia suprastructure (for those in the test group, using digital workflow) and a standardized titanium abutment plus a porcelain-fused-to-metal crown (for those in the control group, using a conventional pathway). The start of the implant prosthetic treatment was established as the baseline. Time-efficiency analysis was defined as the primary outcome, and was measured for every single clinical and laboratory work step in minutes. Statistical analysis was calculated with the Wilcoxon rank sum test. All crowns could be provided within two clinical appointments, independent of the manufacturing process. The mean total production time, as the sum of clinical plus laboratory work steps, was significantly different. The mean ± standard deviation (SD) time was 185.4 ± 17.9 minutes for the digital workflow process and 223.0 ± 26.2 minutes for the conventional pathway (P = .0001). Therefore, digital processing for overall treatment was 16% faster. Detailed analysis for the clinical treatment revealed a significantly reduced mean ± SD chair time of 27.3 ± 3.4 minutes for the test group compared with 33.2 ± 4.9 minutes for the control group (P = .0001). Similar results were found for the mean laboratory work time, with a significant decrease of 158.1 ± 17.2 minutes for the test group vs 189.8 ± 25.3 minutes for the control group (P = .0001). Only a few studies have investigated efficiency parameters of digital workflows compared with conventional pathways in implant dental medicine. This investigation shows that the digital workflow seems to be more time-efficient than the

Disruption of Radiologist Workflow.

PubMed

Kansagra, Akash P; Liu, Kevin; Yu, John-Paul J

2016-01-01

The effect of disruptions has been studied extensively in surgery and emergency medicine, and a number of solutions-such as preoperative checklists-have been implemented to enforce the integrity of critical safety-related workflows. Disruptions of the highly complex and cognitively demanding workflow of modern clinical radiology have only recently attracted attention as a potential safety hazard. In this article, we describe the variety of disruptions that arise in the reading room environment, review approaches that other specialties have taken to mitigate workflow disruption, and suggest possible solutions for workflow improvement in radiology. Copyright © 2015 Mosby, Inc. All rights reserved.

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.

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 Community-Driven Workflow Recommendations and Reuse Infrastructure

NASA Astrophysics Data System (ADS)

Zhang, J.; Votava, P.; Lee, T. J.; Lee, C.; Xiao, S.; Nemani, R. R.; Foster, I.

2013-12-01

Aiming to connect the Earth science community to accelerate the rate of discovery, NASA Earth Exchange (NEX) has established an online repository and platform, so that researchers can publish and share their tools and models with colleagues. In recent years, workflow has become a popular technique at NEX for Earth scientists to define executable multi-step procedures for data processing and analysis. The ability to discover and reuse knowledge (sharable workflows or workflow) is critical to the future advancement of science. However, as reported in our earlier study, the reusability of scientific artifacts at current time is very low. Scientists often do not feel confident in using other researchers' tools and utilities. One major reason is that researchers are often unaware of the existence of others' data preprocessing processes. Meanwhile, researchers often do not have time to fully document the processes and expose them to others in a standard way. These issues cannot be overcome by the existing workflow search technologies used in NEX and other data projects. Therefore, this project aims to develop a proactive recommendation technology based on collective NEX user behaviors. In this way, we aim to promote and encourage process and workflow reuse within NEX. Particularly, we focus on leveraging peer scientists' best practices to support the recommendation of artifacts developed by others. Our underlying theoretical foundation is rooted in the social cognitive theory, which declares people learn by watching what others do. Our fundamental hypothesis is that sharable artifacts have network properties, much like humans in social networks. More generally, reusable artifacts form various types of social relationships (ties), and may be viewed as forming what organizational sociologists who use network analysis to study human interactions call a 'knowledge network.' In particular, we will tackle two research questions: R1: What hidden knowledge may be extracted from

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.

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

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

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

End-to-end workflow for finite element analysis of tumor treating fields in glioblastomas

NASA Astrophysics Data System (ADS)

Timmons, Joshua J.; Lok, Edwin; San, Pyay; Bui, Kevin; Wong, Eric T.

2017-11-01

Tumor Treating Fields (TTFields) therapy is an approved modality of treatment for glioblastoma. Patient anatomy-based finite element analysis (FEA) has the potential to reveal not only how these fields affect tumor control but also how to improve efficacy. While the automated tools for segmentation speed up the generation of FEA models, multi-step manual corrections are required, including removal of disconnected voxels, incorporation of unsegmented structures and the addition of 36 electrodes plus gel layers matching the TTFields transducers. Existing approaches are also not scalable for the high throughput analysis of large patient volumes. A semi-automated workflow was developed to prepare FEA models for TTFields mapping in the human brain. Magnetic resonance imaging (MRI) pre-processing, segmentation, electrode and gel placement, and post-processing were all automated. The material properties of each tissue were applied to their corresponding mask in silico using COMSOL Multiphysics (COMSOL, Burlington, MA, USA). The fidelity of the segmentations with and without post-processing was compared against the full semi-automated segmentation workflow approach using Dice coefficient analysis. The average relative differences for the electric fields generated by COMSOL were calculated in addition to observed differences in electric field-volume histograms. Furthermore, the mesh file formats in MPHTXT and NASTRAN were also compared using the differences in the electric field-volume histogram. The Dice coefficient was less for auto-segmentation without versus auto-segmentation with post-processing, indicating convergence on a manually corrected model. An existent but marginal relative difference of electric field maps from models with manual correction versus those without was identified, and a clear advantage of using the NASTRAN mesh file format was found. The software and workflow outlined in this article may be used to accelerate the investigation of TTFields in

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.

Quantitative workflow based on NN for weighting criteria in landfill suitability mapping

NASA Astrophysics Data System (ADS)

Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Alkhasawneh, Mutasem Sh.; Aziz, Hamidi Abdul

2017-10-01

Our study aims to introduce a new quantitative workflow that integrates neural networks (NNs) and multi criteria decision analysis (MCDA). Existing MCDA workflows reveal a number of drawbacks, because of the reliance on human knowledge in the weighting stage. Thus, new workflow presented to form suitability maps at the regional scale for solid waste planning based on NNs. A feed-forward neural network employed in the workflow. A total of 34 criteria were pre-processed to establish the input dataset for NN modelling. The final learned network used to acquire the weights of the criteria. Accuracies of 95.2% and 93.2% achieved for the training dataset and testing dataset, respectively. The workflow was found to be capable of reducing human interference to generate highly reliable maps. The proposed workflow reveals the applicability of NN in generating landfill suitability maps and the feasibility of integrating them with existing MCDA workflows.

Classical workflow nets and workflow nets with reset arcs: using Lyapunov stability for soundness verification

NASA Astrophysics Data System (ADS)

Clempner, Julio B.

2017-01-01

This paper presents a novel analytical method for soundness verification of workflow nets and reset workflow nets, using the well-known stability results of Lyapunov for Petri nets. We also prove that the soundness property is decidable for workflow nets and reset workflow nets. In addition, we provide evidence of several outcomes related with properties such as boundedness, liveness, reversibility and blocking using stability. Our approach is validated theoretically and by a numerical example related to traffic signal-control synchronisation.

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

Safety and feasibility of STAT RAD: Improvement of a novel rapid tomotherapy-based radiation therapy workflow by failure mode and effects analysis.

PubMed

Jones, Ryan T; Handsfield, Lydia; Read, Paul W; Wilson, David D; Van Ausdal, Ray; Schlesinger, David J; Siebers, Jeffrey V; Chen, Quan

2015-01-01

The clinical challenge of radiation therapy (RT) for painful bone metastases requires clinicians to consider both treatment efficacy and patient prognosis when selecting a radiation therapy regimen. The traditional RT workflow requires several weeks for common palliative RT schedules of 30 Gy in 10 fractions or 20 Gy in 5 fractions. At our institution, we have created a new RT workflow termed "STAT RAD" that allows clinicians to perform computed tomographic (CT) simulation, planning, and highly conformal single fraction treatment delivery within 2 hours. In this study, we evaluate the safety and feasibility of the STAT RAD workflow. A failure mode and effects analysis (FMEA) was performed on the STAT RAD workflow, including development of a process map, identification of potential failure modes, description of the cause and effect, temporal occurrence, and team member involvement in each failure mode, and examination of existing safety controls. A risk probability number (RPN) was calculated for each failure mode. As necessary, workflow adjustments were then made to safeguard failure modes of significant RPN values. After workflow alterations, RPN numbers were again recomputed. A total of 72 potential failure modes were identified in the pre-FMEA STAT RAD workflow, of which 22 met the RPN threshold for clinical significance. Workflow adjustments included the addition of a team member checklist, changing simulation from megavoltage CT to kilovoltage CT, alteration of patient-specific quality assurance testing, and allocating increased time for critical workflow steps. After these modifications, only 1 failure mode maintained RPN significance; patient motion after alignment or during treatment. Performing the FMEA for the STAT RAD workflow before clinical implementation has significantly strengthened the safety and feasibility of STAT RAD. The FMEA proved a valuable evaluation tool, identifying potential problem areas so that we could create a safer workflow

A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

EPA Science Inventory

Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may levera...

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A.; Caron, Christophe

2015-01-01

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org PMID:25527831

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes

PubMed Central

Feliubadaló, Lídia; Lopez-Doriga, Adriana; Castellsagué, Ester; del Valle, Jesús; Menéndez, Mireia; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Gómez, Carolina; Campos, Olga; Pineda, Marta; González, Sara; Moreno, Victor; Brunet, Joan; Blanco, Ignacio; Serra, Eduard; Capellá, Gabriel; Lázaro, Conxi

2013-01-01

Next-generation sequencing (NGS) is changing genetic diagnosis due to its huge sequencing capacity and cost-effectiveness. The aim of this study was to develop an NGS-based workflow for routine diagnostics for hereditary breast and ovarian cancer syndrome (HBOCS), to improve genetic testing for BRCA1 and BRCA2. A NGS-based workflow was designed using BRCA MASTR kit amplicon libraries followed by GS Junior pyrosequencing. Data analysis combined Variant Identification Pipeline freely available software and ad hoc R scripts, including a cascade of filters to generate coverage and variant calling reports. A BRCA homopolymer assay was performed in parallel. A research scheme was designed in two parts. A Training Set of 28 DNA samples containing 23 unique pathogenic mutations and 213 other variants (33 unique) was used. The workflow was validated in a set of 14 samples from HBOCS families in parallel with the current diagnostic workflow (Validation Set). The NGS-based workflow developed permitted the identification of all pathogenic mutations and genetic variants, including those located in or close to homopolymers. The use of NGS for detecting copy-number alterations was also investigated. The workflow meets the sensitivity and specificity requirements for the genetic diagnosis of HBOCS and improves on the cost-effectiveness of current approaches. PMID:23249957

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

PubMed Central

Verdi, Kacy K; Ellis, Heidi JC; Gryk, Michael R

2007-01-01

Background Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. Results We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Conclusion Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using

Conceptual-level workflow modeling of scientific experiments using NMR as a case study.

PubMed

Verdi, Kacy K; Ellis, Heidi Jc; Gryk, Michael R

2007-01-30

Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment.

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.

Potential of knowledge discovery using workflows implemented in the C3Grid

NASA Astrophysics Data System (ADS)

Engel, Thomas; Fink, Andreas; Ulbrich, Uwe; Schartner, Thomas; Dobler, Andreas; Fritzsch, Bernadette; Hiller, Wolfgang; Bräuer, Benny

2013-04-01

With the increasing number of climate simulations, reanalyses and observations, new infrastructures to search and analyse distributed data are necessary. In recent years, the Grid architecture became an important technology to fulfill these demands. For the German project "Collaborative Climate Community Data and Processing Grid" (C3Grid) computer scientists and meteorologists developed a system that offers its users a webinterface to search and download climate data and use implemented analysis tools (called workflows) to further investigate them. In this contribution, two workflows that are implemented in the C3Grid architecture are presented: the Cyclone Tracking (CT) and Stormtrack workflow. They shall serve as an example on how to perform numerous investigations on midlatitude winterstorms on a large amount of analysis and climate model data without having an insight into the data source, program code and a low-to-moderate understanding of the theortical background. CT is based on the work of Murray and Simmonds (1991) to identify and track local minima in the mean sea level pressure (MSLP) field of the selected dataset. Adjustable thresholds for the curvature of the isobars as well as the minimum lifetime of a cyclone allow the distinction of weak subtropical heat low systems and stronger midlatitude cyclones e.g. in the Northern Atlantic. The user gets the resulting track data including statistics about the track density, average central pressure, average central curvature, cyclogenesis and cyclolysis as well as pre-built visualizations of these results. Stormtrack calculates the 2.5-6 day bandpassfiltered standard deviation of the geopotential height on a selected pressure level. Although this workflow needs much less computational effort compared to CT it shows structures that are in good agreement with the track density of the CT workflow. To what extent changes in the mid-level tropospheric storm track are reflected in trough density and intensity

Planning bioinformatics workflows using an expert system

PubMed Central

Chen, Xiaoling; Chang, Jeffrey T.

2017-01-01

Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

Taverna: a tool for building and running workflows of services

PubMed Central

Hull, Duncan; Wolstencroft, Katy; Stevens, Robert; Goble, Carole; Pocock, Mathew R.; Li, Peter; Oinn, Tom

2006-01-01

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from . PMID:16845108

Use of a Hands Free, Instantaneous, Closed-Loop Communication Device Improves Perception of Communication and Workflow Integration in an Academic Teaching Hospital: A Pilot Study.

PubMed

Fang, Daniel Z; Patil, Teja; Belitskaya-Levy, Ilana; Yeung, Marianne; Posley, Keith; Allaudeen, Nazima

2017-11-17

Efficient and effective communication between providers is critical to quality patient care within a hospital system. Hands free communication devices (HFCD) allow instantaneous, closed-loop communication between physicians and other members of a multidisciplinary team, providing a communication advantage over traditional pager systems. HFCD have been shown to decrease emergency room interruptions, improve nursing communication, improve speed of information flow, and eliminate health care waste. We evaluated the integration of an HFCD with an existing alphanumeric paging system on an acute inpatient medicine service. We conducted a prospective, observational, survey-based study over twenty-four weeks in an academic tertiary care center with attending physicians and residents. Our intervention involved the implementation of an HFCD alongside the existing paging system. Fifty-six pre and post surveys evaluated the perception of improvement in communication and the integration of the HFCD into existing workflow. We saw significant improvements in the ability of an HFCD to help physicians communicate thoughts clearly, communicate thoughts effectively, reach team members, reach ancillary staff, and stay informed about patients. Physicians also reported better workflow integration during admissions, rounds, discharge, and teaching sessions. Qualitative data from post surveys demonstrated that the greatest strengths of the HFCD included the ability to reach colleagues and staff quickly, provide instant access to individuals of the care team, and improve overall communication. Integration of an instantaneous, hands free, closed loop communication system alongside the existing pager system can provide improvements in the perceptions of communication and workflow integration in an academic medicine service. Future studies are needed to correlate these subjective findings with objective measures of quality and safety.

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

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

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.

PubMed

Cornwell, MacIntosh; Vangala, Mahesh; Taing, Len; Herbert, Zachary; Köster, Johannes; Li, Bo; Sun, Hanfei; Li, Taiwen; Zhang, Jian; Qiu, Xintao; Pun, Matthew; Jeselsohn, Rinath; Brown, Myles; Liu, X Shirley; Long, Henry W

2018-04-12

RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.

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.

Multivariate Analysis of High Through-Put Adhesively Bonded Single Lap Joints: Experimental and Workflow Protocols

DTIC Science & Technology

2016-06-01

unlimited. v List of Tables Table 1 Single-lap-joint experimental parameters ..............................................7 Table 2 Survey ...Joints: Experimental and Workflow Protocols by Robert E Jensen, Daniel C DeSchepper, and David P Flanagan Approved for...TR-7696 ● JUNE 2016 US Army Research Laboratory Multivariate Analysis of High Through-Put Adhesively Bonded Single Lap Joints: Experimental

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A; Caron, Christophe

2015-05-01

The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). contact@workflow4metabolomics.org. © The Author 2014. Published by Oxford University Press.

Financial and workflow analysis of radiology reporting processes in the planning phase of implementation of a speech recognition system

NASA Astrophysics Data System (ADS)

Whang, Tom; Ratib, Osman M.; Umamoto, Kathleen; Grant, Edward G.; McCoy, Michael J.

2002-05-01

The goal of this study is to determine the financial value and workflow improvements achievable by replacing traditional transcription services with a speech recognition system in a large, university hospital setting. Workflow metrics were measured at two hospitals, one of which exclusively uses a transcription service (UCLA Medical Center), and the other which exclusively uses speech recognition (West Los Angeles VA Hospital). Workflow metrics include time spent per report (the sum of time spent interpreting, dictating, reviewing, and editing), transcription turnaround, and total report turnaround. Compared to traditional transcription, speech recognition resulted in radiologists spending 13-32% more time per report, but it also resulted in reduction of report turnaround time by 22-62% and reduction of marginal cost per report by 94%. The model developed here helps justify the introduction of a speech recognition system by showing that the benefits of reduced operating costs and decreased turnaround time outweigh the cost of increased time spent per report. Whether the ultimate goal is to achieve a financial objective or to improve operational efficiency, it is important to conduct a thorough analysis of workflow before implementation.

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

PubMed Central

Torri, Federica; Dinov, Ivo D.; Zamanyan, Alen; Hobel, Sam; Genco, Alex; Petrosyan, Petros; Clark, Andrew P.; Liu, Zhizhong; Eggert, Paul; Pierce, Jonathan; Knowles, James A.; Ames, Joseph; Kesselman, Carl; Toga, Arthur W.; Potkin, Steven G.; Vawter, Marquis P.; Macciardi, Fabio

2012-01-01

Whole-genome and exome sequencing have already proven to be essential and powerful methods to identify genes responsible for simple Mendelian inherited disorders. These methods can be applied to complex disorders as well, and have been adopted as one of the current mainstream approaches in population genetics. These achievements have been made possible by next generation sequencing (NGS) technologies, which require substantial bioinformatics resources to analyze the dense and complex sequence data. The huge analytical burden of data from genome sequencing might be seen as a bottleneck slowing the publication of NGS papers at this time, especially in psychiatric genetics. We review the existing methods for processing NGS data, to place into context the rationale for the design of a computational resource. We describe our method, the Graphical Pipeline for Computational Genomics (GPCG), to perform the computational steps required to analyze NGS data. The GPCG implements flexible workflows for basic sequence alignment, sequence data quality control, single nucleotide polymorphism analysis, copy number variant identification, annotation, and visualization of results. These workflows cover all the analytical steps required for NGS data, from processing the raw reads to variant calling and annotation. The current version of the pipeline is freely available at http://pipeline.loni.ucla.edu. These applications of NGS analysis may gain clinical utility in the near future (e.g., identifying miRNA signatures in diseases) when the bioinformatics approach is made feasible. Taken together, the annotation tools and strategies that have been developed to retrieve information and test hypotheses about the functional role of variants present in the human genome will help to pinpoint the genetic risk factors for psychiatric disorders. PMID:23139896

Planning bioinformatics workflows using an expert system.

PubMed

Chen, Xiaoling; Chang, Jeffrey T

2017-04-15

Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. https://github.com/jefftc/changlab. jeffrey.t.chang@uth.tmc.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Generic worklist handler for workflow-enabled products

NASA Astrophysics Data System (ADS)

Schmidt, Joachim; Meetz, Kirsten; Wendler, Thomas

1999-07-01

Workflow management (WfM) is an emerging field of medical information technology. It appears as a promising key technology to model, optimize and automate processes, for the sake of improved efficiency, reduced costs and improved patient care. The Application of WfM concepts requires the standardization of architectures and interfaces. A component of central interest proposed in this report is a generic work list handler: A standardized interface between a workflow enactment service and application system. Application systems with embedded work list handlers will be called 'Workflow Enabled Application Systems'. In this paper we discus functional requirements of work list handlers, as well as their integration into workflow architectures and interfaces. To lay the foundation for this specification, basic workflow terminology, the fundamentals of workflow management and - later in the paper - the available standards as defined by the Workflow Management Coalition are briefly reviewed.

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

Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies.

PubMed

Surinova, Silvia; Hüttenhain, Ruth; Chang, Ching-Yun; Espona, Lucia; Vitek, Olga; Aebersold, Ruedi

2013-08-01

Targeted proteomics based on selected reaction monitoring (SRM) mass spectrometry is commonly used for accurate and reproducible quantification of protein analytes in complex biological mixtures. Strictly hypothesis-driven, SRM assays quantify each targeted protein by collecting measurements on its peptide fragment ions, called transitions. To achieve sensitive and accurate quantitative results, experimental design and data analysis must consistently account for the variability of the quantified transitions. This consistency is especially important in large experiments, which increasingly require profiling up to hundreds of proteins over hundreds of samples. Here we describe a robust and automated workflow for the analysis of large quantitative SRM data sets that integrates data processing, statistical protein identification and quantification, and dissemination of the results. The integrated workflow combines three software tools: mProphet for peptide identification via probabilistic scoring; SRMstats for protein significance analysis with linear mixed-effect models; and PASSEL, a public repository for storage, retrieval and query of SRM data. The input requirements for the protocol are files with SRM traces in mzXML format, and a file with a list of transitions in a text tab-separated format. The protocol is especially suited for data with heavy isotope-labeled peptide internal standards. We demonstrate the protocol on a clinical data set in which the abundances of 35 biomarker candidates were profiled in 83 blood plasma samples of subjects with ovarian cancer or benign ovarian tumors. The time frame to realize the protocol is 1-2 weeks, depending on the number of replicates used in the experiment.

Matches, Mismatches, and Methods: Multiple-View Workflows for Energy Portfolio Analysis.

PubMed

Brehmer, Matthew; Ng, Jocelyn; Tate, Kevin; Munzner, Tamara

2016-01-01

The energy performance of large building portfolios is challenging to analyze and monitor, as current analysis tools are not scalable or they present derived and aggregated data at too coarse of a level. We conducted a visualization design study, beginning with a thorough work domain analysis and a characterization of data and task abstractions. We describe generalizable visual encoding design choices for time-oriented data framed in terms of matches and mismatches, as well as considerations for workflow design. Our designs address several research questions pertaining to scalability, view coordination, and the inappropriateness of line charts for derived and aggregated data due to a combination of data semantics and domain convention. We also present guidelines relating to familiarity and trust, as well as methodological considerations for visualization design studies. Our designs were adopted by our collaborators and incorporated into the design of an energy analysis software application that will be deployed to tens of thousands of energy workers in their client base.

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

Radiology information system: a workflow-based approach.

PubMed

Zhang, Jinyan; Lu, Xudong; Nie, Hongchao; Huang, Zhengxing; van der Aalst, W M P

2009-09-01

Introducing workflow management technology in healthcare seems to be prospective in dealing with the problem that the current healthcare Information Systems cannot provide sufficient support for the process management, although several challenges still exist. The purpose of this paper is to study the method of developing workflow-based information system in radiology department as a use case. First, a workflow model of typical radiology process was established. Second, based on the model, the system could be designed and implemented as a group of loosely coupled components. Each component corresponded to one task in the process and could be assembled by the workflow management system. The legacy systems could be taken as special components, which also corresponded to the tasks and were integrated through transferring non-work- flow-aware interfaces to the standard ones. Finally, a workflow dashboard was designed and implemented to provide an integral view of radiology processes. The workflow-based Radiology Information System was deployed in the radiology department of Zhejiang Chinese Medicine Hospital in China. The results showed that it could be adjusted flexibly in response to the needs of changing process, and enhance the process management in the department. It can also provide a more workflow-aware integration method, comparing with other methods such as IHE-based ones. The workflow-based approach is a new method of developing radiology information system with more flexibility, more functionalities of process management and more workflow-aware integration. The work of this paper is an initial endeavor for introducing workflow management technology in healthcare.

Text mining for the biocuration workflow.

PubMed

Hirschman, Lynette; Burns, Gully A P C; Krallinger, Martin; Arighi, Cecilia; Cohen, K Bretonnel; Valencia, Alfonso; Wu, Cathy H; Chatr-Aryamontri, Andrew; Dowell, Karen G; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G

2012-01-01

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on 'Text Mining for the BioCuration Workflow' at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.

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.

[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.

Developing a Workflow Composite Score to Measure Clinical Information Logistics. A Top-down Approach.

PubMed

Liebe, J D; Hübner, U; Straede, M C; Thye, J

2015-01-01

Availability and usage of individual IT applications have been studied intensively in the past years. Recently, IT support of clinical processes is attaining increasing attention. The underlying construct that describes the IT support of clinical workflows is clinical information logistics. This construct needs to be better understood, operationalised and measured. It is therefore the aim of this study to propose and develop a workflow composite score (WCS) for measuring clinical information logistics and to examine its quality based on reliability and validity analyses. We largely followed the procedural model of MacKenzie and colleagues (2011) for defining and conceptualising the construct domain, for developing the measurement instrument, assessing the content validity, pretesting the instrument, specifying the model, capturing the data and computing the WCS and testing the reliability and validity. Clinical information logistics was decomposed into the descriptors data and information, function, integration and distribution, which embraced the framework validated by an analysis of the international literature. This framework was refined selecting representative clinical processes. We chose ward rounds, pre- and post-surgery processes and discharge as sample processes that served as concrete instances for the measurements. They are sufficiently complex, represent core clinical processes and involve different professions, departments and settings. The score was computed on the basis of data from 183 hospitals of different size, ownership, location and teaching status. Testing the reliability and validity yielded encouraging results: the reliability was high with r(split-half) = 0.89, the WCS discriminated between groups; the WCS correlated significantly and moderately with two EHR models and the WCS received good evaluation results by a sample of chief information officers (n = 67). These findings suggest the further utilisation of the WCS. As the WCS does not

Exploring Dental Providers’ Workflow in an Electronic Dental Record Environment

PubMed Central

Schwei, Kelsey M; Cooper, Ryan; Mahnke, Andrea N.; Ye, Zhan

2016-01-01

Summary Background A workflow is defined as a predefined set of work steps and partial ordering of these steps in any environment to achieve the expected outcome. Few studies have investigated the workflow of providers in a dental office. It is important to understand the interaction of dental providers with the existing technologies at point of care to assess breakdown in the workflow which could contribute to better technology designs. Objective The study objective was to assess electronic dental record (EDR) workflows using time and motion methodology in order to identify breakdowns and opportunities for process improvement. Methods A time and motion methodology was used to study the human-computer interaction and workflow of dental providers with an EDR in four dental centers at a large healthcare organization. A data collection tool was developed to capture the workflow of dental providers and staff while they interacted with an EDR during initial, planned, and emergency patient visits, and at the front desk. Qualitative and quantitative analysis was conducted on the observational data. Results Breakdowns in workflow were identified while posting charges, viewing radiographs, e-prescribing, and interacting with patient scheduler. EDR interaction time was significantly different between dentists and dental assistants (6:20 min vs. 10:57 min, p = 0.013) and between dentists and dental hygienists (6:20 min vs. 9:36 min, p = 0.003). Conclusions On average, a dentist spent far less time than dental assistants and dental hygienists in data recording within the EDR. PMID:27437058

chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery.

PubMed

Lee, Man-Ling; Aliagas, Ignacio; Feng, Jianwen A; Gabriel, Thomas; O'Donnell, T J; Sellers, Benjamin D; Wiswedel, Bernd; Gobbi, Alberto

2017-06-12

Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemalot is a set of command line programs with a wide range of functionalities for cheminformatics. The chemalot_knime package allows command line programs that read and write SD files from stdin and to stdout to be wrapped into KNIME nodes. The combination of chemalot and chemalot_knime not only facilitates the compilation and maintenance of sequences of command line programs but also allows KNIME workflows to take advantage of the compute power of a LINUX cluster. Use of the command line programs is demonstrated in three different workflow examples: (1) A workflow to create a data file with project-relevant data for structure-activity or property analysis and other type of investigations, (2) The creation of a quantitative structure-property-relationship model using the command line programs via KNIME nodes, and (3) The analysis of strain energy in small molecule ligand conformations from the Protein Data Bank database. The chemalot and chemalot_knime packages provide lightweight and powerful tools for many tasks in cheminformatics. They are easily integrated with other open source and commercial command line tools and can be combined to build new and even more powerful tools. The chemalot_knime package facilitates the generation and maintenance of user-defined command line workflows, taking advantage of the graphical design capabilities in KNIME. Graphical abstract Example KNIME workflow with chemalot nodes and the corresponding command line pipe.

Nationwide Buildings Energy Research enabled through an integrated Data Intensive Scientific Workflow and Advanced Analysis Environment

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

Kleese van Dam, Kerstin; Lansing, Carina S.; Elsethagen, Todd O.

2014-01-28

Modern workflow systems enable scientists to run ensemble simulations at unprecedented scales and levels of complexity, allowing them to study system sizes previously impossible to achieve, due to the inherent resource requirements needed for the modeling work. However as a result of these new capabilities the science teams suddenly also face unprecedented data volumes that they are unable to analyze with their existing tools and methodologies in a timely fashion. In this paper we will describe the ongoing development work to create an integrated data intensive scientific workflow and analysis environment that offers researchers the ability to easily create andmore » execute complex simulation studies and provides them with different scalable methods to analyze the resulting data volumes. The integration of simulation and analysis environments is hereby not only a question of ease of use, but supports fundamental functions in the correlated analysis of simulation input, execution details and derived results for multi-variant, complex studies. To this end the team extended and integrated the existing capabilities of the Velo data management and analysis infrastructure, the MeDICi data intensive workflow system and RHIPE the R for Hadoop version of the well-known statistics package, as well as developing a new visual analytics interface for the result exploitation by multi-domain users. The capabilities of the new environment are demonstrated on a use case that focusses on the Pacific Northwest National Laboratory (PNNL) building energy team, showing how they were able to take their previously local scale simulations to a nationwide level by utilizing data intensive computing techniques not only for their modeling work, but also for the subsequent analysis of their modeling results. As part of the PNNL research initiative PRIMA (Platform for Regional Integrated Modeling and Analysis) the team performed an initial 3 year study of building energy demands for the US

Integrating Behavioral Health in Primary Care Using Lean Workflow Analysis: A Case Study.

PubMed

van Eeghen, Constance; Littenberg, Benjamin; Holman, Melissa D; Kessler, Rodger

2016-01-01

Primary care offices are integrating behavioral health (BH) clinicians into their practices. Implementing such a change is complex, difficult, and time consuming. Lean workflow analysis may be an efficient, effective, and acceptable method for use during integration. The objectives of this study were to observe BH integration into primary care and to measure its impact. This was a prospective, mixed-methods case study in a primary care practice that served 8,426 patients over a 17-month period, with 652 patients referred to BH services. Secondary measures included primary care visits resulting in BH referrals, referrals resulting in scheduled appointments, time from referral to the scheduled appointment, and time from the referral to the first visit. Providers and staff were surveyed on the Lean method. Referrals increased from 23 to 37 per 1000 visits (P < .001). Referrals resulted in more scheduled (60% to 74%; P < .001) and arrived visits (44% to 53%; P = .025). Time from referral to the first scheduled visit decreased (hazard ratio, 1.60; 95% confidence interval, 1.37-1.88) as did time to first arrived visit (hazard ratio, 1.36; 95% confidence interval, 1.14-1.62). Survey responses and comments were positive. This pilot integration of BH showed significant improvements in treatment initiation and other measures. Strengths of Lean analysis included workflow improvement, system perspective, and project success. Further evaluation is indicated. © Copyright 2016 by the American Board of Family Medicine.

Modeling workflow to design machine translation applications for public health practice

PubMed Central

Turner, Anne M.; Brownstein, Megumu K.; Cole, Kate; Karasz, Hilary; Kirchhoff, Katrin

2014-01-01

Objective Provide a detailed understanding of the information workflow processes related to translating health promotion materials for limited English proficiency individuals in order to inform the design of context-driven machine translation (MT) tools for public health (PH). Materials and Methods We applied a cognitive work analysis framework to investigate the translation information workflow processes of two large health departments in Washington State. Researchers conducted interviews, performed a task analysis, and validated results with PH professionals to model translation workflow and identify functional requirements for a translation system for PH. Results The study resulted in a detailed description of work related to translation of PH materials, an information workflow diagram, and a description of attitudes towards MT technology. We identified a number of themes that hold design implications for incorporating MT in PH translation practice. A PH translation tool prototype was designed based on these findings. Discussion This study underscores the importance of understanding the work context and information workflow for which systems will be designed. Based on themes and translation information workflow processes, we identified key design guidelines for incorporating MT into PH translation work. Primary amongst these is that MT should be followed by human review for translations to be of high quality and for the technology to be adopted into practice. Counclusion The time and costs of creating multilingual health promotion materials are barriers to translation. PH personnel were interested in MT's potential to improve access to low-cost translated PH materials, but expressed concerns about ensuring quality. We outline design considerations and a potential machine translation tool to best fit MT systems into PH practice. PMID:25445922

Building asynchronous geospatial processing workflows with web services

NASA Astrophysics Data System (ADS)

Zhao, Peisheng; Di, Liping; Yu, Genong

2012-02-01

Geoscience research and applications often involve a geospatial processing workflow. This workflow includes a sequence of operations that use a variety of tools to collect, translate, and analyze distributed heterogeneous geospatial data. Asynchronous mechanisms, by which clients initiate a request and then resume their processing without waiting for a response, are very useful for complicated workflows that take a long time to run. Geospatial contents and capabilities are increasingly becoming available online as interoperable Web services. This online availability significantly enhances the ability to use Web service chains to build distributed geospatial processing workflows. This paper focuses on how to orchestrate Web services for implementing asynchronous geospatial processing workflows. The theoretical bases for asynchronous Web services and workflows, including asynchrony patterns and message transmission, are examined to explore different asynchronous approaches to and architecture of workflow code for the support of asynchronous behavior. A sample geospatial processing workflow, issued by the Open Geospatial Consortium (OGC) Web Service, Phase 6 (OWS-6), is provided to illustrate the implementation of asynchronous geospatial processing workflows and the challenges in using Web Services Business Process Execution Language (WS-BPEL) to develop them.

myExperiment: a repository and social network for the sharing of bioinformatics workflows

PubMed Central

Goble, Carole A.; Bhagat, Jiten; Aleksejevs, Sergejs; Cruickshank, Don; Michaelides, Danius; Newman, David; Borkum, Mark; Bechhofer, Sean; Roos, Marco; Li, Peter; De Roure, David

2010-01-01

myExperiment (http://www.myexperiment.org) is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to bugs@myexperiment.org. PMID:20501605

A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology.

PubMed

Yamamoto, Hidekazu; Nir, Dror; Vyas, Lona; Chang, Richard T; Popert, Rick; Cahill, Declan; Challacombe, Ben; Dasgupta, Prokar; Chandra, Ashish

2014-08-01

Evaluation of prostate imaging tests against whole-mount histology specimens requires accurate alignment between radiologic and histologic data sets. Misalignment results in false-positive and -negative zones as assessed by imaging. We describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P < .0001), with higher sensitivity (85% vs. 69%) and specificity (94% vs. 73%) for margin prediction in a 5 × 5-mm grid analysis. A significantly better alignment was observed in the optimized workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Describing and Modeling Workflow and Information Flow in Chronic Disease Care

PubMed Central

Unertl, Kim M.; Weinger, Matthew B.; Johnson, Kevin B.; Lorenzi, Nancy M.

2009-01-01

Objectives The goal of the study was to develop an in-depth understanding of work practices, workflow, and information flow in chronic disease care, to facilitate development of context-appropriate informatics tools. Design The study was conducted over a 10-month period in three ambulatory clinics providing chronic disease care. The authors iteratively collected data using direct observation and semi-structured interviews. Measurements The authors observed all aspects of care in three different chronic disease clinics for over 150 hours, including 157 patient-provider interactions. Observation focused on interactions among people, processes, and technology. Observation data were analyzed through an open coding approach. The authors then developed models of workflow and information flow using Hierarchical Task Analysis and Soft Systems Methodology. The authors also conducted nine semi-structured interviews to confirm and refine the models. Results The study had three primary outcomes: models of workflow for each clinic, models of information flow for each clinic, and an in-depth description of work practices and the role of health information technology (HIT) in the clinics. The authors identified gaps between the existing HIT functionality and the needs of chronic disease providers. Conclusions In response to the analysis of workflow and information flow, the authors developed ten guidelines for design of HIT to support chronic disease care, including recommendations to pursue modular approaches to design that would support disease-specific needs. The study demonstrates the importance of evaluating workflow and information flow in HIT design and implementation. PMID:19717802

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

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.

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.

PubMed

Paraskevopoulou, Maria D; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A G

2013-07-01

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

PubMed Central

Paraskevopoulou, Maria D.; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S.; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A.G.

2013-01-01

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA–gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines. PMID:23680784

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

PubMed Central

2014-01-01

Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Methods Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. Results We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Conclusions Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

PubMed

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

Kwf-Grid workflow management system for Earth science applications

NASA Astrophysics Data System (ADS)

Tran, V.; Hluchy, L.

2009-04-01

In this paper, we present workflow management tool for Earth science applications in EGEE. The workflow management tool was originally developed within K-wf Grid project for GT4 middleware and has many advanced features like semi-automatic workflow composition, user-friendly GUI for managing workflows, knowledge management. In EGEE, we are porting the workflow management tool to gLite middleware for Earth science applications K-wf Grid workflow management system was developed within "Knowledge-based Workflow System for Grid Applications" under the 6th Framework Programme. The workflow mangement system intended to - semi-automatically compose a workflow of Grid services, - execute the composed workflow application in a Grid computing environment, - monitor the performance of the Grid infrastructure and the Grid applications, - analyze the resulting monitoring information, - capture the knowledge that is contained in the information by means of intelligent agents, - and finally to reuse the joined knowledge gathered from all participating users in a collaborative way in order to efficiently construct workflows for new Grid applications. Kwf Grid workflow engines can support different types of jobs (e.g. GRAM job, web services) in a workflow. New class of gLite job has been added to the system, allows system to manage and execute gLite jobs in EGEE infrastructure. The GUI has been adapted to the requirements of EGEE users, new credential management servlet is added to portal. Porting K-wf Grid workflow management system to gLite would allow EGEE users to use the system and benefit from its avanced features. The system is primarly tested and evaluated with applications from ES clusters.

Integrating Behavioral Health in Primary Care Using Lean Workflow Analysis: A Case Study

PubMed Central

van Eeghen, Constance; Littenberg, Benjamin; Holman, Melissa D.; Kessler, Rodger

2016-01-01

Background Primary care offices are integrating behavioral health (BH) clinicians into their practices. Implementing such a change is complex, difficult, and time consuming. Lean workflow analysis may be an efficient, effective, and acceptable method for integration. Objective Observe BH integration into primary care and measure its impact. Design Prospective, mixed methods case study in a primary care practice. Measurements Change in treatment initiation (referrals generating BH visits within the system). Secondary measures: primary care visits resulting in BH referrals, referrals resulting in scheduled appointments, time from referral to scheduled appointment, and time from referral to first visit. Providers and staff were surveyed on the Lean method. Results Referrals increased from 23 to 37/1000 visits (P<.001). Referrals resulted in more scheduled (60% to 74%, P<.001) and arrived visits (44% to 53%, P=.025). Time from referral to first scheduled visit decreased (Hazard Ratio (HR) 1.60; 95% Confidence Interval (CI) 1.37, 1.88; P<0.001) as did time to first arrived visit (HR 1.36; 95% CI 1.14, 1.62; P=0.001). Surveys and comments were positive. Conclusions This pilot integration of BH showed significant improvements in treatment initiation and other measures. Strengths of Lean included workflow improvement, system perspective, and project success. Further evaluation is indicated. PMID:27170796

Building an efficient curation workflow for the Arabidopsis literature corpus

PubMed Central

Li, Donghui; Berardini, Tanya Z.; Muller, Robert J.; Huala, Eva

2012-01-01

TAIR (The Arabidopsis Information Resource) is the model organism database (MOD) for Arabidopsis thaliana, a model plant with a literature corpus of about 39 000 articles in PubMed, with over 4300 new articles added in 2011. We have developed a literature curation workflow incorporating both automated and manual elements to cope with this flood of new research articles. The current workflow can be divided into two phases: article selection and curation. Structured controlled vocabularies, such as the Gene Ontology and Plant Ontology are used to capture free text information in the literature as succinct ontology-based annotations suitable for the application of computational analysis methods. We also describe our curation platform and the use of text mining tools in our workflow. Database URL: www.arabidopsis.org PMID:23221298

Provenance-Powered Automatic Workflow Generation and Composition

NASA Astrophysics Data System (ADS)

Zhang, J.; Lee, S.; Pan, L.; Lee, T. J.

2015-12-01

In recent years, scientists have learned how to codify tools into reusable software modules that can be chained into multi-step executable workflows. Existing scientific workflow tools, created by computer scientists, require domain scientists to meticulously design their multi-step experiments before analyzing data. However, this is oftentimes contradictory to a domain scientist's daily routine of conducting research and exploration. We hope to resolve this dispute. Imagine this: An Earth scientist starts her day applying NASA Jet Propulsion Laboratory (JPL) published climate data processing algorithms over ARGO deep ocean temperature and AMSRE sea surface temperature datasets. Throughout the day, she tunes the algorithm parameters to study various aspects of the data. Suddenly, she notices some interesting results. She then turns to a computer scientist and asks, "can you reproduce my results?" By tracking and reverse engineering her activities, the computer scientist creates a workflow. The Earth scientist can now rerun the workflow to validate her findings, modify the workflow to discover further variations, or publish the workflow to share the knowledge. In this way, we aim to revolutionize computer-supported Earth science. We have developed a prototyping system to realize the aforementioned vision, in the context of service-oriented science. We have studied how Earth scientists conduct service-oriented data analytics research in their daily work, developed a provenance model to record their activities, and developed a technology to automatically generate workflow starting from user behavior and adaptability and reuse of these workflows for replicating/improving scientific studies. A data-centric repository infrastructure is established to catch richer provenance to further facilitate collaboration in the science community. We have also established a Petri nets-based verification instrument for provenance-based automatic workflow generation and recommendation.

Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline.

PubMed

Pappas, Derek J; Marin, Wesley; Hollenbach, Jill A; Mack, Steven J

2016-03-01

Bridging ImmunoGenomic Data-Analysis Workflow Gaps (BIGDAWG) is an integrated data-analysis pipeline designed for the standardized analysis of highly-polymorphic genetic data, specifically for the HLA and KIR genetic systems. Most modern genetic analysis programs are designed for the analysis of single nucleotide polymorphisms, but the highly polymorphic nature of HLA and KIR data require specialized methods of data analysis. BIGDAWG performs case-control data analyses of highly polymorphic genotype data characteristic of the HLA and KIR loci. BIGDAWG performs tests for Hardy-Weinberg equilibrium, calculates allele frequencies and bins low-frequency alleles for k×2 and 2×2 chi-squared tests, and calculates odds ratios, confidence intervals and p-values for each allele. When multi-locus genotype data are available, BIGDAWG estimates user-specified haplotypes and performs the same binning and statistical calculations for each haplotype. For the HLA loci, BIGDAWG performs the same analyses at the individual amino-acid level. Finally, BIGDAWG generates figures and tables for each of these comparisons. BIGDAWG obviates the error-prone reformatting needed to traffic data between multiple programs, and streamlines and standardizes the data-analysis process for case-control studies of highly polymorphic data. BIGDAWG has been implemented as the bigdawg R package and as a free web application at bigdawg.immunogenomics.org. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Barriers to critical thinking: workflow interruptions and task switching among nurses.

PubMed

Cornell, Paul; Riordan, Monica; Townsend-Gervis, Mary; Mobley, Robin

2011-10-01

Nurses are increasingly called upon to engage in critical thinking. However, current workflow inhibits this goal with frequent task switching and unpredictable demands. To assess workflow's cognitive impact, nurses were observed at 2 hospitals with different patient loads and acuity levels. Workflow on a medical/surgical and pediatric oncology unit was observed, recording tasks, tools, collaborators, and locations. Nineteen nurses were observed for a total of 85.2 hours. Tasks were short with a mean duration of 62.4 and 81.6 seconds on the 2 units. More than 50% of the recorded tasks were less than 30 seconds in length. An analysis of task sequence revealed few patterns and little pairwise repetition. Performance on specific tasks differed between the 2 units, but the character of the workflow was highly similar. The nonrepetitive flow and high amount of switching indicate nurses experience a heavy cognitive load with little uninterrupted time. This implies that nurses rarely have the conditions necessary for critical thinking.

xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

PubMed

Duvick, Jon; Standage, Daniel S; Merchant, Nirav; Brendel, Volker P

2016-04-01

Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today's pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant's Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. © 2016 American Society of Plant Biologists. All rights reserved.

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

Structuring clinical workflows for diabetes care: an overview of the OntoHealth approach.

PubMed

Schweitzer, M; Lasierra, N; Oberbichler, S; Toma, I; Fensel, A; Hoerbst, A

2014-01-01

Electronic health records (EHRs) play an important role in the treatment of chronic diseases such as diabetes mellitus. Although the interoperability and selected functionality of EHRs are already addressed by a number of standards and best practices, such as IHE or HL7, the majority of these systems are still monolithic from a user-functionality perspective. The purpose of the OntoHealth project is to foster a functionally flexible, standards-based use of EHRs to support clinical routine task execution by means of workflow patterns and to shift the present EHR usage to a more comprehensive integration concerning complete clinical workflows. The goal of this paper is, first, to introduce the basic architecture of the proposed OntoHealth project and, second, to present selected functional needs and a functional categorization regarding workflow-based interactions with EHRs in the domain of diabetes. A systematic literature review regarding attributes of workflows in the domain of diabetes was conducted. Eligible references were gathered and analyzed using a qualitative content analysis. Subsequently, a functional workflow categorization was derived from diabetes-specific raw data together with existing general workflow patterns. This paper presents the design of the architecture as well as a categorization model which makes it possible to describe the components or building blocks within clinical workflows. The results of our study lead us to identify basic building blocks, named as actions, decisions, and data elements, which allow the composition of clinical workflows within five identified contexts. The categorization model allows for a description of the components or building blocks of clinical workflows from a functional view.

Addressing informatics challenges in Translational Research with workflow technology.

PubMed

Beaulah, Simon A; Correll, Mick A; Munro, Robin E J; Sheldon, Jonathan G

2008-09-01

Interest in Translational Research has been growing rapidly in recent years. In this collision of different data, technologies and cultures lie tremendous opportunities for the advancement of science and business for organisations that are able to integrate, analyse and deliver this information effectively to users. Workflow-based integration and analysis systems are becoming recognised as a fast and flexible way to build applications that are tailored to scientific areas, yet are built on a common platform. Workflow systems are allowing organisations to meet the key informatics challenges in Translational Research and improve disease understanding and patient care.

Workflow in interventional radiology: nerve blocks and facet blocks

NASA Astrophysics Data System (ADS)

Siddoway, Donald; Ingeholm, Mary Lou; Burgert, Oliver; Neumuth, Thomas; Watson, Vance; Cleary, Kevin

2006-03-01

Workflow analysis has the potential to dramatically improve the efficiency and clinical outcomes of medical procedures. In this study, we recorded the workflow for nerve block and facet block procedures in the interventional radiology suite at Georgetown University Hospital in Washington, DC, USA. We employed a custom client/server software architecture developed by the Innovation Center for Computer Assisted Surgery (ICCAS) at the University of Leipzig, Germany. This software runs in an internet browser, and allows the user to record the actions taken by the physician during a procedure. The data recorded during the procedure is stored as an XML document, which can then be further processed. We have successfully gathered data on a number if cases using a tablet PC, and these preliminary results show the feasibility of using this software in an interventional radiology setting. We are currently accruing additional cases and when more data has been collected we will analyze the workflow of these procedures to look for inefficiencies and potential improvements.

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics*

PubMed Central

Li, Jing; Su, Zengliu; Ma, Ze-Qiang; Slebos, Robbert J. C.; Halvey, Patrick; Tabb, David L.; Liebler, Daniel C.; Pao, William; Zhang, Bing

2011-01-01

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics. PMID:21389108

Analysis of Academic Attitudes and Existing Processes to Inform the Design of Teaching and Learning Material Repositories: A User-Centred Approach

ERIC Educational Resources Information Center

King, Melanie; Loddington, Steve; Manuel, Sue; Oppenheim, Charles

2008-01-01

The last couple of years have brought a rise in the number of institutional repositories throughout the world and within UK Higher Education institutions, with the majority of these repositories being devoted to research output. Repositories containing teaching and learning material are less common and the workflows and business processes…

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

A Workflow for Global Sensitivity Analysis of PBPK Models

PubMed Central

McNally, Kevin; Cotton, Richard; Loizou, George D.

2011-01-01

Physiologically based pharmacokinetic (PBPK) models have a potentially significant role in the development of a reliable predictive toxicity testing strategy. The structure of PBPK models are ideal frameworks into which disparate in vitro and in vivo data can be integrated and utilized to translate information generated, using alternative to animal measures of toxicity and human biological monitoring data, into plausible corresponding exposures. However, these models invariably include the description of well known non-linear biological processes such as, enzyme saturation and interactions between parameters such as, organ mass and body mass. Therefore, an appropriate sensitivity analysis (SA) technique is required which can quantify the influences associated with individual parameters, interactions between parameters and any non-linear processes. In this report we have defined the elements of a workflow for SA of PBPK models that is computationally feasible, accounts for interactions between parameters, and can be displayed in the form of a bar chart and cumulative sum line (Lowry plot), which we believe is intuitive and appropriate for toxicologists, risk assessors, and regulators. PMID:21772819

Multidimensional Interactive Radiology Report and Analysis: standardization of workflow and reporting for renal mass tracking and quantification

NASA Astrophysics Data System (ADS)

Hwang, Darryl H.; Ma, Kevin; Yepes, Fernando; Nadamuni, Mridula; Nayyar, Megha; Liu, Brent; Duddalwar, Vinay; Lepore, Natasha

2015-12-01

A conventional radiology report primarily consists of a large amount of unstructured text, and lacks clear, concise, consistent and content-rich information. Hence, an area of unmet clinical need consists of developing better ways to communicate radiology findings and information specific to each patient. Here, we design a new workflow and reporting system that combines and integrates advances in engineering technology with those from the medical sciences, the Multidimensional Interactive Radiology Report and Analysis (MIRRA). Until recently, clinical standards have primarily relied on 2D images for the purpose of measurement, but with the advent of 3D processing, many of the manually measured metrics can be automated, leading to better reproducibility and less subjective measurement placement. Hence, we make use this newly available 3D processing in our workflow. Our pipeline is used here to standardize the labeling, tracking, and quantifying of metrics for renal masses.

Thermal Remote Sensing with Uav-Based Workflows

NASA Astrophysics Data System (ADS)

Boesch, R.

2017-08-01

Climate change will have a significant influence on vegetation health and growth. Predictions of higher mean summer temperatures and prolonged summer draughts may pose a threat to agriculture areas and forest canopies. Rising canopy temperatures can be an indicator of plant stress because of the closure of stomata and a decrease in the transpiration rate. Thermal cameras are available for decades, but still often used for single image analysis, only in oblique view manner or with visual evaluations of video sequences. Therefore remote sensing using a thermal camera can be an important data source to understand transpiration processes. Photogrammetric workflows allow to process thermal images similar to RGB data. But low spatial resolution of thermal cameras, significant optical distortion and typically low contrast require an adapted workflow. Temperature distribution in forest canopies is typically completely unknown and less distinct than for urban or industrial areas, where metal constructions and surfaces yield high contrast and sharp edge information. The aim of this paper is to investigate the influence of interior camera orientation, tie point matching and ground control points on the resulting accuracy of bundle adjustment and dense cloud generation with a typically used photogrammetric workflow for UAVbased thermal imagery in natural environments.

A workflow to investigate exposure and pharmacokinetic ...

EPA Pesticide Factsheets

Adverse outcome pathways (AOP) link known population outcomes to a molecular initiating event (MIE) that can be quantified using high-throughput in vitro methods. Practical application of AOPs in chemical-specific risk assessment requires consideration of exposure and absorption, distribution, metabolism, excretion (ADME) properties of chemicals. We developed a conceptual workflow to consider exposure and ADME properties in relationship to an MIE and demonstrated the utility of this workflow using a previously established AOP, acetylcholinesterase (AChE) inhibition. Thirty active chemicals found to inhibit AChE in the ToxCastTM assay were examined with respect to their exposure and absorption potentials, and their ability to cross the blood-brain barrier. Structural similarities of active compounds were compared against structures of inactive compounds to detect possible non-active parents that might have active metabolites. Fifty-two of the 1,029 inactive compounds exhibited a similarity threshold above 75% with their nearest active neighbors. Excluding compounds that may not be absorbed, 22 could be potentially toxic following metabolism. The incorporation of exposure and ADME properties into the conceptual workflow resulted in prioritization of 20 out of 30 active compounds identified in an AChE inhibition assay for further analysis, along with identification of several inactive parent compounds of active metabolites. This qualitative approach can minimize co

xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud[OPEN

PubMed Central

Merchant, Nirav

2016-01-01

Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today’s pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant’s Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. PMID:27020957

Traversing the many paths of workflow research: developing a conceptual framework of workflow terminology through a systematic literature review

PubMed Central

Novak, Laurie L; Johnson, Kevin B; Lorenzi, Nancy M

2010-01-01

The objective of this review was to describe methods used to study and model workflow. The authors included studies set in a variety of industries using qualitative, quantitative and mixed methods. Of the 6221 matching abstracts, 127 articles were included in the final corpus. The authors collected data from each article on researcher perspective, study type, methods type, specific methods, approaches to evaluating quality of results, definition of workflow and dependent variables. Ethnographic observation and interviews were the most frequently used methods. Long study durations revealed the large time commitment required for descriptive workflow research. The most frequently discussed technique for evaluating quality of study results was triangulation. The definition of the term “workflow” and choice of methods for studying workflow varied widely across research areas and researcher perspectives. The authors developed a conceptual framework of workflow-related terminology for use in future research and present this model for use by other researchers. PMID:20442143

Teaching meta-analysis using MetaLight.

PubMed

Thomas, James; Graziosi, Sergio; Higgins, Steve; Coe, Robert; Torgerson, Carole; Newman, Mark

2012-10-18

Meta-analysis is a statistical method for combining the results of primary studies. It is often used in systematic reviews and is increasingly a method and topic that appears in student dissertations. MetaLight is a freely available software application that runs simple meta-analyses and contains specific functionality to facilitate the teaching and learning of meta-analysis. While there are many courses and resources for meta-analysis available and numerous software applications to run meta-analyses, there are few pieces of software which are aimed specifically at helping those teaching and learning meta-analysis. Valuable teaching time can be spent learning the mechanics of a new software application, rather than on the principles and practices of meta-analysis. We discuss ways in which the MetaLight tool can be used to present some of the main issues involved in undertaking and interpreting a meta-analysis. While there are many software tools available for conducting meta-analysis, in the context of a teaching programme such software can require expenditure both in terms of money and in terms of the time it takes to learn how to use it. MetaLight was developed specifically as a tool to facilitate the teaching and learning of meta-analysis and we have presented here some of the ways it might be used in a training situation.

Make Your Workflows Smarter

NASA Technical Reports Server (NTRS)

Jones, Corey; Kapatos, Dennis; Skradski, Cory

2012-01-01

Do you have workflows with many manual tasks that slow down your business? Or, do you scale back workflows because there are simply too many manual tasks? Basic workflow robots can automate some common tasks, but not everything. This presentation will show how advanced robots called "expression robots" can be set up to perform everything from simple tasks such as: moving, creating folders, renaming, changing or creating an attribute, and revising, to more complex tasks like: creating a pdf, or even launching a session of Creo Parametric and performing a specific modeling task. Expression robots are able to utilize the Java API and Info*Engine to do almost anything you can imagine! Best of all, these tools are supported by PTC and will work with later releases of Windchill. Limited knowledge of Java, Info*Engine, and XML are required. The attendee will learn what task expression robots are capable of performing. The attendee will learn what is involved in setting up an expression robot. The attendee will gain a basic understanding of simple Info*Engine tasks

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.

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.

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.

Worklist handling in workflow-enabled radiological application systems

NASA Astrophysics Data System (ADS)

Wendler, Thomas; Meetz, Kirsten; Schmidt, Joachim; von Berg, Jens

2000-05-01

For the next generation integrated information systems for health care applications, more emphasis has to be put on systems which, by design, support the reduction of cost, the increase inefficiency and the improvement of the quality of services. A substantial contribution to this will be the modeling. optimization, automation and enactment of processes in health care institutions. One of the perceived key success factors for the system integration of processes will be the application of workflow management, with workflow management systems as key technology components. In this paper we address workflow management in radiology. We focus on an important aspect of workflow management, the generation and handling of worklists, which provide workflow participants automatically with work items that reflect tasks to be performed. The display of worklists and the functions associated with work items are the visible part for the end-users of an information system using a workflow management approach. Appropriate worklist design and implementation will influence user friendliness of a system and will largely influence work efficiency. Technically, in current imaging department information system environments (modality-PACS-RIS installations), a data-driven approach has been taken: Worklist -- if present at all -- are generated from filtered views on application data bases. In a future workflow-based approach, worklists will be generated by autonomous workflow services based on explicit process models and organizational models. This process-oriented approach will provide us with an integral view of entire health care processes or sub- processes. The paper describes the basic mechanisms of this approach and summarizes its benefits.

Automatic Image Processing Workflow for the Keck/NIRC2 Vortex Coronagraph

NASA Astrophysics Data System (ADS)

Xuan, Wenhao; Cook, Therese; Ngo, Henry; Zawol, Zoe; Ruane, Garreth; Mawet, Dimitri

2018-01-01

The Keck/NIRC2 camera, equipped with the vortex coronagraph, is an instrument targeted at the high contrast imaging of extrasolar planets. To uncover a faint planet signal from the overwhelming starlight, we utilize the Vortex Image Processing (VIP) library, which carries out principal component analysis to model and remove the stellar point spread function. To bridge the gap between data acquisition and data reduction, we implement a workflow that 1) downloads, sorts, and processes data with VIP, 2) stores the analysis products into a database, and 3) displays the reduced images, contrast curves, and auxiliary information on a web interface. Both angular differential imaging and reference star differential imaging are implemented in the analysis module. A real-time version of the workflow runs during observations, allowing observers to make educated decisions about time distribution on different targets, hence optimizing science yield. The post-night version performs a standardized reduction after the observation, building up a valuable database that not only helps uncover new discoveries, but also enables a statistical study of the instrument itself. We present the workflow, and an examination of the contrast performance of the NIRC2 vortex with respect to factors including target star properties and observing conditions.

a Workflow for UAV's Integration Into a Geodesign Platform

NASA Astrophysics Data System (ADS)

Anca, P.; Calugaru, A.; Alixandroae, I.; Nazarie, R.

2016-06-01

This paper presents a workflow for the development of various Geodesign scenarios. The subject is important in the context of identifying patterns and designing solutions for a Smart City with optimized public transportation, efficient buildings, efficient utilities, recreational facilities a.s.o.. The workflow describes the procedures starting with acquiring data in the field, data processing, orthophoto generation, DTM generation, integration into a GIS platform and analyzing for a better support for Geodesign. Esri's City Engine is used mostly for 3D modeling capabilities that enable the user to obtain 3D realistic models. The workflow uses as inputs information extracted from images acquired using UAVs technologies, namely eBee, existing 2D GIS geodatabases, and a set of CGA rules. The method that we used further, is called procedural modeling, and uses rules in order to extrude buildings, the street network, parcel zoning and side details, based on the initial attributes from the geodatabase. The resulted products are various scenarios for redesigning, for analyzing new exploitation sites. Finally, these scenarios can be published as interactive web scenes for internal, groups or pubic consultation. In this way, problems like the impact of new constructions being build, re-arranging green spaces or changing routes for public transportation, etc. are revealed through impact and visibility analysis or shadowing analysis and are brought to the citizen's attention. This leads to better decisions.

geoKepler Workflow Module for Computationally Scalable and Reproducible Geoprocessing and Modeling

NASA Astrophysics Data System (ADS)

Cowart, C.; Block, J.; Crawl, D.; Graham, J.; Gupta, A.; Nguyen, M.; de Callafon, R.; Smarr, L.; Altintas, I.

2015-12-01

The NSF-funded WIFIRE project has developed an open-source, online geospatial workflow platform for unifying geoprocessing tools and models for for fire and other geospatially dependent modeling applications. It is a product of WIFIRE's objective to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. geoKepler includes a set of reusable GIS components, or actors, for the Kepler Scientific Workflow System (https://kepler-project.org). Actors exist for reading and writing GIS data in formats such as Shapefile, GeoJSON, KML, and using OGC web services such as WFS. The actors also allow for calling geoprocessing tools in other packages such as GDAL and GRASS. Kepler integrates functions from multiple platforms and file formats into one framework, thus enabling optimal GIS interoperability, model coupling, and scalability. Products of the GIS actors can be fed directly to models such as FARSITE and WRF. Kepler's ability to schedule and scale processes using Hadoop and Spark also makes geoprocessing ultimately extensible and computationally scalable. The reusable workflows in geoKepler can be made to run automatically when alerted by real-time environmental conditions. Here, we show breakthroughs in the speed of creating complex data for hazard assessments with this platform. We also demonstrate geoKepler workflows that use Data Assimilation to ingest real-time weather data into wildfire simulations, and for data mining techniques to gain insight into environmental conditions affecting fire behavior. Existing machine learning tools and libraries such as R and MLlib are being leveraged for this purpose in Kepler, as well as Kepler's Distributed Data Parallel (DDP) capability to provide a framework for scalable processing. geoKepler workflows can be executed via an iPython notebook as a part of a Jupyter hub at UC San Diego for sharing and reporting of the scientific analysis and results from

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

PubMed

Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

2015-06-30

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

Text mining for the biocuration workflow

PubMed Central

Hirschman, Lynette; Burns, Gully A. P. C; Krallinger, Martin; Arighi, Cecilia; Cohen, K. Bretonnel; Valencia, Alfonso; Wu, Cathy H.; Chatr-Aryamontri, Andrew; Dowell, Karen G.; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G.

2012-01-01

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community. PMID:22513129

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

PubMed

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down

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.

Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

PubMed

Arshad, Junaid; Hoffmann, Alexander; Gesing, Sandra; Grunzke, Richard; Krüger, Jens; Kiss, Tamas; Herres-Pawlis, Sonja; Terstyanszky, Gabor

2016-01-01

In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Graphical AbstractMeta-workflows and embedded workflows in the template representation.

Teaching Content Analysis through "Harry Potter"

ERIC Educational Resources Information Center

Messinger, Adam M.

2012-01-01

Content analysis is a valuable research tool for social scientists that unfortunately can prove challenging to teach to undergraduate students. Published classroom exercises designed to teach content analysis have thus far been predominantly envisioned as lengthy projects for upper-level courses. A brief and engaging exercise may be more…

Resident training in a teaching hospital: How do attendings teach in the real operative environment?

PubMed

Glarner, Carly E; Law, Katherine E; Zelenski, Amy B; McDonald, Robert J; Greenberg, Jacob A; Foley, Eugene F; Wiegmann, Douglas A; Greenberg, Caprice C

2017-07-01

The study aim was to explore the nature of intraoperative education and its interaction with the environment where surgical education occurs. Video and audio recording captured teaching interactions between colorectal surgeons and general surgery residents during laparoscopic segmental colectomies. Cases and collected data were analyzed for teaching behaviors and workflow disruptions. Flow disruptions (FDs) are considered deviations from natural case progression. Across 10 cases (20.4 operative hours), attendings spent 11.2 hours (54.7%) teaching, using directing (M = 250.1), and confirming (M = 236.1) most. FDs occurred 410 times, accounting for 4.4 hours of case time (21.57%). Teaching occurred with FD events for 2.4 hours (22.2%), whereas 77.8% of teaching happened outside FD occurrence. Teaching methods shifted from active to passive during FD events to compensate for patient safety. Understanding how FDs impact operative learning will inform faculty development in managing interruptions and improve its integration into resident education. Copyright © 2016. Published by Elsevier Inc.

Implementing bioinformatic workflows within the bioextract server

USDA-ARS?s Scientific Manuscript database

Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

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 Model of Workflow Composition for Emergency Management

NASA Astrophysics Data System (ADS)

Xin, Chen; Bin-ge, Cui; Feng, Zhang; Xue-hui, Xu; Shan-shan, Fu

The common-used workflow technology is not flexible enough in dealing with concurrent emergency situations. The paper proposes a novel model for defining emergency plans, in which workflow segments appear as a constituent part. A formal abstraction, which contains four operations, is defined to compose workflow segments under constraint rule. The software system of the business process resources construction and composition is implemented and integrated into Emergency Plan Management Application System.

The TimeStudio Project: An open source scientific workflow system for the behavioral and brain sciences.

PubMed

Nyström, Pär; Falck-Ytter, Terje; Gredebäck, Gustaf

2016-06-01

This article describes a new open source scientific workflow system, the TimeStudio Project, dedicated to the behavioral and brain sciences. The program is written in MATLAB and features a graphical user interface for the dynamic pipelining of computer algorithms developed as TimeStudio plugins. TimeStudio includes both a set of general plugins (for reading data files, modifying data structures, visualizing data structures, etc.) and a set of plugins specifically developed for the analysis of event-related eyetracking data as a proof of concept. It is possible to create custom plugins to integrate new or existing MATLAB code anywhere in a workflow, making TimeStudio a flexible workbench for organizing and performing a wide range of analyses. The system also features an integrated sharing and archiving tool for TimeStudio workflows, which can be used to share workflows both during the data analysis phase and after scientific publication. TimeStudio thus facilitates the reproduction and replication of scientific studies, increases the transparency of analyses, and reduces individual researchers' analysis workload. The project website ( http://timestudioproject.com ) contains the latest releases of TimeStudio, together with documentation and user forums.

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis.

PubMed

Costa, Raquel L; Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis

PubMed Central

Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results

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

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

Deploying and sharing U-Compare workflows as web services.

PubMed

Kontonatsios, Georgios; Korkontzelos, Ioannis; Kolluru, Balakrishna; Thompson, Paul; Ananiadou, Sophia

2013-02-18

U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare's components. Workflows developed using U-Compare can be exported and sent to other users who, in turn, can import and re-use them. However, the resulting workflows are standalone applications, i.e., software tools that run and are accessible only via a local machine, and that can only be run with the U-Compare platform. We address the above issues by extending U-Compare to convert standalone workflows into web services automatically, via a two-click process. The resulting web services can be registered on a central server and made publicly available. Alternatively, users can make web services available on their own servers, after installing the web application framework, which is part of the extension to U-Compare. We have performed a user-oriented evaluation of the proposed extension, by asking users who have tested the enhanced functionality of U-Compare to complete questionnaires that assess its functionality, reliability, usability, efficiency and maintainability. The results obtained reveal that the new functionality is well received by users. The web services produced by U-Compare are built on top of open standards, i.e., REST and SOAP protocols, and therefore, they are decoupled from the underlying platform. Exported workflows can be integrated with any application that supports these open standards. We demonstrate how the newly extended U-Compare enhances the cross-platform interoperability of workflows, by seamlessly importing a number of text mining workflow web services exported from U-Compare into Taverna, i.e., a generic scientific workflow construction platform.

Deploying and sharing U-Compare workflows as web services

PubMed Central

2013-01-01

Background U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare’s components. Workflows developed using U-Compare can be exported and sent to other users who, in turn, can import and re-use them. However, the resulting workflows are standalone applications, i.e., software tools that run and are accessible only via a local machine, and that can only be run with the U-Compare platform. Results We address the above issues by extending U-Compare to convert standalone workflows into web services automatically, via a two-click process. The resulting web services can be registered on a central server and made publicly available. Alternatively, users can make web services available on their own servers, after installing the web application framework, which is part of the extension to U-Compare. We have performed a user-oriented evaluation of the proposed extension, by asking users who have tested the enhanced functionality of U-Compare to complete questionnaires that assess its functionality, reliability, usability, efficiency and maintainability. The results obtained reveal that the new functionality is well received by users. Conclusions The web services produced by U-Compare are built on top of open standards, i.e., REST and SOAP protocols, and therefore, they are decoupled from the underlying platform. Exported workflows can be integrated with any application that supports these open standards. We demonstrate how the newly extended U-Compare enhances the cross-platform interoperability of workflows, by seamlessly importing a number of text mining workflow web services exported from U-Compare into Taverna, i.e., a generic scientific workflow construction platform. PMID:23419017

a Standardized Approach to Topographic Data Processing and Workflow Management

NASA Astrophysics Data System (ADS)

Wheaton, J. M.; Bailey, P.; Glenn, N. F.; Hensleigh, J.; Hudak, A. T.; Shrestha, R.; Spaete, L.

2013-12-01

An ever-increasing list of options exist for collecting high resolution topographic data, including airborne LIDAR, terrestrial laser scanners, bathymetric SONAR and structure-from-motion. An equally rich, arguably overwhelming, variety of tools exists with which to organize, quality control, filter, analyze and summarize these data. However, scientists are often left to cobble together their analysis as a series of ad hoc steps, often using custom scripts and one-time processes that are poorly documented and rarely shared with the community. Even when literature-cited software tools are used, the input and output parameters differ from tool to tool. These parameters are rarely archived and the steps performed lost, making the analysis virtually impossible to replicate precisely. What is missing is a coherent, robust, framework for combining reliable, well-documented topographic data-processing steps into a workflow that can be repeated and even shared with others. We have taken several popular topographic data processing tools - including point cloud filtering and decimation as well as DEM differencing - and defined a common protocol for passing inputs and outputs between them. This presentation describes a free, public online portal that enables scientists to create custom workflows for processing topographic data using a number of popular topographic processing tools. Users provide the inputs required for each tool and in what sequence they want to combine them. This information is then stored for future reuse (and optionally sharing with others) before the user then downloads a single package that contains all the input and output specifications together with the software tools themselves. The user then launches the included batch file that executes the workflow on their local computer against their topographic data. This ZCloudTools architecture helps standardize, automate and archive topographic data processing. It also represents a forum for discovering and

A workflow learning model to improve geovisual analytics utility

PubMed Central

Roth, Robert E; MacEachren, Alan M; McCabe, Craig A

2011-01-01

concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. Results/Conclusions In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009. PMID:21983545

A workflow learning model to improve geovisual analytics utility.

PubMed

Roth, Robert E; Maceachren, Alan M; McCabe, Craig A

2009-01-01

the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. RESULTS/CONCLUSIONS: In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009.

A characterization of workflow management systems for extreme-scale applications

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

Ferreira da Silva, Rafael; Filgueira, Rosa; Pietri, Ilia

We present that the automation of the execution of computational tasks is at the heart of improving scientific productivity. Over the last years, scientific workflows have been established as an important abstraction that captures data processing and computation of large and complex scientific applications. By allowing scientists to model and express entire data processing steps and their dependencies, workflow management systems relieve scientists from the details of an application and manage its execution on a computational infrastructure. As the resource requirements of today’s computational and data science applications that process vast amounts of data keep increasing, there is a compellingmore » case for a new generation of advances in high-performance computing, commonly termed as extreme-scale computing, which will bring forth multiple challenges for the design of workflow applications and management systems. This paper presents a novel characterization of workflow management systems using features commonly associated with extreme-scale computing applications. We classify 15 popular workflow management systems in terms of workflow execution models, heterogeneous computing environments, and data access methods. Finally, the paper also surveys workflow applications and identifies gaps for future research on the road to extreme-scale workflows and management systems.« less

A characterization of workflow management systems for extreme-scale applications

DOE PAGES

Ferreira da Silva, Rafael; Filgueira, Rosa; Pietri, Ilia; ...

2017-02-16

We present that the automation of the execution of computational tasks is at the heart of improving scientific productivity. Over the last years, scientific workflows have been established as an important abstraction that captures data processing and computation of large and complex scientific applications. By allowing scientists to model and express entire data processing steps and their dependencies, workflow management systems relieve scientists from the details of an application and manage its execution on a computational infrastructure. As the resource requirements of today’s computational and data science applications that process vast amounts of data keep increasing, there is a compellingmore » case for a new generation of advances in high-performance computing, commonly termed as extreme-scale computing, which will bring forth multiple challenges for the design of workflow applications and management systems. This paper presents a novel characterization of workflow management systems using features commonly associated with extreme-scale computing applications. We classify 15 popular workflow management systems in terms of workflow execution models, heterogeneous computing environments, and data access methods. Finally, the paper also surveys workflow applications and identifies gaps for future research on the road to extreme-scale workflows and management systems.« less

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.

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.

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.

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.

Emergency Medicine Resident Physicians’ Perceptions of Electronic Documentation and Workflow

PubMed Central

Neri, P.M.; Redden, L.; Poole, S.; Pozner, C.N.; Horsky, J.; Raja, A.S.; Poon, E.; Schiff, G.

2015-01-01

Summary Objective To understand emergency department (ED) physicians’ use of electronic documentation in order to identify usability and workflow considerations for the design of future ED information system (EDIS) physician documentation modules. Methods We invited emergency medicine resident physicians to participate in a mixed methods study using task analysis and qualitative interviews. Participants completed a simulated, standardized patient encounter in a medical simulation center while documenting in the test environment of a currently used EDIS. We recorded the time on task, type and sequence of tasks performed by the participants (including tasks performed in parallel). We then conducted semi-structured interviews with each participant. We analyzed these qualitative data using the constant comparative method to generate themes. Results Eight resident physicians participated. The simulation session averaged 17 minutes and participants spent 11 minutes on average on tasks that included electronic documentation. Participants performed tasks in parallel, such as history taking and electronic documentation. Five of the 8 participants performed a similar workflow sequence during the first part of the session while the remaining three used different workflows. Three themes characterize electronic documentation: (1) physicians report that location and timing of documentation varies based on patient acuity and workload, (2) physicians report a need for features that support improved efficiency; and (3) physicians like viewing available patient data but struggle with integration of the EDIS with other information sources. Conclusion We confirmed that physicians spend much of their time on documentation (65%) during an ED patient visit. Further, we found that resident physicians did not all use the same workflow and approach even when presented with an identical standardized patient scenario. Future EHR design should consider these varied workflows while trying to

Modeling Complex Workflow in Molecular Diagnostics

PubMed Central

Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

2010-01-01

One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

Conventions and workflows for using Situs

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

Wriggers, Willy, E-mail: wriggers@biomachina.org

2012-04-01

Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described. Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs tomore » be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.« less

Grid workflow validation using ontology-based tacit knowledge: A case study for quantitative remote sensing applications

NASA Astrophysics Data System (ADS)

Liu, Jia; Liu, Longli; Xue, Yong; Dong, Jing; Hu, Yingcui; Hill, Richard; Guang, Jie; Li, Chi

2017-01-01

Workflow for remote sensing quantitative retrieval is the ;bridge; between Grid services and Grid-enabled application of remote sensing quantitative retrieval. Workflow averts low-level implementation details of the Grid and hence enables users to focus on higher levels of application. The workflow for remote sensing quantitative retrieval plays an important role in remote sensing Grid and Cloud computing services, which can support the modelling, construction and implementation of large-scale complicated applications of remote sensing science. The validation of workflow is important in order to support the large-scale sophisticated scientific computation processes with enhanced performance and to minimize potential waste of time and resources. To research the semantic correctness of user-defined workflows, in this paper, we propose a workflow validation method based on tacit knowledge research in the remote sensing domain. We first discuss the remote sensing model and metadata. Through detailed analysis, we then discuss the method of extracting the domain tacit knowledge and expressing the knowledge with ontology. Additionally, we construct the domain ontology with Protégé. Through our experimental study, we verify the validity of this method in two ways, namely data source consistency error validation and parameters matching error validation.

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

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.

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.

A reliable computational workflow for the selection of optimal screening libraries.

PubMed

Gilad, Yocheved; Nadassy, Katalin; Senderowitz, Hanoch

2015-01-01

The experimental screening of compound collections is a common starting point in many drug discovery projects. Successes of such screening campaigns critically depend on the quality of the screened library. Many libraries are currently available from different vendors yet the selection of the optimal screening library for a specific project is challenging. We have devised a novel workflow for the rational selection of project-specific screening libraries. The workflow accepts as input a set of virtual candidate libraries and applies the following steps to each library: (1) data curation; (2) assessment of ADME/T profile; (3) assessment of the number of promiscuous binders/frequent HTS hitters; (4) assessment of internal diversity; (5) assessment of similarity to known active compound(s) (optional); (6) assessment of similarity to in-house or otherwise accessible compound collections (optional). For ADME/T profiling, Lipinski's and Veber's rule-based filters were implemented and a new blood brain barrier permeation model was developed and validated (85 and 74 % success rate for training set and test set, respectively). Diversity and similarity descriptors which demonstrated best performances in terms of their ability to select either diverse or focused sets of compounds from three databases (Drug Bank, CMC and CHEMBL) were identified and used for diversity and similarity assessments. The workflow was used to analyze nine common screening libraries available from six vendors. The results of this analysis are reported for each library providing an assessment of its quality. Furthermore, a consensus approach was developed to combine the results of these analyses into a single score for selecting the optimal library under different scenarios. We have devised and tested a new workflow for the rational selection of screening libraries under different scenarios. The current workflow was implemented using the Pipeline Pilot software yet due to the usage of generic

Seamless online science workflow development and collaboration using IDL and the ENVI Services Engine

NASA Astrophysics Data System (ADS)

Harris, A. T.; Ramachandran, R.; Maskey, M.

2013-12-01

The Exelis-developed IDL and ENVI software are ubiquitous tools in Earth science research environments. The IDL Workbench is used by the Earth science community for programming custom data analysis and visualization modules. ENVI is a software solution for processing and analyzing geospatial imagery that combines support for multiple Earth observation scientific data types (optical, thermal, multi-spectral, hyperspectral, SAR, LiDAR) with advanced image processing and analysis algorithms. The ENVI & IDL Services Engine (ESE) is an Earth science data processing engine that allows researchers to use open standards to rapidly create, publish and deploy advanced Earth science data analytics within any existing enterprise infrastructure. Although powerful in many ways, the tools lack collaborative features out-of-box. Thus, as part of the NASA funded project, Collaborative Workbench to Accelerate Science Algorithm Development, researchers at the University of Alabama in Huntsville and Exelis have developed plugins that allow seamless research collaboration from within IDL workbench. Such additional features within IDL workbench are possible because IDL workbench is built using the Eclipse Rich Client Platform (RCP). RCP applications allow custom plugins to be dropped in for extended functionalities. Specific functionalities of the plugins include creating complex workflows based on IDL application source code, submitting workflows to be executed by ESE in the cloud, and sharing and cloning of workflows among collaborators. All these functionalities are available to scientists without leaving their IDL workbench. Because ESE can interoperate with any middleware, scientific programmers can readily string together IDL processing tasks (or tasks written in other languages like C++, Java or Python) to create complex workflows for deployment within their current enterprise architecture (e.g. ArcGIS Server, GeoServer, Apache ODE or SciFlo from JPL). Using the collaborative IDL

Workflow Dynamics and the Imaging Value Chain: Quantifying the Effect of Designating a Nonimage-Interpretive Task Workflow.

PubMed

Lee, Matthew H; Schemmel, Andrew J; Pooler, B Dustin; Hanley, Taylor; Kennedy, Tabassum A; Field, Aaron S; Wiegmann, Douglas; Yu, John-Paul J

To assess the impact of separate non-image interpretive task and image-interpretive task workflows in an academic neuroradiology practice. A prospective, randomized, observational investigation of a centralized academic neuroradiology reading room was performed. The primary reading room fellow was observed over a one-month period using a time-and-motion methodology, recording frequency and duration of tasks performed. Tasks were categorized into separate image interpretive and non-image interpretive workflows. Post-intervention observation of the primary fellow was repeated following the implementation of a consult assistant responsible for non-image interpretive tasks. Pre- and post-intervention data were compared. Following separation of image-interpretive and non-image interpretive workflows, time spent on image-interpretive tasks by the primary fellow increased from 53.8% to 73.2% while non-image interpretive tasks decreased from 20.4% to 4.4%. Mean time duration of image interpretation nearly doubled, from 05:44 to 11:01 (p = 0.002). Decreases in specific non-image interpretive tasks, including phone calls/paging (2.86/hr versus 0.80/hr), in-room consultations (1.36/hr versus 0.80/hr), and protocoling (0.99/hr versus 0.10/hr), were observed. The consult assistant experienced 29.4 task switching events per hour. Rates of specific non-image interpretive tasks for the CA were 6.41/hr for phone calls/paging, 3.60/hr for in-room consultations, and 3.83/hr for protocoling. Separating responsibilities into NIT and IIT workflows substantially increased image interpretation time and decreased TSEs for the primary fellow. Consolidation of NITs into a separate workflow may allow for more efficient task completion. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Using telephony data to facilitate discovery of clinical workflows.

PubMed

Rucker, Donald W

2017-04-19

Discovery of clinical workflows to target for redesign using methods such as Lean and Six Sigma is difficult. VoIP telephone call pattern analysis may complement direct observation and EMR-based tools in understanding clinical workflows at the enterprise level by allowing visualization of institutional telecommunications activity. To build an analytic framework mapping repetitive and high-volume telephone call patterns in a large medical center to their associated clinical units using an enterprise unified communications server log file and to support visualization of specific call patterns using graphical networks. Consecutive call detail records from the medical center's unified communications server were parsed to cross-correlate telephone call patterns and map associated phone numbers to a cost center dictionary. Hashed data structures were built to allow construction of edge and node files representing high volume call patterns for display with an open source graph network tool. Summary statistics for an analysis of exactly one week's call detail records at a large academic medical center showed that 912,386 calls were placed with a total duration of 23,186 hours. Approximately half of all calling called number pairs had an average call duration under 60 seconds and of these the average call duration was 27 seconds. Cross-correlation of phone calls identified by clinical cost center can be used to generate graphical displays of clinical enterprise communications. Many calls are short. The compact data transfers within short calls may serve as automation or re-design targets. The large absolute amount of time medical center employees were engaged in VoIP telecommunications suggests that analysis of telephone call patterns may offer additional insights into core clinical workflows.

Scientific workflows as productivity tools for drug discovery.

PubMed

Shon, John; Ohkawa, Hitomi; Hammer, Juergen

2008-05-01

Large pharmaceutical companies annually invest tens to hundreds of millions of US dollars in research informatics to support their early drug discovery processes. Traditionally, most of these investments are designed to increase the efficiency of drug discovery. The introduction of do-it-yourself scientific workflow platforms has enabled research informatics organizations to shift their efforts toward scientific innovation, ultimately resulting in a possible increase in return on their investments. Unlike the handling of most scientific data and application integration approaches, researchers apply scientific workflows to in silico experimentation and exploration, leading to scientific discoveries that lie beyond automation and integration. This review highlights some key requirements for scientific workflow environments in the pharmaceutical industry that are necessary for increasing research productivity. Examples of the application of scientific workflows in research and a summary of recent platform advances are also provided.

A three-level atomicity model for decentralized workflow management systems

NASA Astrophysics Data System (ADS)

Ben-Shaul, Israel Z.; Heineman, George T.

1996-12-01

A workflow management system (WFMS) employs a workflow manager (WM) to execute and automate the various activities within a workflow. To protect the consistency of data, the WM encapsulates each activity with a transaction; a transaction manager (TM) then guarantees the atomicity of activities. Since workflows often group several activities together, the TM is responsible for guaranteeing the atomicity of these units. There are scalability issues, however, with centralized WFMSs. Decentralized WFMSs provide an architecture for multiple autonomous WFMSs to interoperate, thus accommodating multiple workflows and geographically-dispersed teams. When atomic units are composed of activities spread across multiple WFMSs, however, there is a conflict between global atomicity and local autonomy of each WFMS. This paper describes a decentralized atomicity model that enables workflow administrators to specify the scope of multi-site atomicity based upon the desired semantics of multi-site tasks in the decentralized WFMS. We describe an architecture that realizes our model and execution paradigm.

Teaching Information Security with Workflow Technology--A Case Study Approach

ERIC Educational Resources Information Center

He, Wu; Kshirsagar, Ashish; Nwala, Alexander; Li, Yaohang

2014-01-01

In recent years, there has been a significant increase in the demand from professionals in different areas for improving the curricula regarding information security. The use of authentic case studies in teaching information security offers the potential to effectively engage students in active learning. In this paper, the authors introduce the…

CamBAfx: Workflow Design, Implementation and Application for Neuroimaging

PubMed Central

Ooi, Cinly; Bullmore, Edward T.; Wink, Alle-Meije; Sendur, Levent; Barnes, Anna; Achard, Sophie; Aspden, John; Abbott, Sanja; Yue, Shigang; Kitzbichler, Manfred; Meunier, David; Maxim, Voichita; Salvador, Raymond; Henty, Julian; Tait, Roger; Subramaniam, Naresh; Suckling, John

2009-01-01

CamBAfx is a workflow application designed for both researchers who use workflows to process data (consumers) and those who design them (designers). It provides a front-end (user interface) optimized for data processing designed in a way familiar to consumers. The back-end uses a pipeline model to represent workflows since this is a common and useful metaphor used by designers and is easy to manipulate compared to other representations like programming scripts. As an Eclipse Rich Client Platform application, CamBAfx's pipelines and functions can be bundled with the software or downloaded post-installation. The user interface contains all the workflow facilities expected by consumers. Using the Eclipse Extension Mechanism designers are encouraged to customize CamBAfx for their own pipelines. CamBAfx wraps a workflow facility around neuroinformatics software without modification. CamBAfx's design, licensing and Eclipse Branding Mechanism allow it to be used as the user interface for other software, facilitating exchange of innovative computational tools between originating labs. PMID:19826470

The complete digital workflow in fixed prosthodontics: a systematic review.

PubMed

Joda, Tim; Zarone, Fernando; Ferrari, Marco

2017-09-19

The continuous development in dental processing ensures new opportunities in the field of fixed prosthodontics in a complete virtual environment without any physical model situations. The aim was to compare fully digitalized workflows to conventional and/or mixed analog-digital workflows for the treatment with tooth-borne or implant-supported fixed reconstructions. A PICO strategy was executed using an electronic (MEDLINE, EMBASE, Google Scholar) plus manual search up to 2016-09-16 focusing on RCTs investigating complete digital workflows in fixed prosthodontics with regard to economics or esthetics or patient-centered outcomes with or without follow-up or survival/success rate analysis as well as complication assessment of at least 1 year under function. The search strategy was assembled from MeSH-Terms and unspecific free-text words: {(("Dental Prosthesis" [MeSH]) OR ("Crowns" [MeSH]) OR ("Dental Prosthesis, Implant-Supported" [MeSH])) OR ((crown) OR (fixed dental prosthesis) OR (fixed reconstruction) OR (dental bridge) OR (implant crown) OR (implant prosthesis) OR (implant restoration) OR (implant reconstruction))} AND {("Computer-Aided Design" [MeSH]) OR ((digital workflow) OR (digital technology) OR (computerized dentistry) OR (intraoral scan) OR (digital impression) OR (scanbody) OR (virtual design) OR (digital design) OR (cad/cam) OR (rapid prototyping) OR (monolithic) OR (full-contour))} AND {("Dental Technology" [MeSH) OR ((conventional workflow) OR (lost-wax-technique) OR (porcelain-fused-to-metal) OR (PFM) OR (implant impression) OR (hand-layering) OR (veneering) OR (framework))} AND {(("Study, Feasibility" [MeSH]) OR ("Survival" [MeSH]) OR ("Success" [MeSH]) OR ("Economics" [MeSH]) OR ("Costs, Cost Analysis" [MeSH]) OR ("Esthetics, Dental" [MeSH]) OR ("Patient Satisfaction" [MeSH])) OR ((feasibility) OR (efficiency) OR (patient-centered outcome))}. Assessment of risk of bias in selected studies was done at a 'trial level' including random sequence

An Optimized DNA Analysis Workflow for the Sampling, Extraction, and Concentration of DNA obtained from Archived Latent Fingerprints.

PubMed

Solomon, April D; Hytinen, Madison E; McClain, Aryn M; Miller, Marilyn T; Dawson Cruz, Tracey

2018-01-01

DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases. © 2017 American Academy of Forensic Sciences.

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow

PubMed Central

Wonczak, Stephan; Thiele, Holger; Nieroda, Lech; Jabbari, Kamel; Borowski, Stefan; Sinha, Vishal; Gunia, Wilfried; Lang, Ulrich; Achter, Viktor; Nürnberg, Peter

2015-01-01

Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files. PMID:25942438

Identifying impact of software dependencies on replicability of biomedical workflows.

PubMed

Miksa, Tomasz; Rauber, Andreas; Mina, Eleni

2016-12-01

Complex data driven experiments form the basis of biomedical research. Recent findings warn that the context in which the software is run, that is the infrastructure and the third party dependencies, can have a crucial impact on the final results delivered by a computational experiment. This implies that in order to replicate the same result, not only the same data must be used, but also it must be run on an equivalent software stack. In this paper we present the VFramework that enables assessing replicability of workflows. It identifies whether any differences in software dependencies among two executions of the same workflow exist and whether they have impact on the produced results. We also conduct a case study in which we investigate the impact of software dependencies on replicability of Taverna workflows used in biomedical research of Huntington's disease. We re-execute analysed workflows in environments differing in operating system distribution and configuration. The results show that the VFramework can be used to identify the impact of software dependencies on the replicability of biomedical workflows. Furthermore, we observe that despite the fact that the workflows are executed in a controlled environment, they still depend on specific tools installed in the environment. The context model used by the VFramework improves the deficiencies of provenance traces and documents also such tools. Based on our findings we define guidelines for workflow owners that enable them to improve replicability of their workflows. Copyright © 2016 Elsevier Inc. All rights reserved.

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

A computational workflow for designing silicon donor qubits

DOE PAGES

Humble, Travis S.; Ericson, M. Nance; Jakowski, Jacek; ...

2016-09-19

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to performmore » detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. In conclusion, the resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.« less

Workflow in interventional radiology: uterine fibroid embolization (UFE)

NASA Astrophysics Data System (ADS)

Lindisch, David; Neumuth, Thomas; Burgert, Oliver; Spies, James; Cleary, Kevin

2008-03-01

Workflow analysis can be used to record the steps taken during clinical interventions with the goal of identifying bottlenecks and streamlining the procedure efficiency. In this study, we recorded the workflow for uterine fibroid embolization (UFE) procedures in the interventional radiology suite at Georgetown University Hospital in Washington, DC, USA. We employed a custom client/server software architecture developed by the Innovation Center for Computer Assisted Surgery (ICCAS) at the University of Leipzig, Germany. This software runs in a JAVA environment and enables an observer to record the actions taken by the physician and surgical team during these interventions. The data recorded is stored as an XML document, which can then be further processed. We recorded data from 30 patients and found a mean intervention time of 01:49:46 (+/- 16:04) minutes. The critical intervention step, the embolization, had a mean time of 00:15:42 (+/- 05:49) minutes, which was only 15% of the total intervention time.

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

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.

Large-Scale Compute-Intensive Analysis via a Combined In-situ and Co-scheduling Workflow Approach

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

Messer, Bronson; Sewell, Christopher; Heitmann, Katrin

2015-01-01

Large-scale simulations can produce tens of terabytes of data per analysis cycle, complicating and limiting the efficiency of workflows. Traditionally, outputs are stored on the file system and analyzed in post-processing. With the rapidly increasing size and complexity of simulations, this approach faces an uncertain future. Trending techniques consist of performing the analysis in situ, utilizing the same resources as the simulation, and/or off-loading subsets of the data to a compute-intensive analysis system. We introduce an analysis framework developed for HACC, a cosmological N-body code, that uses both in situ and co-scheduling approaches for handling Petabyte-size outputs. An initial inmore » situ step is used to reduce the amount of data to be analyzed, and to separate out the data-intensive tasks handled off-line. The analysis routines are implemented using the PISTON/VTK-m framework, allowing a single implementation of an algorithm that simultaneously targets a variety of GPU, multi-core, and many-core architectures.« less

Teach-Discover-Treat (TDT): Collaborative Computational Drug Discovery for Neglected Diseases

PubMed Central

Jansen, Johanna M.; Cornell, Wendy; Tseng, Y. Jane; Amaro, Rommie E.

2012-01-01

Teach – Discover – Treat (TDT) is an initiative to promote the development and sharing of computational tools solicited through a competition with the aim to impact education and collaborative drug discovery for neglected diseases. Collaboration, multidisciplinary integration, and innovation are essential for successful drug discovery. This requires a workforce that is trained in state-of-the-art workflows and equipped with the ability to collaborate on platforms that are accessible and free. The TDT competition solicits high quality computational workflows for neglected disease targets, using freely available, open access tools. PMID:23085175

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.

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.

A Metric and Workflow for Quality Control in the Analysis of Heterogeneity in Phenotypic Profiles and Screens

PubMed Central

Gough, Albert; Shun, Tongying; Taylor, D. Lansing; Schurdak, Mark

2016-01-01

Heterogeneity is well recognized as a common property of cellular systems that impacts biomedical research and the development of therapeutics and diagnostics. Several studies have shown that analysis of heterogeneity: gives insight into mechanisms of action of perturbagens; can be used to predict optimal combination therapies; and to quantify heterogeneity in tumors where heterogeneity is believed to be associated with adaptation and resistance. Cytometry methods including high content screening (HCS), high throughput microscopy, flow cytometry, mass spec imaging and digital pathology capture cell level data for populations of cells. However it is often assumed that the population response is normally distributed and therefore that the average adequately describes the results. A deeper understanding of the results of the measurements and more effective comparison of perturbagen effects requires analysis that takes into account the distribution of the measurements, i.e. the heterogeneity. However, the reproducibility of heterogeneous data collected on different days, and in different plates/slides has not previously been evaluated. Here we show that conventional assay quality metrics alone are not adequate for quality control of the heterogeneity in the data. To address this need, we demonstrate the use of the Kolmogorov-Smirnov statistic as a metric for monitoring the reproducibility of heterogeneity in an SAR screen, describe a workflow for quality control in heterogeneity analysis. One major challenge in high throughput biology is the evaluation and interpretation of heterogeneity in thousands of samples, such as compounds in a cell-based screen. In this study we also demonstrate that three heterogeneity indices previously reported, capture the shapes of the distributions and provide a means to filter and browse big data sets of cellular distributions in order to compare and identify distributions of interest. These metrics and methods are presented as a

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

DOE PAGES

Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge; ...

2016-05-19

Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proofmore » of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks.« less

SU-E-T-419: Workflow and FMEA in a New Proton Therapy (PT) Facility

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

Cheng, C; Wessels, B; Hamilton, H

2014-06-01

Purpose: Workflow is an important component in the operational planning of a new proton facility. By integrating the concept of failure mode and effect analysis (FMEA) and traditional QA requirements, a workflow for a proton therapy treatment course is set up. This workflow serves as the blue print for the planning of computer hardware/software requirements and network flow. A slight modification of the workflow generates a process map(PM) for FMEA and the planning of QA program in PT. Methods: A flowchart is first developed outlining the sequence of processes involved in a PT treatment course. Each process consists of amore » number of sub-processes to encompass a broad scope of treatment and QA procedures. For each subprocess, the personnel involved, the equipment needed and the computer hardware/software as well as network requirements are defined by a team of clinical staff, administrators and IT personnel. Results: Eleven intermediate processes with a total of 70 sub-processes involved in a PT treatment course are identified. The number of sub-processes varies, ranging from 2-12. The sub-processes within each process are used for the operational planning. For example, in the CT-Sim process, there are 12 sub-processes: three involve data entry/retrieval from a record-and-verify system, two controlled by the CT computer, two require department/hospital network, and the other five are setup procedures. IT then decides the number of computers needed and the software and network requirement. By removing the traditional QA procedures from the workflow, a PM is generated for FMEA analysis to design a QA program for PT. Conclusion: Significant efforts are involved in the development of the workflow in a PT treatment course. Our hybrid model of combining FMEA and traditional QA program serves a duo purpose of efficient operational planning and designing of a QA program in PT.« less

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

The MPO system for automatic workflow documentation

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

Abla, G.; Coviello, E. N.; Flanagan, S. M.

Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for critical applications. However, it is not the mere existence of data that is important, but our ability to make use of it. Experience has shown that when metadata is better organized and more complete, the underlying data becomes more useful. Traditionally, capturing the steps of scientific workflows and metadata was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing, and annotation. Here, this article presents the Metadata, Provenance, and Ontology (MPO) System, the softwaremore » that can automate the documentation of scientific workflows and associated information. Based on recorded metadata, it provides explicit information about the relationships among the elements of workflows in notebook form augmented with directed acyclic graphs. A set of web-based graphical navigation tools and Application Programming Interface (API) have been created for searching and browsing, as well as programmatically accessing the workflows and data. We describe the MPO concepts and its software architecture. We also report the current status of the software as well as the initial deployment experience.« less

The MPO system for automatic workflow documentation

DOE PAGES

Abla, G.; Coviello, E. N.; Flanagan, S. M.; ...

2016-04-18

Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for critical applications. However, it is not the mere existence of data that is important, but our ability to make use of it. Experience has shown that when metadata is better organized and more complete, the underlying data becomes more useful. Traditionally, capturing the steps of scientific workflows and metadata was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing, and annotation. Here, this article presents the Metadata, Provenance, and Ontology (MPO) System, the softwaremore » that can automate the documentation of scientific workflows and associated information. Based on recorded metadata, it provides explicit information about the relationships among the elements of workflows in notebook form augmented with directed acyclic graphs. A set of web-based graphical navigation tools and Application Programming Interface (API) have been created for searching and browsing, as well as programmatically accessing the workflows and data. We describe the MPO concepts and its software architecture. We also report the current status of the software as well as the initial deployment experience.« less

Successful adaption of a forensic toxicological screening workflow employing nontargeted liquid chromatography-tandem mass spectrometry to water analysis.

PubMed

Steger, Julia; Arnhard, Kathrin; Haslacher, Sandra; Geiger, Klemens; Singer, Klaus; Schlapp, Michael; Pitterl, Florian; Oberacher, Herbert

2016-04-01

Forensic toxicology and environmental water analysis share the common interest and responsibility in ensuring comprehensive and reliable confirmation of drugs and pharmaceutical compounds in samples analyzed. Dealing with similar analytes, detection and identification techniques should be exchangeable between scientific disciplines. Herein, we demonstrate the successful adaption of a forensic toxicological screening workflow employing nontargeted LC/MS/MS under data-dependent acquisition control and subsequent database search to water analysis. The main modification involved processing of an increased sample volume with SPE (500 mL vs. 1-10 mL) to reach LODs in the low ng/L range. Tandem mass spectra acquired with a qTOF instrument were submitted to database search. The targeted data mining strategy was found to be sensitive and specific; automated search produced hardly any false results. To demonstrate the applicability of the adapted workflow to complex samples, 14 wastewater effluent samples collected on seven consecutive days at the local wastewater-treatment plant were analyzed. Of the 88,970 fragment ion mass spectra produced, 8.8% of spectra were successfully assigned to one of the 1040 reference compounds included in the database, and this enabled the identification of 51 compounds representing important illegal drugs, members of various pharmaceutical compound classes, and metabolites thereof. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrating prediction, provenance, and optimization into high energy workflows

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

Schram, M.; Bansal, V.; Friese, R. D.

We propose a novel approach for efficient execution of workflows on distributed resources. The key components of this framework include: performance modeling to quantitatively predict workflow component behavior; optimization-based scheduling such as choosing an optimal subset of resources to meet demand and assignment of tasks to resources; distributed I/O optimizations such as prefetching; and provenance methods for collecting performance data. In preliminary results, these techniques improve throughput on a small Belle II workflow by 20%.

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

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

PubMed

Aranguren, Mikel Egaña; Wilkinson, Mark D

2015-01-01

Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

PubMed Central

Callahan, Ben J.; Sankaran, Kris; Fukuyama, Julia A.; McMurdie, Paul J.; Holmes, Susan P.

2016-01-01

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork package. PMID:27508062

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data

PubMed Central

2014-01-01

Background Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Analysis of raw microarray data files (e.g. Affymetrix CEL files) can be time consuming, complex, and requires fundamental computational and bioinformatics skills. The development of analytical workflows to automate these tasks simplifies the processing of, improves the efficiency of, and serves to standardize multiple and sequential analyses. Once installed, workflows facilitate the tedious steps required to run rapid intra- and inter-dataset comparisons. Results We developed a workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray Data analysis (MAAMD) in Kepler. Two freely available stand-alone software tools, R and AltAnalyze were embedded in MAAMD. The inputs of MAAMD are user-editable csv files, which contain sample information and parameters describing the locations of input files and required tools. MAAMD was tested by analyzing 4 different GEO datasets from mice and drosophila. MAAMD automates data downloading, data organization, data quality control assesment, differential gene expression analysis, clustering analysis, pathway visualization, gene-set enrichment analysis, and cross-species orthologous-gene comparisons. MAAMD was utilized to identify gene orthologues responding to hypoxia or hyperoxia in both mice and drosophila. The entire set of analyses for 4 datasets (34 total microarrays) finished in ~ one hour. Conclusions MAAMD saves time, minimizes the required computer skills, and offers a standardized procedure for users to analyze microarray datasets and make new intra- and inter-dataset comparisons. PMID:24621103

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.

PubMed

Cormier, Nathan; Kolisnik, Tyler; Bieda, Mark

2016-07-05

There has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized graphical outputs. A number of systems have emphasized custom development of ChIP-seq pipelines. These systems are primarily based on custom programming of a single, complex pipeline or supply libraries of modules and do not produce the full range of outputs commonly produced for ChIP-seq datasets. It is desirable to have more comprehensive pipelines, in particular ones addressing common metadata tasks, such as pathway analysis, and pipelines producing standard complex graphical outputs. It is advantageous if these are highly modular systems, available as both turnkey pipelines and individual modules, that are easily comprehensible, modifiable and extensible to allow rapid alteration in response to new analysis developments in this growing area. Furthermore, it is advantageous if these pipelines allow data provenance tracking. We present a set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full turnkey pipelines and 16 component modules. The turnkey pipelines in Kepler allow data provenance tracking. Implementation emphasized use of common R packages and widely-used external tools (e.g., MACS for peak finding), along with custom programming. This software presents comprehensive solutions and easily repurposed code blocks for ChIP-seq analysis and pipeline creation. Tasks include mapping raw reads, peakfinding via MACS, summary statistics, peak location statistics, summary plots centered on the transcription start site (TSS), gene ontology, pathway analysis, and de novo motif finding, among others. These pipelines range from those performing a single task to those performing full analyses of

Common Data Models and Efficient Reproducible Workflows for Distributed Ocean Model Skill Assessment

NASA Astrophysics Data System (ADS)

Signell, R. P.; Snowden, D. P.; Howlett, E.; Fernandes, F. A.

2014-12-01

Model skill assessment requires discovery, access, analysis, and visualization of information from both sensors and models, and traditionally has been possible only by a few experts. The US Integrated Ocean Observing System (US-IOOS) consists of 17 Federal Agencies and 11 Regional Associations that produce data from various sensors and numerical models; exactly the information required for model skill assessment. US-IOOS is seeking to develop documented skill assessment workflows that are standardized, efficient, and reproducible so that a much wider community can participate in the use and assessment of model results. Standardization requires common data models for observational and model data. US-IOOS relies on the CF Conventions for observations and structured grid data, and on the UGRID Conventions for unstructured (e.g. triangular) grid data. This allows applications to obtain only the data they require in a uniform and parsimonious way using web services: OPeNDAP for model output and OGC Sensor Observation Service (SOS) for observed data. Reproducibility is enabled with IPython Notebooks shared on GitHub (http://github.com/ioos). These capture the entire skill assessment workflow, including user input, search, access, analysis, and visualization, ensuring that workflows are self-documenting and reproducible by anyone, using free software. Python packages for common data models are Pyugrid and the British Met Office Iris package. Python packages required to run the workflows (pyugrid, pyoos, and the British Met Office Iris package) are also available on GitHub and on Binstar.org so that users can run scenarios using the free Anaconda Python distribution. Hosted services such as Wakari enable anyone to reproduce these workflows for free, without installing any software locally, using just their web browser. We are also experimenting with Wakari Enterprise, which allows multi-user access from a web browser to an IPython Server running where large quantities of

Principal Component Clustering Approach to Teaching Quality Discriminant Analysis

ERIC Educational Resources Information Center

Xian, Sidong; Xia, Haibo; Yin, Yubo; Zhai, Zhansheng; Shang, Yan

2016-01-01

Teaching quality is the lifeline of the higher education. Many universities have made some effective achievement about evaluating the teaching quality. In this paper, we establish the Students' evaluation of teaching (SET) discriminant analysis model and algorithm based on principal component clustering analysis. Additionally, we classify the SET…

Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge.

PubMed

Lin, Chi-Hung; Krisp, Christoph; Packer, Nicolle H; Molloy, Mark P

2018-02-10

Glycoproteomics investigates glycan moieties in a site specific manner to reveal the functional roles of protein glycosylation. Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. In this study, we investigated pseudo-MRM (MRM-HR) and data-independent acquisition (DIA) as alternative acquisition strategies for glycopeptide analysis. These approaches allow data acquisition over the full MS/MS scan range allowing data re-analysis post-acquisition, without data re-acquisition. The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. To overcome the duty cycle limitation of MRM-HR acquisition needed for analysis of complex samples such as plasma we trialed DIA. This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. We developed a data-independent mass spectrometry workflow to identify specific glycopeptides from complex biological mixtures. The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. This is demonstrated through the analysis of immunoglobulins in human plasma where we detected two IgG1 glycoforms that are rarely observed. Copyright © 2017 Elsevier B.V. All rights reserved.

A framework for streamlining research workflow in neuroscience and psychology

PubMed Central

Kubilius, Jonas

2014-01-01

Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on ad-hoc workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce psychopy_ext, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tools by choosing reasonable defaults and implementing relatively rigid patterns of workflow. This structure allows for automation of multiple tasks, such as generated user interfaces, unit testing, control analyses of stimuli, single-command access to descriptive statistics, and publication quality plotting. Taken together, psychopy_ext opens an exciting possibility for a faster, more robust code development and collaboration for researchers. PMID:24478691

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

MetaboLyzer: A Novel Statistical Workflow for Analyzing Post-Processed LC/MS Metabolomics Data

PubMed Central

Mak, Tytus D.; Laiakis, Evagelia C.; Goudarzi, Maryam; Fornace, Albert J.

2014-01-01

Metabolomics, the global study of small molecules in a particular system, has in the last few years risen to become a primary –omics platform for the study of metabolic processes. With the ever-increasing pool of quantitative data yielded from metabolomic research, specialized methods and tools with which to analyze and extract meaningful conclusions from these data are becoming more and more crucial. Furthermore, the depth of knowledge and expertise required to undertake a metabolomics oriented study is a daunting obstacle to investigators new to the field. As such, we have created a new statistical analysis workflow, MetaboLyzer, which aims to both simplify analysis for investigators new to metabolomics, as well as provide experienced investigators the flexibility to conduct sophisticated analysis. MetaboLyzer’s workflow is specifically tailored to the unique characteristics and idiosyncrasies of postprocessed liquid chromatography/mass spectrometry (LC/MS) based metabolomic datasets. It utilizes a wide gamut of statistical tests, procedures, and methodologies that belong to classical biostatistics, as well as several novel statistical techniques that we have developed specifically for metabolomics data. Furthermore, MetaboLyzer conducts rapid putative ion identification and putative biologically relevant analysis via incorporation of four major small molecule databases: KEGG, HMDB, Lipid Maps, and BioCyc. MetaboLyzer incorporates these aspects into a comprehensive workflow that outputs easy to understand statistically significant and potentially biologically relevant information in the form of heatmaps, volcano plots, 3D visualization plots, correlation maps, and metabolic pathway hit histograms. For demonstration purposes, a urine metabolomics data set from a previously reported radiobiology study in which samples were collected from mice exposed to gamma radiation was analyzed. MetaboLyzer was able to identify 243 statistically significant ions out of a

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

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

Teaching Instrumentation and Methodology in Human Motion Analysis

DTIC Science & Technology

2001-10-25

TEACHING INSTRUMENTATION AND METHODOLOGY IN HUMAN MOTION ANALYSIS V. Medved Faculty of Physical Education , University of Zagreb, Zagreb, Croatia...the introducement of teaching curricula to implement the apropriate knowledge. Problems are discussed of educating professionals and disseminating...University of Zagreb, undergraduate teaching of locomotion biomechanics is provided only at the Faculty of Physical Education . Following a need to teach

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.

Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.

PubMed

Davidson, Robert L; Weber, Ralf J M; Liu, Haoyu; Sharma-Oates, Archana; Viant, Mark R

2016-01-01

Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardization and reproducibility of computational metabolomics tools must be improved significantly. Here we present our end-to-end mass spectrometry metabolomics workflow in the widely used platform, Galaxy. Named Galaxy-M, our workflow has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. The range of tools presented spans from processing of raw data, e.g. peak picking and alignment, through data cleansing, e.g. missing value imputation, to preparation for statistical analysis, e.g. normalization and scaling, and principal components analysis (PCA) with associated statistical evaluation. We demonstrate the ease of using these Galaxy workflows via the analysis of DIMS and LC-MS datasets, and provide PCA scores and associated statistics to help other users to ensure that they can accurately repeat the processing and analysis of these two datasets. Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub. The Galaxy platform has enabled us to produce an easily accessible and reproducible computational metabolomics workflow. More tools could be added by the community to expand its functionality. We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility.

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

Optimizing high performance computing workflow for protein functional annotation

PubMed Central

Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

2014-01-01

Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data. PMID:25313296

Optimizing high performance computing workflow for protein functional annotation.

PubMed

Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

2014-09-10

Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P.

2011-01-01

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. PMID:21546552

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

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

The impact of electronic medical record systems on outpatient workflows: a longitudinal evaluation of its workflow effects.

PubMed

Vishwanath, Arun; Singh, Sandeep Rajan; Winkelstein, Peter

2010-11-01

The promise of the electronic medical record (EMR) lies in its ability to reduce the costs of health care delivery and improve the overall quality of care--a promise that is realized through major changes in workflows within the health care organization. Yet little systematic information exists about the workflow effects of EMRs. Moreover, some of the research to-date points to reduced satisfaction among physicians after implementation of the EMR and increased time, i.e., negative workflow effects. A better understanding of the impact of the EMR on workflows is, hence, vital to understanding what the technology really does offer that is new and unique. (i) To empirically develop a physician centric conceptual model of the workflow effects of EMRs; (ii) To use the model to understand the antecedents to the physicians' workflow expectation from the new EMR; (iii) To track physicians' satisfaction overtime, 3 months and 20 months after implementation of the EMR; (iv) To explore the impact of technology learning curves on physicians' reported satisfaction levels. The current research uses the mixed-method technique of concept mapping to empirically develop the conceptual model of an EMR's workflow effects. The model is then used within a controlled study to track physician expectations from a new EMR system as well as their assessments of the EMR's performance 3 months and 20 months after implementation. The research tracks the actual implementation of a new EMR within the outpatient clinics of a large northeastern research hospital. The pre-implementation survey netted 20 physician responses; post-implementation Time 1 survey netted 22 responses, and Time 2 survey netted 26 physician responses. The implementation of the actual EMR served as the intervention. Since the study was conducted within the same setting and tracked a homogenous group of respondents, the overall study design ensured against extraneous influences on the results. Outcome measures were derived

A practical workflow for making anatomical atlases for biological research.

PubMed

Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

2012-01-01

The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

A data-independent acquisition workflow for qualitative screening of new psychoactive substances in biological samples.

PubMed

Kinyua, Juliet; Negreira, Noelia; Ibáñez, María; Bijlsma, Lubertus; Hernández, Félix; Covaci, Adrian; van Nuijs, Alexander L N

2015-11-01

Identification of new psychoactive substances (NPS) is challenging. Developing targeted methods for their analysis can be difficult and costly due to their impermanence on the drug scene. Accurate-mass mass spectrometry (AMMS) using a quadrupole time-of-flight (QTOF) analyzer can be useful for wide-scope screening since it provides sensitive, full-spectrum MS data. Our article presents a qualitative screening workflow based on data-independent acquisition mode (all-ions MS/MS) on liquid chromatography (LC) coupled to QTOFMS for the detection and identification of NPS in biological matrices. The workflow combines and structures fundamentals of target and suspect screening data processing techniques in a structured algorithm. This allows the detection and tentative identification of NPS and their metabolites. We have applied the workflow to two actual case studies involving drug intoxications where we detected and confirmed the parent compounds ketamine, 25B-NBOMe, 25C-NBOMe, and several predicted phase I and II metabolites not previously reported in urine and serum samples. The screening workflow demonstrates the added value for the detection and identification of NPS in biological matrices.

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.

Development of HEATHER for cochlear implant stimulation using a new modeling workflow.

PubMed

Tran, Phillip; Sue, Andrian; Wong, Paul; Li, Qing; Carter, Paul

2015-02-01

The current conduction pathways resulting from monopolar stimulation of the cochlear implant were studied by developing a human electroanatomical total head reconstruction (namely, HEATHER). HEATHER was created from serially sectioned images of the female Visible Human Project dataset to encompass a total of 12 different tissues, and included computer-aided design geometries of the cochlear implant. Since existing methods were unable to generate the required complexity for HEATHER, a new modeling workflow was proposed. The results of the finite-element analysis agree with the literature, showing that the injected current exits the cochlea via the modiolus (14%), the basal end of the cochlea (22%), and through the cochlear walls (64%). It was also found that, once leaving the cochlea, the current travels to the implant body via the cranial cavity or scalp. The modeling workflow proved to be robust and flexible, allowing for meshes to be generated with substantial user control. Furthermore, the workflow could easily be employed to create realistic anatomical models of the human head for different bioelectric applications, such as deep brain stimulation, electroencephalography, and other biophysical phenomena.

A practical data processing workflow for multi-OMICS projects.

PubMed

Kohl, Michael; Megger, Dominik A; Trippler, Martin; Meckel, Hagen; Ahrens, Maike; Bracht, Thilo; Weber, Frank; Hoffmann, Andreas-Claudius; Baba, Hideo A; Sitek, Barbara; Schlaak, Jörg F; Meyer, Helmut E; Stephan, Christian; Eisenacher, Martin

2014-01-01

Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques. This article is part of a Special Issue entitled: Computational Proteomics in the Post

Research Infrastructure for Collaborative Team Science: Challenges in Technology-Supported Workflows in and Across Laboratories, Institutions, and Geographies.

PubMed

Mirel, Barbara; Luo, Airong; Harris, Marcelline

2015-05-01

Collaborative research has many challenges. One under-researched challenge is how to align collaborators' research practices and evolving analytical reasoning with technologies and configurations of technologies that best support them. The goal of such alignment is to enhance collaborative problem solving capabilities in research. Toward this end, we draw on our own research and a synthesis of the literature to characterize the workflow of collaborating scientists in systems-level renal disease research. We describe the various phases of a hypothetical workflow among diverse collaborators within and across laboratories, extending from their primary analysis through secondary analysis. For each phase, we highlight required technology supports, and. At time, complementary organizational supports. This survey of supports matching collaborators' analysis practices and needs in research projects to technological support is preliminary, aimed ultimately at developing a research capability framework that can help scientists and technologists mutually understand workflows and technologies that can help enable and enhance them. Copyright © 2015 Elsevier Inc. All rights reserved.

A lightweight messaging-based distributed processing and workflow execution framework for real-time and big data analysis

NASA Astrophysics Data System (ADS)

Laban, Shaban; El-Desouky, Aly

2014-05-01

To achieve a rapid, simple and reliable parallel processing of different types of tasks and big data processing on any compute cluster, a lightweight messaging-based distributed applications processing and workflow execution framework model is proposed. The framework is based on Apache ActiveMQ and Simple (or Streaming) Text Oriented Message Protocol (STOMP). ActiveMQ , a popular and powerful open source persistence messaging and integration patterns server with scheduler capabilities, acts as a message broker in the framework. STOMP provides an interoperable wire format that allows framework programs to talk and interact between each other and ActiveMQ easily. In order to efficiently use the message broker a unified message and topic naming pattern is utilized to achieve the required operation. Only three Python programs and simple library, used to unify and simplify the implementation of activeMQ and STOMP protocol, are needed to use the framework. A watchdog program is used to monitor, remove, add, start and stop any machine and/or its different tasks when necessary. For every machine a dedicated one and only one zoo keeper program is used to start different functions or tasks, stompShell program, needed for executing the user required workflow. The stompShell instances are used to execute any workflow jobs based on received message. A well-defined, simple and flexible message structure, based on JavaScript Object Notation (JSON), is used to build any complex workflow systems. Also, JSON format is used in configuration, communication between machines and programs. The framework is platform independent. Although, the framework is built using Python the actual workflow programs or jobs can be implemented by any programming language. The generic framework can be used in small national data centres for processing seismological and radionuclide data received from the International Data Centre (IDC) of the Preparatory Commission for the Comprehensive Nuclear

Teaching with Stereoscopic Video: Opportunities and Challenges

NASA Astrophysics Data System (ADS)

Variano, Evan

2017-11-01

I will present my work on creating stereoscopic videos for fluid pedagogy. I discuss a variety of workflows for content creation and a variety of platforms for content delivery. I review the qualitative lessons learned when teaching with this material, and discuss outlook for the future. This work was partially supported by the NSF award ENG-1604026 and the UC Berkeley Student Technology Fund.

A software tool to analyze clinical workflows from direct observations.

PubMed

Schweitzer, Marco; Lasierra, Nelia; Hoerbst, Alexander

2015-01-01

Observational data of clinical processes need to be managed in a convenient way, so that process information is reliable, valid and viable for further analysis. However, existing tools for allocating observations fail in systematic data collection of specific workflow recordings. We present a software tool which was developed to facilitate the analysis of clinical process observations. The tool was successfully used in the project OntoHealth, to build, store and analyze observations of diabetes routine consultations.

Using Importance-Performance Analysis To Evaluate Teaching Effectiveness.

ERIC Educational Resources Information Center

Attarian, Aram

This paper introduces Importance-Performance (IP) analysis as a method to evaluate teaching effectiveness in a university outdoor program. Originally developed for use in the field of marketing, IP analysis is simple and easy to administer, and provides the instructor with a visual representation of what teaching attributes are important, how…

Sensor-based architecture for medical imaging workflow analysis.

PubMed

Silva, Luís A Bastião; Campos, Samuel; Costa, Carlos; Oliveira, José Luis

2014-08-01

The growing use of computer systems in medical institutions has been generating a tremendous quantity of data. While these data have a critical role in assisting physicians in the clinical practice, the information that can be extracted goes far beyond this utilization. This article proposes a platform capable of assembling multiple data sources within a medical imaging laboratory, through a network of intelligent sensors. The proposed integration framework follows a SOA hybrid architecture based on an information sensor network, capable of collecting information from several sources in medical imaging laboratories. Currently, the system supports three types of sensors: DICOM repository meta-data, network workflows and examination reports. Each sensor is responsible for converting unstructured information from data sources into a common format that will then be semantically indexed in the framework engine. The platform was deployed in the Cardiology department of a central hospital, allowing identification of processes' characteristics and users' behaviours that were unknown before the utilization of this solution.

A Workflow to Investigate Exposure and Pharmacokinetic ...

EPA Pesticide Factsheets

Background: Adverse outcome pathways (AOPs) link adverse effects in individuals or populations to a molecular initiating event (MIE) that can be quantified using in vitro methods. Practical application of AOPs in chemical-specific risk assessment requires incorporation of knowledge on exposure, along with absorption, distribution, metabolism, and excretion (ADME) properties of chemicals.Objectives: We developed a conceptual workflow to examine exposure and ADME properties in relation to an MIE. The utility of this workflow was evaluated using a previously established AOP, acetylcholinesterase (AChE) inhibition.Methods: Thirty chemicals found to inhibit human AChE in the ToxCast™ assay were examined with respect to their exposure, absorption potential, and ability to cross the blood–brain barrier (BBB). Structures of active chemicals were compared against structures of 1,029 inactive chemicals to detect possible parent compounds that might have active metabolites.Results: Application of the workflow screened 10 “low-priority” chemicals of 30 active chemicals. Fifty-two of the 1,029 inactive chemicals exhibited a similarity threshold of ≥ 75% with their nearest active neighbors. Of these 52 compounds, 30 were excluded due to poor absorption or distribution. The remaining 22 compounds may inhibit AChE in vivo either directly or as a result of metabolic activation.Conclusions: The incorporation of exposure and ADME properties into the conceptual workflow e

Integrate Data into Scientific Workflows for Terrestrial Biosphere Model Evaluation through Brokers

NASA Astrophysics Data System (ADS)

Wei, Y.; Cook, R. B.; Du, F.; Dasgupta, A.; Poco, J.; Huntzinger, D. N.; Schwalm, C. R.; Boldrini, E.; Santoro, M.; Pearlman, J.; Pearlman, F.; Nativi, S.; Khalsa, S.

2013-12-01

Terrestrial biosphere models (TBMs) have become integral tools for extrapolating local observations and process-level understanding of land-atmosphere carbon exchange to larger regions. Model-model and model-observation intercomparisons are critical to understand the uncertainties within model outputs, to improve model skill, and to improve our understanding of land-atmosphere carbon exchange. The DataONE Exploration, Visualization, and Analysis (EVA) working group is evaluating TBMs using scientific workflows in UV-CDAT/VisTrails. This workflow-based approach promotes collaboration and improved tracking of evaluation provenance. But challenges still remain. The multi-scale and multi-discipline nature of TBMs makes it necessary to include diverse and distributed data resources in model evaluation. These include, among others, remote sensing data from NASA, flux tower observations from various organizations including DOE, and inventory data from US Forest Service. A key challenge is to make heterogeneous data from different organizations and disciplines discoverable and readily integrated for use in scientific workflows. This presentation introduces the brokering approach taken by the DataONE EVA to fill the gap between TBMs' evaluation scientific workflows and cross-organization and cross-discipline data resources. The DataONE EVA started the development of an Integrated Model Intercomparison Framework (IMIF) that leverages standards-based discovery and access brokers to dynamically discover, access, and transform (e.g. subset and resampling) diverse data products from DataONE, Earth System Grid (ESG), and other data repositories into a format that can be readily used by scientific workflows in UV-CDAT/VisTrails. The discovery and access brokers serve as an independent middleware that bridge existing data repositories and TBMs evaluation scientific workflows but introduce little overhead to either component. In the initial work, an OpenSearch-based discovery broker

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

Developing a workflow to identify inconsistencies in volunteered geographic information: a phenological case study

USGS Publications Warehouse

Mehdipoor, Hamed; Zurita-Milla, Raul; Rosemartin, Alyssa; Gerst, Katharine L.; Weltzin, Jake F.

2015-01-01

Recent improvements in online information communication and mobile location-aware technologies have led to the production of large volumes of volunteered geographic information. Widespread, large-scale efforts by volunteers to collect data can inform and drive scientific advances in diverse fields, including ecology and climatology. Traditional workflows to check the quality of such volunteered information can be costly and time consuming as they heavily rely on human interventions. However, identifying factors that can influence data quality, such as inconsistency, is crucial when these data are used in modeling and decision-making frameworks. Recently developed workflows use simple statistical approaches that assume that the majority of the information is consistent. However, this assumption is not generalizable, and ignores underlying geographic and environmental contextual variability that may explain apparent inconsistencies. Here we describe an automated workflow to check inconsistency based on the availability of contextual environmental information for sampling locations. The workflow consists of three steps: (1) dimensionality reduction to facilitate further analysis and interpretation of results, (2) model-based clustering to group observations according to their contextual conditions, and (3) identification of inconsistent observations within each cluster. The workflow was applied to volunteered observations of flowering in common and cloned lilac plants (Syringa vulgaris and Syringa x chinensis) in the United States for the period 1980 to 2013. About 97% of the observations for both common and cloned lilacs were flagged as consistent, indicating that volunteers provided reliable information for this case study. Relative to the original dataset, the exclusion of inconsistent observations changed the apparent rate of change in lilac bloom dates by two days per decade, indicating the importance of inconsistency checking as a key step in data quality

A Drupal-Based Collaborative Framework for Science Workflows

NASA Astrophysics Data System (ADS)

Pinheiro da Silva, P.; Gandara, A.

2010-12-01

Cyber-infrastructure is built from utilizing technical infrastructure to support organizational practices and social norms to provide support for scientific teams working together or dependent on each other to conduct scientific research. Such cyber-infrastructure enables the sharing of information and data so that scientists can leverage knowledge and expertise through automation. Scientific workflow systems have been used to build automated scientific systems used by scientists to conduct scientific research and, as a result, create artifacts in support of scientific discoveries. These complex systems are often developed by teams of scientists who are located in different places, e.g., scientists working in distinct buildings, and sometimes in different time zones, e.g., scientist working in distinct national laboratories. The sharing of these specifications is currently supported by the use of version control systems such as CVS or Subversion. Discussions about the design, improvement, and testing of these specifications, however, often happen elsewhere, e.g., through the exchange of email messages and IM chatting. Carrying on a discussion about these specifications is challenging because comments and specifications are not necessarily connected. For instance, the person reading a comment about a given workflow specification may not be able to see the workflow and even if the person can see the workflow, the person may not specifically know to which part of the workflow a given comments applies to. In this paper, we discuss the design, implementation and use of CI-Server, a Drupal-based infrastructure, to support the collaboration of both local and distributed teams of scientists using scientific workflows. CI-Server has three primary goals: to enable information sharing by providing tools that scientists can use within their scientific research to process data, publish and share artifacts; to build community by providing tools that support discussions between

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

Big data analytics workflow management for eScience

NASA Astrophysics Data System (ADS)

Fiore, Sandro; D'Anca, Alessandro; Palazzo, Cosimo; Elia, Donatello; Mariello, Andrea; Nassisi, Paola; Aloisio, Giovanni

2015-04-01

In many domains such as climate and astrophysics, scientific data is often n-dimensional and requires tools that support specialized data types and primitives if it is to be properly stored, accessed, analysed and visualized. Currently, scientific data analytics relies on domain-specific software and libraries providing a huge set of operators and functionalities. However, most of these software fail at large scale since they: (i) are desktop based, rely on local computing capabilities and need the data locally; (ii) cannot benefit from available multicore/parallel machines since they are based on sequential codes; (iii) do not provide declarative languages to express scientific data analysis tasks, and (iv) do not provide newer or more scalable storage models to better support the data multidimensionality. Additionally, most of them: (v) are domain-specific, which also means they support a limited set of data formats, and (vi) do not provide a workflow support, to enable the construction, execution and monitoring of more 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 several parallel operators to manipulate large datasets. Some relevant examples include: (i) data sub-setting (slicing and dicing), (ii) data aggregation, (iii) array-based primitives (the same operator applies to all the implemented UDF extensions), (iv) data cube duplication, (v) data cube pivoting, (vi) NetCDF-import and export. Metadata operators are available too. Additionally, the Ophidia framework provides array-based primitives to perform data sub-setting, data aggregation (i.e. max, min, avg), array concatenation, algebraic expressions and predicate evaluation on large arrays of scientific data. Bit-oriented plugins have also been implemented to manage binary data cubes. Defining processing chains and workflows with tens, hundreds of data analytics operators is the

High-volume workflow management in the ITN/FBI system

NASA Astrophysics Data System (ADS)

Paulson, Thomas L.

1997-02-01

The Identification Tasking and Networking (ITN) Federal Bureau of Investigation system will manage the processing of more than 70,000 submissions per day. The workflow manager controls the routing of each submission through a combination of automated and manual processing steps whose exact sequence is dynamically determined by the results at each step. For most submissions, one or more of the steps involve the visual comparison of fingerprint images. The ITN workflow manager is implemented within a scaleable client/server architecture. The paper describes the key aspects of the ITN workflow manager design which allow the high volume of daily processing to be successfully accomplished.

A Framework for Modeling Workflow Execution by an Interdisciplinary Healthcare Team.

PubMed

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

2015-01-01

The use of business workflow models in healthcare is limited because of insufficient capture of complexities associated with behavior of interdisciplinary healthcare teams that execute healthcare workflows. In this paper we present a novel framework that builds on the well-founded business workflow model formalism and related infrastructures and introduces a formal semantic layer that describes selected aspects of team dynamics and supports their real-time operationalization.

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.

Thematic Progression Analysis in Teaching Explanation Writing

ERIC Educational Resources Information Center

Yang, Xueqian

2008-01-01

Thematic Progression theory explains textual meanings of how experiential and interpersonal meanings are organized in a linear and coherent way. Employing the rationale of T-P theory, this article analyses a lesson plan of teaching Explanation, and shows that T-P analysis can be employed in teaching writing.

How does peer teaching compare to faculty teaching? A systematic review and meta-analysis (.).

PubMed

Rees, Eliot L; Quinn, Patrick J; Davies, Benjamin; Fotheringham, Victoria

2016-08-01

In undergraduate medical education, peer-teaching has become an established and common method to enhance student learning. Evidence suggests that peer-teaching provides learning benefits for both learners and tutors. We aimed to describe the outcomes for medical students taught by peers through systematic review and meta-analysis of existing literature. Seven databases were searched through 21 terms and their Boolean combinations. Studies reporting knowledge or skills outcomes of students taught by peers compared to those taught by faculty or qualified clinicians were included. Extracted data on students' knowledge and skills outcomes were synthesised through a random effects model meta-analysis. The search yielded 2292 studies. Five hundred and fifty-three duplicates and 1611 irrelevant articles were removed during title-screening. The abstracts of 128 papers were screened against the inclusion and exclusion criteria. Ten studies have been included in the review. Meta-analyses showed no significant difference in peer-teaching compared to faculty teaching for knowledge or skills outcomes, standardised mean differences were 0.07 (95% CI: -0.07, 0.21) and 0.11 (95% CI: -0.07, 1.29), respectively. Students taught by peers do not have significantly different outcomes to those taught by faculty. As the process of teaching helps to develop both tutor knowledge and teaching skills, peer-teaching should be supported.

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.

An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

PubMed Central

Li, Jian; Batcha, Aarif Mohamed Nazeer; Grüning, Björn; Mansmann, Ulrich R.

2015-01-01

Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility. PMID:27081306

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.

An Adaptable Seismic Data Format for Modern Scientific Workflows

NASA Astrophysics Data System (ADS)

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

2013-12-01

Data storage, exchange, and access play a critical role in modern seismology. Current seismic data formats, such as SEED, SAC, and SEG-Y, were designed with specific applications in mind and are frequently a major bottleneck in implementing efficient workflows. We propose a new modern parallel format that can be adapted for a variety of seismic workflows. The Adaptable Seismic Data Format (ASDF) features high-performance parallel read and write support and the ability to store an arbitrary number of traces of varying sizes. Provenance information is stored inside the file so that users know the origin of the data as well as the precise operations that have been applied to the waveforms. The design of the new format is based on several real-world use cases, including earthquake seismology and seismic interferometry. The metadata is based on the proven XML schemas StationXML and QuakeML. Existing time-series analysis tool-kits are easily interfaced with this new format so that seismologists can use robust, previously developed software packages, such as ObsPy and the SAC library. ADIOS, netCDF4, and HDF5 can be used as the underlying container format. At Princeton University, we have chosen to use ADIOS as the container format because it has shown superior scalability for certain applications, such as dealing with big data on HPC systems. In the context of high-performance computing, we have implemented ASDF into the global adjoint tomography workflow on Oak Ridge National Laboratory's supercomputer Titan.

Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

PubMed

Ramus, Claire; Hovasse, Agnès; Marcellin, Marlène; Hesse, Anne-Marie; Mouton-Barbosa, Emmanuelle; Bouyssié, David; Vaca, Sebastian; Carapito, Christine; Chaoui, Karima; Bruley, Christophe; Garin, Jérôme; Cianférani, Sarah; Ferro, Myriam; Van Dorssaeler, Alain; Burlet-Schiltz, Odile; Schaeffer, Christine; Couté, Yohann; Gonzalez de Peredo, Anne

2016-01-30

Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an attractive way to analyze differential protein expression in complex biological samples. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we used a proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). The spiked standard dataset has been deposited to the ProteomeXchange repository with the identifier PXD001819 and can be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods. Bioinformatic pipelines for label-free quantitative analysis must be objectively evaluated in their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. This can be done through the use of complex spiked samples, for which the "ground truth" of variant proteins is known, allowing a statistical evaluation of the performances of the data processing workflow. We provide here such a controlled standard dataset and used it to evaluate the performances of several label-free bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments.

PubMed

Lott, Steffen C; Wolfien, Markus; Riege, Konstantin; Bagnacani, Andrea; Wolkenhauer, Olaf; Hoffmann, Steve; Hess, Wolfgang R

2017-11-10

RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. In this review, we aim to explain the impact of structured pre-selection, classification and integration of best-performing tools within modularized data analysis workflows and ready-to-use computing infrastructures towards experimental data analyses. We highlight examples for workflows and use cases that are presented for pro-, eukaryotic and mixed dual RNA-Seq (meta-transcriptomics) experiments. In addition, we are summarizing the expertise of the laboratories participating in the project consortium "Structured Analysis and Integration of RNA-Seq experiments" (de.STAIR) and its integration with the Galaxy-workbench of the RNA Bioinformatics Center (RBC). Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Exploring the impact of an automated prescription-filling device on community pharmacy technician workflow.

PubMed

Walsh, Kristin E; Chui, Michelle Anne; Kieser, Mara A; Williams, Staci M; Sutter, Susan L; Sutter, John G

2011-01-01

To explore community pharmacy technician workflow change after implementation of an automated robotic prescription-filling device. At an independent community pharmacy in rural Mayville, WI, pharmacy technicians were observed before and 3 months after installation of an automated robotic prescription-filling device. The main outcome measures were sequences and timing of technician workflow steps, workflow interruptions, automation surprises, and workarounds. Of the 77 and 80 observations made before and 3 months after robot installation, respectively, 17 different workflow sequences were observed before installation and 38 after installation. Average prescription filling time was reduced by 40 seconds per prescription with use of the robot. Workflow interruptions per observation increased from 1.49 to 1.79 (P = 0.11), and workarounds increased from 10% to 36% after robot use. Although automated prescription-filling devices can increase efficiency, workflow interruptions and workarounds may negate that efficiency. Assessing changes in workflow and sequencing of tasks that may result from the use of automation can help uncover opportunities for workflow policy and procedure redesign.

Exploring the impact of an automated prescription-filling device on community pharmacy technician workflow

PubMed Central

Walsh, Kristin E.; Chui, Michelle Anne; Kieser, Mara A.; Williams, Staci M.; Sutter, Susan L.; Sutter, John G.

2012-01-01

Objective To explore community pharmacy technician workflow change after implementation of an automated robotic prescription-filling device. Methods At an independent community pharmacy in rural Mayville, WI, pharmacy technicians were observed before and 3 months after installation of an automated robotic prescription-filling device. The main outcome measures were sequences and timing of technician workflow steps, workflow interruptions, automation surprises, and workarounds. Results Of the 77 and 80 observations made before and 3 months after robot installation, respectively, 17 different workflow sequences were observed before installation and 38 after installation. Average prescription filling time was reduced by 40 seconds per prescription with use of the robot. Workflow interruptions per observation increased from 1.49 to 1.79 (P = 0.11), and workarounds increased from 10% to 36% after robot use. Conclusion Although automated prescription-filling devices can increase efficiency, workflow interruptions and workarounds may negate that efficiency. Assessing changes in workflow and sequencing of tasks that may result from the use of automation can help uncover opportunities for workflow policy and procedure redesign. PMID:21896459

The VERCE platform: Enabling Computational Seismology via Streaming Workflows and Science Gateways

NASA Astrophysics Data System (ADS)

Spinuso, Alessandro; Filgueira, Rosa; Krause, Amrey; Matser, Jonas; Casarotti, Emanuele; Magnoni, Federica; Gemund, Andre; Frobert, Laurent; Krischer, Lion; Atkinson, Malcolm

2015-04-01

The VERCE project is creating an e-Science platform to facilitate innovative data analysis and coding methods that fully exploit the wealth of data in global seismology. One of the technologies developed within the project is the Dispel4Py python library, which allows to describe abstract stream-based workflows for data-intensive applications and to execute them in a distributed environment. At runtime Dispel4Py is able to map workflow descriptions dynamically onto a number of computational resources (Apache Storm clusters, MPI powered clusters, and shared-memory multi-core machines, single-core machines), setting it apart from other workflow frameworks. Therefore, Dispel4Py enables scientists to focus on their computation instead of being distracted by details of the computing infrastructure they use. Among the workflows developed with Dispel4Py in VERCE, we mention here those for Seismic Ambient Noise Cross-Correlation and MISFIT calculation, which address two data-intensive problems that are common in computational seismology. The former, also called Passive Imaging, allows the detection of relative seismic-wave velocity variations during the time of recording, to be associated with the stress-field changes that occurred in the test area. The MISFIT instead, takes as input the synthetic seismograms generated from HPC simulations for a certain Earth model and earthquake and, after a preprocessing stage, compares them with real observations in order to foster subsequent model updates and improvement (Inversion). The VERCE Science Gateway exposes the MISFIT calculation workflow as a service, in combination with the simulation phase. Both phases can be configured, controlled and monitored by the user via a rich user interface which is integrated within the gUSE Science Gateway framework, hiding the complexity of accessing third parties data services, security mechanisms and enactment on the target resources. Thanks to a modular extension to the Dispel4Py framework

Mathematics Teaching Anxiety and Self-Efficacy Beliefs toward Mathematics Teaching: A Path Analysis

ERIC Educational Resources Information Center

Peker, Murat

2016-01-01

The purpose of this study was to investigate the relationship between pre-service primary school teachers' mathematics teaching anxiety and their self-efficacy beliefs toward mathematics teaching through path analysis. There were a total of 250 pre-service primary school teachers involved in this study. Of the total, 202 were female and 48 were…

Parallel and Efficient Sensitivity Analysis of Microscopy Image Segmentation Workflows in Hybrid Systems

PubMed Central

Barreiros, Willian; Teodoro, George; Kurc, Tahsin; Kong, Jun; Melo, Alba C. M. A.; Saltz, Joel

2017-01-01

We investigate efficient sensitivity analysis (SA) of algorithms that segment and classify image features in a large dataset of high-resolution images. Algorithm SA is the process of evaluating variations of methods and parameter values to quantify differences in the output. A SA can be very compute demanding because it requires re-processing the input dataset several times with different parameters to assess variations in output. In this work, we introduce strategies to efficiently speed up SA via runtime optimizations targeting distributed hybrid systems and reuse of computations from runs with different parameters. We evaluate our approach using a cancer image analysis workflow on a hybrid cluster with 256 nodes, each with an Intel Phi and a dual socket CPU. The SA attained a parallel efficiency of over 90% on 256 nodes. The cooperative execution using the CPUs and the Phi available in each node with smart task assignment strategies resulted in an additional speedup of about 2×. Finally, multi-level computation reuse lead to an additional speedup of up to 2.46× on the parallel version. The level of performance attained with the proposed optimizations will allow the use of SA in large-scale studies. PMID:29081725

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

Considering Time in Orthophotography Production: from a General Workflow to a Shortened Workflow for a Faster Disaster Response

NASA Astrophysics Data System (ADS)

Lucas, G.

2015-08-01

This article overall deals with production time with orthophoto imagery with medium size digital frame camera. The workflow examination follows two main parts: data acquisition and post-processing. The objectives of the research are fourfold: 1/ gathering time references for the most important steps of orthophoto production (it turned out that literature is missing on this topic); these figures are used later for total production time estimation; 2/ identifying levers for reducing orthophoto production time; 3/ building a simplified production workflow for emergency response: less exigent with accuracy and faster; and compare it to a classical workflow; 4/ providing methodical elements for the estimation of production time with a custom project. In the data acquisition part a comprehensive review lists and describes all the factors that may affect the acquisition efficiency. Using a simulation with different variables (average line length, time of the turns, flight speed) their effect on acquisition efficiency is quantitatively examined. Regarding post-processing, the time references figures were collected from the processing of a 1000 frames case study with 15 cm GSD covering a rectangular area of 447 km2; the time required to achieve each step during the production is written down. When several technical options are possible, each one is tested and time documented so as all alternatives are available. Based on a technical choice with the workflow and using the compiled time reference of the elementary steps, a total time is calculated for the post-processing of the 1000 frames. Two scenarios are compared as regards to time and accuracy. The first one follows the "normal" practices, comprising triangulation, orthorectification and advanced mosaicking methods (feature detection, seam line editing and seam applicator); the second is simplified and make compromise over positional accuracy (using direct geo-referencing) and seamlines preparation in order to achieve

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

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

Research and Implementation of Key Technologies in Multi-Agent System to Support Distributed Workflow

NASA Astrophysics Data System (ADS)

Pan, Tianheng

2018-01-01

In recent years, the combination of workflow management system and Multi-agent technology is a hot research field. The problem of lack of flexibility in workflow management system can be improved by introducing multi-agent collaborative management. The workflow management system adopts distributed structure. It solves the problem that the traditional centralized workflow structure is fragile. In this paper, the agent of Distributed workflow management system is divided according to its function. The execution process of each type of agent is analyzed. The key technologies such as process execution and resource management are analyzed.

Assembling Large, Multi-Sensor Climate Datasets Using the SciFlo Grid Workflow System

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Manipon, G.; Xing, Z.; Fetzer, E.

2008-12-01

NASA's Earth Observing System (EOS) is the world's most ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the A-Train platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over periods of years to decades. However, moving from predominantly single-instrument studies to a multi-sensor, measurement-based model for long-duration analysis of important climate variables presents serious challenges for large-scale data mining and data fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another instrument (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the cloud scenes from CloudSat, and repeat the entire analysis over years of AIRS data. To perform such an analysis, one must discover & access multiple datasets from remote sites, find the space/time matchups between instruments swaths and model grids, understand the quality flags and uncertainties for retrieved physical variables, and assemble merged datasets for further scientific and statistical analysis. To meet these large-scale challenges, we are utilizing a Grid computing and dataflow framework, named SciFlo, in which we are deploying a set of versatile and reusable operators for data query, access, subsetting, co-registration, mining, fusion, and advanced statistical analysis. SciFlo is a semantically-enabled ("smart") Grid Workflow system that ties together a peer-to-peer network of computers into an efficient engine for distributed computation. The SciFlo workflow engine enables scientists to do multi-instrument Earth Science by assembling remotely-invokable Web Services (SOAP or http GET URLs), native executables, command-line scripts, and Python codes into a distributed computing flow. A scientist visually authors the graph of operation in the VizFlow GUI, or uses a

Assembling Large, Multi-Sensor Climate Datasets Using the SciFlo Grid Workflow System

NASA Astrophysics Data System (ADS)

Wilson, B.; Manipon, G.; Xing, Z.; Fetzer, E.

2009-04-01

NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the "A-Train" platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over periods of years to decades. However, moving from predominantly single-instrument studies to a multi-sensor, measurement-based model for long-duration analysis of important climate variables presents serious challenges for large-scale data mining and data fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another instrument (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the "cloud scenes" from CloudSat, and repeat the entire analysis over years of AIRS data. To perform such an analysis, one must discover & access multiple datasets from remote sites, find the space/time "matchups" between instruments swaths and model grids, understand the quality flags and uncertainties for retrieved physical variables, assemble merged datasets, and compute fused products for further scientific and statistical analysis. To meet these large-scale challenges, we are utilizing a Grid computing and dataflow framework, named SciFlo, in which we are deploying a set of versatile and reusable operators for data query, access, subsetting, co-registration, mining, fusion, and advanced statistical analysis. SciFlo is a semantically-enabled ("smart") Grid Workflow system that ties together a peer-to-peer network of computers into an efficient engine for distributed computation. The SciFlo workflow engine enables scientists to do multi-instrument Earth Science by assembling remotely-invokable Web Services (SOAP or http GET URLs), native executables, command-line scripts, and Python codes into a distributed computing flow. A scientist visually authors the graph of operation in the Viz

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.

The View from a Few Hundred Feet : A New Transparent and Integrated Workflow for UAV-collected Data

NASA Astrophysics Data System (ADS)

Peterson, F. S.; Barbieri, L.; Wyngaard, J.

2015-12-01

Unmanned Aerial Vehicles (UAVs) allow scientists and civilians to monitor earth and atmospheric conditions in remote locations. To keep up with the rapid evolution of UAV technology, data workflows must also be flexible, integrated, and introspective. Here, we present our data workflow for a project to assess the feasibility of detecting threshold levels of methane, carbon-dioxide, and other aerosols by mounting consumer-grade gas analysis sensors on UAV's. Particularly, we highlight our use of Project Jupyter, a set of open-source software tools and documentation designed for developing "collaborative narratives" around scientific workflows. By embracing the GitHub-backed, multi-language systems available in Project Jupyter, we enable interaction and exploratory computation while simultaneously embracing distributed version control. Additionally, the transparency of this method builds trust with civilians and decision-makers and leverages collaboration and communication to resolve problems. The goal of this presentation is to provide a generic data workflow for scientific inquiries involving UAVs and to invite the participation of the AGU community in its improvement and curation.

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.

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

Workflow interruptions, cognitive failure and near-accidents in health care.

PubMed

Elfering, Achim; Grebner, Simone; Ebener, Corinne

2015-01-01

Errors are frequent in health care. A specific model was tested that affirms failure in cognitive action regulation to mediate the influence of nurses' workflow interruptions and safety conscientiousness on near-accidents in health care. One hundred and sixty-five nurses from seven Swiss hospitals participated in a questionnaire survey. Structural equation modelling confirmed the hypothesised mediation model. Cognitive failure in action regulation significantly mediated the influence of workflow interruptions on near-accidents (p < .05). An indirect path from conscientiousness to near-accidents via cognitive failure in action regulation was also significant (p < .05). Compliance with safety regulations was significantly related to cognitive failure and near-accidents; moreover, cognitive failure mediated the association between compliance and near-accidents (p < .05). Contrary to expectations, compliance with safety regulations was not related to workflow interruptions. Workflow interruptions caused by colleagues, patients and organisational constraints are likely to trigger errors in nursing. Work redesign is recommended to reduce cognitive failure and improve safety of nurses and patients.

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.

Predicting Team Performance through Human Behavioral Sensing and Quantitative Workflow Instrumentation

DTIC Science & Technology

2016-07-27

make risk-informed decisions during serious games . Statistical models of intra- game performance were developed to determine whether behaviors in...specific facets of the gameplay workflow were predictive of analytical performance and games outcomes. A study of over seventy instrumented teams revealed...more accurate game decisions. 2 Keywords: Humatics · Serious Games · Human-System Interaction · Instrumentation · Teamwork · Communication Analysis

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

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 Cyber

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

Design and implementation of a secure workflow system based on PKI/PMI

NASA Astrophysics Data System (ADS)

Yan, Kai; Jiang, Chao-hui

2013-03-01

As the traditional workflow system in privilege management has the following weaknesses: low privilege management efficiency, overburdened for administrator, lack of trust authority etc. A secure workflow model based on PKI/PMI is proposed after studying security requirements of the workflow systems in-depth. This model can achieve static and dynamic authorization after verifying user's ID through PKC and validating user's privilege information by using AC in workflow system. Practice shows that this system can meet the security requirements of WfMS. Moreover, it can not only improve system security, but also ensures integrity, confidentiality, availability and non-repudiation of the data in the system.

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

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

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.

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

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

PubMed

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

2014-01-01

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.

SMITH: a LIMS for handling next-generation sequencing workflows

PubMed Central

2014-01-01

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

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

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

Extension of specification language for soundness and completeness of service workflow

NASA Astrophysics Data System (ADS)

Viriyasitavat, Wattana; Xu, Li Da; Bi, Zhuming; Sapsomboon, Assadaporn

2018-05-01

A Service Workflow is an aggregation of distributed services to fulfill specific functionalities. With ever increasing available services, the methodologies for the selections of the services against the given requirements become main research subjects in multiple disciplines. A few of researchers have contributed to the formal specification languages and the methods for model checking; however, existing methods have the difficulties to tackle with the complexity of workflow compositions. In this paper, we propose to formalize the specification language to reduce the complexity of the workflow composition. To this end, we extend a specification language with the consideration of formal logic, so that some effective theorems can be derived for the verification of syntax, semantics, and inference rules in the workflow composition. The logic-based approach automates compliance checking effectively. The Service Workflow Specification (SWSpec) has been extended and formulated, and the soundness, completeness, and consistency of SWSpec applications have been verified; note that a logic-based SWSpec is mandatory for the development of model checking. The application of the proposed SWSpec has been demonstrated by the examples with the addressed soundness, completeness, and consistency.

Teaching audience analysis to the technical student

NASA Technical Reports Server (NTRS)

Debs, M. B.; Brillhart, L. V.

1981-01-01

Teaching audience analysis, as practiced in a technical writing course for engineering students, is discussed. Audience analysis is described as the task of defining the audience for a particular piece of writing and determining those characteristics of the audience which constrain the writer and effect reception of the message. A mature technical writing style that shows the tension produced when a text is written to be read and understood is considered in terms of audience analysis. Techniques include: (1) conveying to students the concept that a reader with certain expectations exist, (2) team teaching to preserve the context of a given technical discipline, and (3) assigning a technical report that addresses a variety of readers, thus establishing the complexity of audience oriented writing.

A Systematic Analysis of Quality of Teaching Surveys

ERIC Educational Resources Information Center

Davies, Martin; Hirschberg, Joe; Lye, Jenny; Johnston, Carol

2010-01-01

All tertiary institutions in Australia use the same Course Experience Questionnaire (CEQ); however, for the internal evaluation of teaching they use their own surveys. This paper performs an analysis of the internal Quality of Teaching Surveys (QTS) used in Australian universities. We classify the questions within the QTS surveys. This…

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

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.

Automation and workflow considerations for embedding Digimarc Barcodes at scale

NASA Astrophysics Data System (ADS)

Rodriguez, Tony; Haaga, Don; Calhoon, Sean

2015-03-01

The Digimarc® Barcode is a digital watermark applied to packages and variable data labels that carries GS1 standard GTIN-14 data traditionally carried by a 1-D barcode. The Digimarc Barcode can be read with smartphones and imaging-based barcode readers commonly used in grocery and retail environments. Using smartphones, consumers can engage with products and retailers can materially increase the speed of check-out, increasing store margins and providing a better experience for shoppers. Internal testing has shown an average of 53% increase in scanning throughput, enabling 100's of millions of dollars in cost savings [1] for retailers when deployed at scale. To get to scale, the process of embedding a digital watermark must be automated and integrated within existing workflows. Creating the tools and processes to do so represents a new challenge for the watermarking community. This paper presents a description and an analysis of the workflow implemented by Digimarc to deploy the Digimarc Barcode at scale. An overview of the tools created and lessons learned during the introduction of technology to the market are provided.

Workflow-Oriented Cyberinfrastructure for Sensor Data Analytics

NASA Astrophysics Data System (ADS)

Orcutt, J. A.; Rajasekar, A.; Moore, R. W.; Vernon, F.

2015-12-01

Sensor streams comprise an increasingly large part of Earth Science data. Analytics based on sensor data require an easy way to perform operations such as acquisition, conversion to physical units, metadata linking, sensor fusion, analysis and visualization on distributed sensor streams. Furthermore, embedding real-time sensor data into scientific workflows is of growing interest. We have implemented a scalable networked architecture that can be used to dynamically access packets of data in a stream from multiple sensors, and perform synthesis and analysis across a distributed network. Our system is based on the integrated Rule Oriented Data System (irods.org), which accesses sensor data from the Antelope Real Time Data System (brtt.com), and provides virtualized access to collections of data streams. We integrate real-time data streaming from different sources, collected for different purposes, on different time and spatial scales, and sensed by different methods. iRODS, noted for its policy-oriented data management, brings to sensor processing features and facilities such as single sign-on, third party access control lists ( ACLs), location transparency, logical resource naming, and server-side modeling capabilities while reducing the burden on sensor network operators. Rich integrated metadata support also makes it straightforward to discover data streams of interest and maintain data provenance. The workflow support in iRODS readily integrates sensor processing into any analytical pipeline. The system is developed as part of the NSF-funded Datanet Federation Consortium (datafed.org). APIs for selecting, opening, reaping and closing sensor streams are provided, along with other helper functions to associate metadata and convert sensor packets into NetCDF and JSON formats. Near real-time sensor data including seismic sensors, environmental sensors, LIDAR and video streams are available through this interface. A system for archiving sensor data and metadata in Net

Performance of an Automated Versus a Manual Whole-Body Magnetic Resonance Imaging Workflow.

PubMed

Stocker, Daniel; Finkenstaedt, Tim; Kuehn, Bernd; Nanz, Daniel; Klarhoefer, Markus; Guggenberger, Roman; Andreisek, Gustav; Kiefer, Berthold; Reiner, Caecilia S

2018-04-24

The aim of this study was to evaluate the performance of an automated workflow for whole-body magnetic resonance imaging (WB-MRI), which reduces user interaction compared with the manual WB-MRI workflow. This prospective study was approved by the local ethics committee. Twenty patients underwent WB-MRI for myopathy evaluation on a 3 T MRI scanner. Ten patients (7 women; age, 52 ± 13 years; body weight, 69.9 ± 13.3 kg; height, 173 ± 9.3 cm; body mass index, 23.2 ± 3.0) were examined with a prototypical automated WB-MRI workflow, which automatically segments the whole body, and 10 patients (6 women; age, 35.9 ± 12.4 years; body weight, 72 ± 21 kg; height, 169.2 ± 10.4 cm; body mass index, 24.9 ± 5.6) with a manual scan. Overall image quality (IQ; 5-point scale: 5, excellent; 1, poor) and coverage of the study volume were assessed by 2 readers for each sequence (coronal T2-weighted turbo inversion recovery magnitude [TIRM] and axial contrast-enhanced T1-weighted [ce-T1w] gradient dual-echo sequence). Interreader agreement was evaluated with intraclass correlation coefficients. Examination time, number of user interactions, and MR technicians' acceptance rating (1, highest; 10, lowest) was compared between both groups. Total examination time was significantly shorter for automated WB-MRI workflow versus manual WB-MRI workflow (30.0 ± 4.2 vs 41.5 ± 3.4 minutes, P < 0.0001) with significantly shorter planning time (2.5 ± 0.8 vs 14.0 ± 7.0 minutes, P < 0.0001). Planning took 8% of the total examination time with automated versus 34% with manual WB-MRI workflow (P < 0.0001). The number of user interactions with automated WB-MRI workflow was significantly lower compared with manual WB-MRI workflow (10.2 ± 4.4 vs 48.2 ± 17.2, P < 0.0001). Planning efforts were rated significantly lower by the MR technicians for the automated WB-MRI workflow than for the manual WB-MRI workflow (2.20 ± 0.92 vs 4.80 ± 2.39, respectively; P = 0.005). Overall IQ was similar

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

Grid workflow job execution service 'Pilot'

NASA Astrophysics Data System (ADS)

Shamardin, Lev; Kryukov, Alexander; Demichev, Andrey; Ilyin, Vyacheslav

2011-12-01

'Pilot' is a grid job execution service for workflow jobs. The main goal for the service is to automate computations with multiple stages since they can be expressed as simple workflows. Each job is a directed acyclic graph of tasks and each task is an execution of something on a grid resource (or 'computing element'). Tasks may be submitted to any WS-GRAM (Globus Toolkit 4) service. The target resources for the tasks execution are selected by the Pilot service from the set of available resources which match the specific requirements from the task and/or job definition. Some simple conditional execution logic is also provided. The 'Pilot' service is built on the REST concepts and provides a simple API through authenticated HTTPS. This service is deployed and used in production in a Russian national grid project GridNNN.

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.

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

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

PubMed Central

Bontempi, Gianluca; Ceccarelli, Michele; Noushmehr, Houtan

2016-01-01

Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox,  TCGAbiolinks. PMID:28232861

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.

PubMed

Silva, Tiago C; Colaprico, Antonio; Olsen, Catharina; D'Angelo, Fulvio; Bontempi, Gianluca; Ceccarelli, Michele; Noushmehr, Houtan

2016-01-01

Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox,  TCGAbiolinks.

Using Multimedia for Teaching Analysis in History of Modern Architecture.

ERIC Educational Resources Information Center

Perryman, Garry

This paper presents a case for the development and support of a computer-based interactive multimedia program for teaching analysis in community college architecture design programs. Analysis in architecture design is an extremely important strategy for the teaching of higher-order thinking skills, which senior schools of architecture look for in…

Parallel workflow tools to facilitate human brain MRI post-processing

PubMed Central

Cui, Zaixu; Zhao, Chenxi; Gong, Gaolang

2015-01-01

Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues. PMID:26029043

Aligning HST Images to Gaia: A Faster Mosaicking Workflow

NASA Astrophysics Data System (ADS)

Bajaj, V.

2017-11-01

We present a fully programmatic workflow for aligning HST images using the high-quality astrometry provided by Gaia Data Release 1. Code provided in a Jupyter Notebook works through this procedure, including parsing the data to determine the query area parameters, querying Gaia for the coordinate catalog, and using the catalog with TweakReg as reference catalog. This workflow greatly simplifies the normally time-consuming process of aligning HST images, especially those taken as part of mosaics.

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.

NOW: A Workflow Language for Orchestration in Nomadic Networks

NASA Astrophysics Data System (ADS)

Philips, Eline; van der Straeten, Ragnhild; Jonckers, Viviane

Existing workflow languages for nomadic or mobile ad hoc networks do not offer adequate support for dealing with the volatile connections inherent to these environments. Services residing on mobile devices are exposed to (temporary) network failures, which should be considered the rule rather than the exception. This paper proposes a nomadic workflow language built on top of an ambient-oriented programming language which supports dynamic service discovery and communication primitives resilient to network failures. Our proposed language provides high level workflow abstractions for control flow and supports rich network and service failure detection and handling through compensating actions. Moreover, we introduce a powerful variable binding mechanism which enables dynamic data flow between services in a nomadic environment. By adding this extra layer of abstraction on top of an ambient-oriented programming language, the application programmer is offered a flexible way to develop applications for nomadic networks.

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters.

PubMed

Cheng, Gong; Lu, Quan; Ma, Ling; Zhang, Guocai; Xu, Liang; Zhou, Zongshan

2017-01-01

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters

PubMed Central

Cheng, Gong; Zhang, Guocai; Xu, Liang

2017-01-01

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily. PMID:29204317

Towards seamless workflows in agile data science

NASA Astrophysics Data System (ADS)

Klump, J. F.; Robertson, J.

2017-12-01

Agile workflows are a response to projects with requirements that may change over time. They prioritise rapid and flexible responses to change, preferring to adapt to changes in requirements rather than predict them before a project starts. This suits the needs of research very well because research is inherently agile in its methodology. The adoption of agile methods has made collaborative data analysis much easier in a research environment fragmented across institutional data stores, HPC, personal and lab computers and more recently cloud environments. Agile workflows use tools that share a common worldview: in an agile environment, there may be more that one valid version of data, code or environment in play at any given time. All of these versions need references and identifiers. For example, a team of developers following the git-flow conventions (github.com/nvie/gitflow) may have several active branches, one for each strand of development. These workflows allow rapid and parallel iteration while maintaining identifiers pointing to individual snapshots of data and code and allowing rapid switching between strands. In contrast, the current focus of versioning in research data management is geared towards managing data for reproducibility and long-term preservation of the record of science. While both are important goals in the persistent curation domain of the institutional research data infrastructure, current tools emphasise planning over adaptation and can introduce unwanted rigidity by insisting on a single valid version or point of truth. In the collaborative curation domain of a research project, things are more fluid. However, there is no equivalent to the "versioning iso-surface" of the git protocol for the management and versioning of research data. At CSIRO we are developing concepts and tools for the agile management of software code and research data for virtual research environments, based on our experiences of actual data analytics projects in the

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor

PubMed Central

Collado-Torres, Leonardo; Nellore, Abhinav; Jaffe, Andrew E.

2017-01-01

The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The processed data can be accessed via the recount2 website and the recountBioconductor package. This workflow explains in detail how to use the recountpackage and how to integrate it with other Bioconductor packages for several analyses that can be carried out with the recount2 resource. In particular, we describe how the coverage count matrices were computed in recount2 as well as different ways of obtaining public metadata, which can facilitate downstream analyses. Step-by-step directions show how to do a gene-level differential expression analysis, visualize base-level genome coverage data, and perform an analyses at multiple feature levels. This workflow thus provides further information to understand the data in recount2 and a compendium of R code to use the data. PMID:29043067

A Multivariate Methodological Workflow for the Analysis of FTIR Chemical Mapping Applied on Historic Paint Stratigraphies

PubMed Central

Sciutto, Giorgia; Oliveri, Paolo; Catelli, Emilio; Bonacini, Irene

2017-01-01

In the field of applied researches in heritage science, the use of multivariate approach is still quite limited and often chemometric results obtained are often underinterpreted. Within this scenario, the present paper is aimed at disseminating the use of suitable multivariate methodologies and proposes a procedural workflow applied on a representative group of case studies, of considerable importance for conservation purposes, as a sort of guideline on the processing and on the interpretation of this FTIR data. Initially, principal component analysis (PCA) is performed and the score values are converted into chemical maps. Successively, the brushing approach is applied, demonstrating its usefulness for a deep understanding of the relationships between the multivariate map and PC score space, as well as for the identification of the spectral bands mainly involved in the definition of each area localised within the score maps. PMID:29333162

Microprocessors as a Vehicle for Teaching Circuit Analysis.

ERIC Educational Resources Information Center

Neu, Emil C.

1982-01-01

Based on the premise that most engineering students will own their own microcomputers, discusses the teaching of circuit analysis, possible directions to be taken in hardware analysis, and impact on the mathematics related to circuit analysis. (SK)

Time-efficiency analysis of the treatment with monolithic implant crowns in a digital workflow: a randomized controlled trial.

PubMed

Joda, Tim; Brägger, Urs

2016-11-01

The aim of the randomized controlled trial was to analyze time-efficiency of a treatment with implant crowns made of monolithic lithium disilicate (LS2) plus titanium base vs. porcelain fuse to zirconium dioxide (ZrO 2 ) in a digital workflow. Twenty study participants were included for single-tooth replacement in premolar and molar sites. Baseline was the start of the prosthetic treatment. All patients received transocclusal screw-retained implant reconstructions on a soft tissue level-type implant. The 3D implant position was captured with intraoral optical scanning (IOS). After randomization, ten patients were restored with CAD-/CAM-produced monolithic LS2-crowns bonded to prefabricated titanium abutments without any physical models (test), and ten patients with CAD-/CAM-fabricated ZrO 2 -suprastructures and hand-layered ceramic veneering with milled master models (control). Every single clinical and laboratory work step was timed in minutes and then analyzed for time-efficiency with Wilcoxon Rank Sum Tests. Direct costs were assessed for laboratory fees for first line production in Swiss Francs (CHF). Two clinical appointments were necessary for IOS and seating of all implant crowns. The mean total production time, as the sum of clinical plus laboratory work steps, was significantly different, resulting in 75.3 min (SD ± 2.1) for test and 156.6 min (SD ± 4.6) for control [P = 0.0001]. Analysis for clinical treatment sessions showed a significantly shorter mean chair time for the complete digital workflow of 20.8 min (SD ± 0.3) compared to 24.1 min (SD ± 1.1) [P = 0.001]. Even more obvious were the results for the mean laboratory work time with a significant reduction of 54.5 min (SD ± 4.9) vs. 132.5 min (SD ± 8.7), respectively [P = 0.0001]. The test workflow was more time-efficient than the controls for implant-supported crowns; notably, laboratory fabrication steps could be effectively shortened with the digital process of

The chromosomal analysis of teaching: the search for promoter genes.

PubMed

Skeff, Kelley M

2007-01-01

The process of teaching is ubiquitous in medicine, both in the practice of medicine and the promotion of medical science. Yet, until the last 50 years, the process of medical teaching had been neglected. To improve this process, the research group at the Stanford Faculty Development Center for Medical Teachers developed an educational framework to assist teachers to analyze and improve the teaching process. Utilizing empirical data drawn from videotapes of actual clinical teaching and educational literature, we developed a seven-category systematic scheme for the analysis of medical teaching, identifying key areas and behaviors that could enable teachers to enhance their effectiveness. The organizational system of this scheme is similar to that used in natural sciences, such as genetics. Whereas geneticists originally identified chromosomes and ultimately individual and related genes, this classification system identifies major categories and specific teaching behaviors that can enhance teaching effectiveness. Over the past two decades, this organizational framework has provided the basis for a variety of faculty development programs for improving teaching effectiveness. Results of those programs have revealed several positive findings, including the usefulness of the methods for a wide variety of medical teachers in a variety of settings. This research indicates that the development of a framework for analysis has been, as in the natural sciences, an important way to improve the science of the art of teaching.

Data processing workflows from low-cost digital survey to various applications: three case studies of Chinese historic architecture

NASA Astrophysics Data System (ADS)

Sun, Z.; Cao, Y. K.

2015-08-01

The paper focuses on the versatility of data processing workflows ranging from BIM-based survey to structural analysis and reverse modeling. In China nowadays, a large number of historic architecture are in need of restoration, reinforcement and renovation. But the architects are not prepared for the conversion from the booming AEC industry to architectural preservation. As surveyors working with architects in such projects, we have to develop efficient low-cost digital survey workflow robust to various types of architecture, and to process the captured data for architects. Although laser scanning yields high accuracy in architectural heritage documentation and the workflow is quite straightforward, the cost and portability hinder it from being used in projects where budget and efficiency are of prime concern. We integrate Structure from Motion techniques with UAV and total station in data acquisition. The captured data is processed for various purposes illustrated with three case studies: the first one is as-built BIM for a historic building based on registered point clouds according to Ground Control Points; The second one concerns structural analysis for a damaged bridge using Finite Element Analysis software; The last one relates to parametric automated feature extraction from captured point clouds for reverse modeling and fabrication.

Model-based Vestibular Afferent Stimulation: Modular Workflow for Analyzing Stimulation Scenarios in Patient Specific and Statistical Vestibular Anatomy.

PubMed

Handler, Michael; Schier, Peter P; Fritscher, Karl D; Raudaschl, Patrik; Johnson Chacko, Lejo; Glueckert, Rudolf; Saba, Rami; Schubert, Rainer; Baumgarten, Daniel; Baumgartner, Christian

2017-01-01

Our sense of balance and spatial orientation strongly depends on the correct functionality of our vestibular system. Vestibular dysfunction can lead to blurred vision and impaired balance and spatial orientation, causing a significant decrease in quality of life. Recent studies have shown that vestibular implants offer a possible treatment for patients with vestibular dysfunction. The close proximity of the vestibular nerve bundles, the facial nerve and the cochlear nerve poses a major challenge to targeted stimulation of the vestibular system. Modeling the electrical stimulation of the vestibular system allows for an efficient analysis of stimulation scenarios previous to time and cost intensive in vivo experiments. Current models are based on animal data or CAD models of human anatomy. In this work, a (semi-)automatic modular workflow is presented for the stepwise transformation of segmented vestibular anatomy data of human vestibular specimens to an electrical model and subsequently analyzed. The steps of this workflow include (i) the transformation of labeled datasets to a tetrahedra mesh, (ii) nerve fiber anisotropy and fiber computation as a basis for neuron models, (iii) inclusion of arbitrary electrode designs, (iv) simulation of quasistationary potential distributions, and (v) analysis of stimulus waveforms on the stimulation outcome. Results obtained by the workflow based on human datasets and the average shape of a statistical model revealed a high qualitative agreement and a quantitatively comparable range compared to data from literature, respectively. Based on our workflow, a detailed analysis of intra- and extra-labyrinthine electrode configurations with various stimulation waveforms and electrode designs can be performed on patient specific anatomy, making this framework a valuable tool for current optimization questions concerning vestibular implants in humans.

Cytoscape: the network visualization tool for GenomeSpace workflows.

PubMed

Demchak, Barry; Hull, Tim; Reich, Michael; Liefeld, Ted; Smoot, Michael; Ideker, Trey; Mesirov, Jill P

2014-01-01

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

Cytoscape: the network visualization tool for GenomeSpace workflows

PubMed Central

Demchak, Barry; Hull, Tim; Reich, Michael; Liefeld, Ted; Smoot, Michael; Ideker, Trey; Mesirov, Jill P.

2014-01-01

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013. PMID:25165537

Integrated Sensitivity Analysis Workflow

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

Friedman-Hill, Ernest J.; Hoffman, Edward L.; Gibson, Marcus J.

2014-08-01

Sensitivity analysis is a crucial element of rigorous engineering analysis, but performing such an analysis on a complex model is difficult and time consuming. The mission of the DART Workbench team at Sandia National Laboratories is to lower the barriers to adoption of advanced analysis tools through software integration. The integrated environment guides the engineer in the use of these integrated tools and greatly reduces the cycle time for engineering analysis.

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

Load-sensitive dynamic workflow re-orchestration and optimisation for faster patient healthcare.

PubMed

Meli, Christopher L; Khalil, Ibrahim; Tari, Zahir

2014-01-01

Hospital waiting times are considerably long, with no signs of reducing any-time soon. A number of factors including population growth, the ageing population and a lack of new infrastructure are expected to further exacerbate waiting times in the near future. In this work, we show how healthcare services can be modelled as queueing nodes, together with healthcare service workflows, such that these workflows can be optimised during execution in order to reduce patient waiting times. Services such as X-ray, computer tomography, and magnetic resonance imaging often form queues, thus, by taking into account the waiting times of each service, the workflow can be re-orchestrated and optimised. Experimental results indicate average waiting time reductions are achievable by optimising workflows using dynamic re-orchestration. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Bioprocess development workflow: Transferable physiological knowledge instead of technological correlations.

PubMed

Reichelt, Wieland N; Haas, Florian; Sagmeister, Patrick; Herwig, Christoph

2017-01-01

Microbial bioprocesses need to be designed to be transferable from lab scale to production scale as well as between setups. Although substantial effort is invested to control technological parameters, usually the only true constant parameter is the actual producer of the product: the cell. Hence, instead of solely controlling technological process parameters, the focus should be increasingly laid on physiological parameters. This contribution aims at illustrating a workflow of data life cycle management with special focus on physiology. Information processing condenses the data into physiological variables, while information mining condenses the variables further into physiological descriptors. This basis facilitates data analysis for a physiological explanation for observed phenomena in productivity. Targeting transferability, we demonstrate this workflow using an industrially relevant Escherichia coli process for recombinant protein production and substantiate the following three points: (1) The postinduction phase is independent in terms of productivity and physiology from the preinduction variables specific growth rate and biomass at induction. (2) The specific substrate uptake rate during induction phase was found to significantly impact the maximum specific product titer. (3) The time point of maximum specific titer can be predicted by an easy accessible physiological variable: while the maximum specific titers were reached at different time points (19.8 ± 7.6 h), those maxima were reached all within a very narrow window of cumulatively consumed substrate dSn (3.1 ± 0.3 g/g). Concluding, this contribution provides a workflow on how to gain a physiological view on the process and illustrates potential benefits. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:261-270, 2017. © 2016 American Institute of Chemical Engineers.

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.

The radiologist's workflow environment: evaluation of disruptors and potential implications.

PubMed

Yu, John-Paul J; Kansagra, Akash P; Mongan, John

2014-06-01

Workflow interruptions in the health care delivery environment are a major contributor to medical errors and have been extensively studied within numerous hospital settings, including the nursing environment and the operating room, along with their effects on physician workflow. Less understood, though, is the role of interruptions in other highly specialized clinical domains and subspecialty services, such as diagnostic radiology. The workflow of the on-call radiologist, in particular, is especially susceptible to disruption by telephone calls and other modes of physician-to-physician communication. Herein, the authors describe their initial efforts to quantify the degree of interruption experienced by on-call radiologists and examine its potential implications in patient safety and overall clinical care. Copyright © 2014 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

PubMed

Hartman, Amber L; Riddle, Sean; McPhillips, Timothy; Ludäscher, Bertram; Eisen, Jonathan A

2010-06-12

For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable

Teaching Audience Analysis with Presidential "Victory" Speeches

ERIC Educational Resources Information Center

Jones, Kevin T.

2015-01-01

Teaching students to understand the importance of audience analysis can be challenging. In fact, many public-speaking texts suggest methods for engaging audience analysis that is not always practical or possible (e.g., polling audiences before you speak to them). One practical way of understanding audience analysis is to see it at work in the text…

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…

Automating radiologist workflow, part 3: education and training.

PubMed

Reiner, Bruce

2008-12-01

The current model for radiologist education consists largely of mentorship during residency, followed by peer-to-peer training thereafter. The traditional focus of this radiologist education has historically been restricted to anatomy, pathology, and imaging modality. This "human" mentoring model becomes a limiting factor in the current practice environment because of rapid and dramatic changes in imaging and information technologies, along with the increased time demands placed on practicing radiologists. One novel way to address these burgeoning education and training challenges is to leverage technology, with the creation of user-specific and context-specific automated workflow templates. These automated templates would provide a low-stress, time-efficient, and easy-to-use equivalent of "computerized" mentoring. A radiologist could identify the workflow template of interest on the basis of the specific computer application, pathology, anatomy, or modality of interest. While the corresponding workflow template is activated, the radiologist "student" could effectively start and stop at areas of interest and use the functionality of an electronic wizard to identify additional educational resource of interest. An additional training feature of the technology is the ability to review "proven" cases for the purposes of establishing competence and credentialing.

Formalizing an integrative, multidisciplinary cancer therapy discovery workflow

PubMed Central

McGuire, Mary F.; Enderling, Heiko; Wallace, Dorothy I.; Batra, Jaspreet; Jordan, Marie; Kumar, Sushil; Panetta, John C.; Pasquier, Eddy

2014-01-01

Although many clinicians and researchers work to understand cancer, there has been limited success to effectively combine forces and collaborate over time, distance, data and budget constraints. Here we present a workflow template for multidisciplinary cancer therapy that was developed during the 2nd Annual Workshop on Cancer Systems Biology sponsored by Tufts University, Boston, MA in July 2012. The template was applied to the development of a metronomic therapy backbone for neuroblastoma. Three primary groups were identified: clinicians, biologists, and scientists (mathematicians, computer scientists, physicists and engineers). The workflow described their integrative interactions; parallel or sequential processes; data sources and computational tools at different stages as well as the iterative nature of therapeutic development from clinical observations to in vitro, in vivo, and clinical trials. We found that theoreticians in dialog with experimentalists could develop calibrated and parameterized predictive models that inform and formalize sets of testable hypotheses, thus speeding up discovery and validation while reducing laboratory resources and costs. The developed template outlines an interdisciplinary collaboration workflow designed to systematically investigate the mechanistic underpinnings of a new therapy and validate that therapy to advance development and clinical acceptance. PMID:23955390

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.

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.

Implementing an excellence in teaching recognition system: needs analysis and recommendations.

PubMed

Schindler, Nancy; Corcoran, Julia C; Miller, Megan; Wang, Chih-Hsiung; Roggin, Kevin; Posner, Mitchell; Fryer, Jonathan; DaRosa, Debra A

2013-01-01

Teaching awards have been suggested to serve a variety of purposes. The specific characteristics of teaching awards and the associated effectiveness at achieving planned purposes are poorly understood. A needs analysis was performed to inform recommendations for an Excellence in Teaching Recognition System to meet the needs of surgical education leadership. We performed a 2-part needs analysis beginning with a review of the literature. We then, developed, piloted, and administered a survey instrument to General Surgery program leaders. The survey examined the features and perceived effectiveness of existing teaching awards systems. A multi-institution committee of program directors, clerkship directors, and Vice-Chairs of education then met to identify goals and develop recommendations for implementation of an "Excellence in Teaching Recognition System." There is limited evidence demonstrating effectiveness of existing teaching awards in medical education. Evidence supports the ability of such awards to demonstrate value placed on teaching, to inspire faculty to teach, and to contribute to promotion. Survey findings indicate that existing awards strive to achieve these purposes and that educational leaders believe awards have the potential to do this and more. Leaders are moderately satisfied with existing awards for providing recognition and demonstrating value placed on teaching, but they are less satisfied with awards for motivating faculty to participate in teaching or for contributing to promotion. Most departments and institutions honor only a few recipients annually. There is a paucity of literature addressing teaching recognition systems in medical education and little evidence to support the success of such systems in achieving their intended purposes. The ability of awards to affect outcomes such as participation in teaching and promotion may be limited by the small number of recipients for most existing awards. We propose goals for a Teaching Recognition

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.

RetroPath2.0: A retrosynthesis workflow for metabolic engineers.

PubMed

Delépine, Baudoin; Duigou, Thomas; Carbonell, Pablo; Faulon, Jean-Loup

2018-01-01

Synthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering, the research and development process still remains costly. In order to expand the chemical repertoire for the production of next generation compounds, a major engineering biology effort is required in the development of novel design tools that target chemical diversity through rapid and predictable protocols. Addressing that goal involves retrosynthesis approaches that explore the chemical biosynthetic space. However, the complexity associated with the large combinatorial retrosynthesis design space has often been recognized as the main challenge hindering the approach. Here, we provide RetroPath2.0, an automated open source workflow for retrosynthesis based on generalized reaction rules that perform the retrosynthesis search from chassis to target through an efficient and well-controlled protocol. Its easiness of use and the versatility of its applications make this tool a valuable addition to the biological engineer bench desk. We show through several examples the application of the workflow to biotechnological relevant problems, including the identification of alternative biosynthetic routes through enzyme promiscuity or the development of biosensors. We demonstrate in that way the ability of the workflow to streamline retrosynthesis pathway design and its major role in reshaping the design, build, test and learn pipeline by driving the process toward the objective of optimizing bioproduction. The RetroPath2.0 workflow is built using tools developed by the bioinformatics and cheminformatics community, because it is open source we anticipate community contributions will likely expand further the features of the workflow. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Observing health professionals' workflow patterns for diabetes care - First steps towards an ontology for EHR services.

PubMed

Schweitzer, M; Lasierra, N; Hoerbst, A

2015-01-01

Increasing the flexibility from a user-perspective and enabling a workflow based interaction, facilitates an easy user-friendly utilization of EHRs for healthcare professionals' daily work. To offer such versatile EHR-functionality, our approach is based on the execution of clinical workflows by means of a composition of semantic web-services. The backbone of such architecture is an ontology which enables to represent clinical workflows and facilitates the selection of suitable services. In this paper we present the methods and results after running observations of diabetes routine consultations which were conducted in order to identify those workflows and the relation among the included tasks. Mentioned workflows were first modeled by BPMN and then generalized. As a following step in our study, interviews will be conducted with clinical personnel to validate modeled workflows.

Automation of lidar-based hydrologic feature extraction workflows using GIS

NASA Astrophysics Data System (ADS)

Borlongan, Noel Jerome B.; de la Cruz, Roel M.; Olfindo, Nestor T.; Perez, Anjillyn Mae C.

2016-10-01

With the advent of LiDAR technology, higher resolution datasets become available for use in different remote sensing and GIS applications. One significant application of LiDAR datasets in the Philippines is in resource features extraction. Feature extraction using LiDAR datasets require complex and repetitive workflows which can take a lot of time for researchers through manual execution and supervision. The Development of the Philippine Hydrologic Dataset for Watersheds from LiDAR Surveys (PHD), a project under the Nationwide Detailed Resources Assessment Using LiDAR (Phil-LiDAR 2) program, created a set of scripts, the PHD Toolkit, to automate its processes and workflows necessary for hydrologic features extraction specifically Streams and Drainages, Irrigation Network, and Inland Wetlands, using LiDAR Datasets. These scripts are created in Python and can be added in the ArcGIS® environment as a toolbox. The toolkit is currently being used as an aid for the researchers in hydrologic feature extraction by simplifying the workflows, eliminating human errors when providing the inputs, and providing quick and easy-to-use tools for repetitive tasks. This paper discusses the actual implementation of different workflows developed by Phil-LiDAR 2 Project 4 in Streams, Irrigation Network and Inland Wetlands extraction.

High‐resolution trench photomosaics from image‐based modeling: Workflow and error analysis

USGS Publications Warehouse

Reitman, Nadine G.; Bennett, Scott E. K.; Gold, Ryan D.; Briggs, Richard; Duross, Christopher

2015-01-01

Photomosaics are commonly used to construct maps of paleoseismic trench exposures, but the conventional process of manually using image‐editing software is time consuming and produces undesirable artifacts and distortions. Herein, we document and evaluate the application of image‐based modeling (IBM) for creating photomosaics and 3D models of paleoseismic trench exposures, illustrated with a case‐study trench across the Wasatch fault in Alpine, Utah. Our results include a structure‐from‐motion workflow for the semiautomated creation of seamless, high‐resolution photomosaics designed for rapid implementation in a field setting. Compared with conventional manual methods, the IBM photomosaic method provides a more accurate, continuous, and detailed record of paleoseismic trench exposures in approximately half the processing time and 15%–20% of the user input time. Our error analysis quantifies the effect of the number and spatial distribution of control points on model accuracy. For this case study, an ∼87  m2 exposure of a benched trench photographed at viewing distances of 1.5–7 m yields a model with <2  cm root mean square error (rmse) with as few as six control points. Rmse decreases as more control points are implemented, but the gains in accuracy are minimal beyond 12 control points. Spreading control points throughout the target area helps to minimize error. We propose that 3D digital models and corresponding photomosaics should be standard practice in paleoseismic exposure archiving. The error analysis serves as a guide for future investigations that seek balance between speed and accuracy during photomosaic and 3D model construction.

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

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

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME

PubMed Central

Berthold, Michael R.; Hedrick, Michael P.; Gilson, Michael K.

2015-01-01

Today’s large, public databases of protein–small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to custom scripting for informatics and data analysis. Here, we illustrate how the large protein-ligand database BindingDB may be incorporated into KNIME workflows as a step toward the integration of pharmacological data with broader biomolecular analyses. Thus, we describe a collection of KNIME workflows that access BindingDB data via RESTful webservices and, for more intensive queries, via a local distillation of the full BindingDB dataset. We focus in particular on the KNIME implementation of knowledge-based tools to generate informed hypotheses regarding protein targets of bioactive compounds, based on notions of chemical similarity. A number of variants of this basic approach are tested for seven existing drugs with relatively ill-defined therapeutic targets, leading to replication of some previously confirmed results and discovery of new, high-quality hits. Implications for future development are discussed. Database URL: www.bindingdb.org PMID:26384374

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.

Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry

PubMed Central

Kolluru, BalaKrishna; Hawizy, Lezan; Murray-Rust, Peter; Tsujii, Junichi; Ananiadou, Sophia

2011-01-01

Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR. PMID:21633495

Using workflows to explore and optimise named entity recognition for chemistry.

PubMed

Kolluru, Balakrishna; Hawizy, Lezan; Murray-Rust, Peter; Tsujii, Junichi; Ananiadou, Sophia

2011-01-01

Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR.

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.

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.

Workflow for high-content, individual cell quantification of fluorescent markers from universal microscope data, supported by open source software.

PubMed

Stockwell, Simon R; Mittnacht, Sibylle

2014-12-16

Advances in understanding the control mechanisms governing the behavior of cells in adherent mammalian tissue culture models are becoming increasingly dependent on modes of single-cell analysis. Methods which deliver composite data reflecting the mean values of biomarkers from cell populations risk losing subpopulation dynamics that reflect the heterogeneity of the studied biological system. In keeping with this, traditional approaches are being replaced by, or supported with, more sophisticated forms of cellular assay developed to allow assessment by high-content microscopy. These assays potentially generate large numbers of images of fluorescent biomarkers, which enabled by accompanying proprietary software packages, allows for multi-parametric measurements per cell. However, the relatively high capital costs and overspecialization of many of these devices have prevented their accessibility to many investigators. Described here is a universally applicable workflow for the quantification of multiple fluorescent marker intensities from specific subcellular regions of individual cells suitable for use with images from most fluorescent microscopes. Key to this workflow is the implementation of the freely available Cell Profiler software(1) to distinguish individual cells in these images, segment them into defined subcellular regions and deliver fluorescence marker intensity values specific to these regions. The extraction of individual cell intensity values from image data is the central purpose of this workflow and will be illustrated with the analysis of control data from a siRNA screen for G1 checkpoint regulators in adherent human cells. However, the workflow presented here can be applied to analysis of data from other means of cell perturbation (e.g., compound screens) and other forms of fluorescence based cellular markers and thus should be useful for a wide range of laboratories.

Psychometric Properties on Lecturers' Beliefs on Teaching Function: Rasch Model Analysis

ERIC Educational Resources Information Center

Mofreh, Samah Ali Mohsen; Ghafar, Mohammed Najib Abdul; Omar, Abdul Hafiz Hj; Mosaku, Monsurat; Ma'ruf, Amar

2014-01-01

This paper focuses on the psychometric analysis of lecturers' beliefs on teaching function (LBTF) survey using Rasch Model analysis. The sample comprised 34 Community Colleges' lecturers. The Rasch Model is applied to produce specific measurements on the lecturers' beliefs on teaching function in order to generalize results and inferential…

Multi-Objective Approach for Energy-Aware Workflow Scheduling in Cloud Computing Environments

PubMed Central

Kadima, Hubert; Granado, Bertrand

2013-01-01

We address the problem of scheduling workflow applications on heterogeneous computing systems like cloud computing infrastructures. In general, the cloud workflow scheduling is a complex optimization problem which requires considering different criteria so as to meet a large number of QoS (Quality of Service) requirements. Traditional research in workflow scheduling mainly focuses on the optimization constrained by time or cost without paying attention to energy consumption. The main contribution of this study is to propose a new approach for multi-objective workflow scheduling in clouds, and present the hybrid PSO algorithm to optimize the scheduling performance. Our method is based on the Dynamic Voltage and Frequency Scaling (DVFS) technique to minimize energy consumption. This technique allows processors to operate in different voltage supply levels by sacrificing clock frequencies. This multiple voltage involves a compromise between the quality of schedules and energy. Simulation results on synthetic and real-world scientific applications highlight the robust performance of the proposed approach. PMID:24319361

Multi-objective approach for energy-aware workflow scheduling in cloud computing environments.

PubMed

Yassa, Sonia; Chelouah, Rachid; Kadima, Hubert; Granado, Bertrand

2013-01-01

We address the problem of scheduling workflow applications on heterogeneous computing systems like cloud computing infrastructures. In general, the cloud workflow scheduling is a complex optimization problem which requires considering different criteria so as to meet a large number of QoS (Quality of Service) requirements. Traditional research in workflow scheduling mainly focuses on the optimization constrained by time or cost without paying attention to energy consumption. The main contribution of this study is to propose a new approach for multi-objective workflow scheduling in clouds, and present the hybrid PSO algorithm to optimize the scheduling performance. Our method is based on the Dynamic Voltage and Frequency Scaling (DVFS) technique to minimize energy consumption. This technique allows processors to operate in different voltage supply levels by sacrificing clock frequencies. This multiple voltage involves a compromise between the quality of schedules and energy. Simulation results on synthetic and real-world scientific applications highlight the robust performance of the proposed approach.

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.

High precision quantification of human plasma proteins using the automated SISCAPA Immuno-MS workflow.

PubMed

Razavi, Morteza; Leigh Anderson, N; Pope, Matthew E; Yip, Richard; Pearson, Terry W

2016-09-25

Efficient robotic workflows for trypsin digestion of human plasma and subsequent antibody-mediated peptide enrichment (the SISCAPA method) were developed with the goal of improving assay precision and throughput for multiplexed protein biomarker quantification. First, an 'addition only' tryptic digestion protocol was simplified from classical methods, eliminating the need for sample cleanup, while improving reproducibility, scalability and cost. Second, methods were developed to allow multiplexed enrichment and quantification of peptide surrogates of protein biomarkers representing a very broad range of concentrations and widely different molecular masses in human plasma. The total workflow coefficients of variation (including the 3 sequential steps of digestion, SISCAPA peptide enrichment and mass spectrometric analysis) for 5 proteotypic peptides measured in 6 replicates of each of 6 different samples repeated over 6 days averaged 3.4% within-run and 4.3% across all runs. An experiment to identify sources of variation in the workflow demonstrated that MRM measurement and tryptic digestion steps each had average CVs of ∼2.7%. Because of the high purity of the peptide analytes enriched by antibody capture, the liquid chromatography step is minimized and in some cases eliminated altogether, enabling throughput levels consistent with requirements of large biomarker and clinical studies. Copyright © 2016 Elsevier B.V. All rights reserved.

What Not To Do: Anti-patterns for Developing Scientific Workflow Software Components

NASA Astrophysics Data System (ADS)

Futrelle, J.; Maffei, A. R.; Sosik, H. M.; Gallager, S. M.; York, A.

2013-12-01

Scientific workflows promise to enable efficient scaling-up of researcher code to handle large datasets and workloads, as well as documentation of scientific processing via standardized provenance records, etc. Workflow systems and related frameworks for coordinating the execution of otherwise separate components are limited, however, in their ability to overcome software engineering design problems commonly encountered in pre-existing components, such as scripts developed externally by scientists in their laboratories. In practice, this often means that components must be rewritten or replaced in a time-consuming, expensive process. In the course of an extensive workflow development project involving large-scale oceanographic image processing, we have begun to identify and codify 'anti-patterns'--problematic design characteristics of software--that make components fit poorly into complex automated workflows. We have gone on to develop and document low-effort solutions and best practices that efficiently address the anti-patterns we have identified. The issues, solutions, and best practices can be used to evaluate and improve existing code, as well as guiding the development of new components. For example, we have identified a common anti-pattern we call 'batch-itis' in which a script fails and then cannot perform more work, even if that work is not precluded by the failure. The solution we have identified--removing unnecessary looping over independent units of work--is often easier to code than the anti-pattern, as it eliminates the need for complex control flow logic in the component. Other anti-patterns we have identified are similarly easy to identify and often easy to fix. We have drawn upon experience working with three science teams at Woods Hole Oceanographic Institution, each of which has designed novel imaging instruments and associated image analysis code. By developing use cases and prototypes within these teams, we have undertaken formal evaluations of

Development of a user customizable imaging informatics-based intelligent workflow engine system to enhance rehabilitation clinical trials

NASA Astrophysics Data System (ADS)

Wang, Ximing; Martinez, Clarisa; Wang, Jing; Liu, Ye; Liu, Brent

2014-03-01

Clinical trials usually have a demand to collect, track and analyze multimedia data according to the workflow. Currently, the clinical trial data management requirements are normally addressed with custom-built systems. Challenges occur in the workflow design within different trials. The traditional pre-defined custom-built system is usually limited to a specific clinical trial and normally requires time-consuming and resource-intensive software development. To provide a solution, we present a user customizable imaging informatics-based intelligent workflow engine system for managing stroke rehabilitation clinical trials with intelligent workflow. The intelligent workflow engine provides flexibility in building and tailoring the workflow in various stages of clinical trials. By providing a solution to tailor and automate the workflow, the system will save time and reduce errors for clinical trials. Although our system is designed for clinical trials for rehabilitation, it may be extended to other imaging based clinical trials as well.

Critical care physician cognitive task analysis: an exploratory study.

PubMed

Fackler, James C; Watts, Charles; Grome, Anna; Miller, Thomas; Crandall, Beth; Pronovost, Peter

2009-01-01

For better or worse, the imposition of work-hour limitations on house-staff has imperiled continuity and/or improved decision-making. Regardless, the workflow of every physician team in every academic medical centre has been irrevocably altered. We explored the use of cognitive task analysis (CTA) techniques, most commonly used in other high-stress and time-sensitive environments, to analyse key cognitive activities in critical care medicine. The study objective was to assess the usefulness of CTA as an analytical tool in order that physician cognitive tasks may be understood and redistributed within the work-hour limited medical decision-making teams. After approval from each Institutional Review Board, two intensive care units (ICUs) within major university teaching hospitals served as data collection sites for CTA observations and interviews of critical care providers. Five broad categories of cognitive activities were identified: pattern recognition; uncertainty management; strategic vs. tactical thinking; team coordination and maintenance of common ground; and creation and transfer of meaning through stories. CTA within the framework of Naturalistic Decision Making is a useful tool to understand the critical care process of decision-making and communication. The separation of strategic and tactical thinking has implications for workflow redesign. Given the global push for work-hour limitations, such workflow redesign is occurring. Further work with CTA techniques will provide important insights toward rational, rather than random, workflow changes.

Differentiated protection services with failure probability guarantee for workflow-based applications

NASA Astrophysics Data System (ADS)

Zhong, Yaoquan; Guo, Wei; Jin, Yaohui; Sun, Weiqiang; Hu, Weisheng

2010-12-01

A cost-effective and service-differentiated provisioning strategy is very desirable to service providers so that they can offer users satisfactory services, while optimizing network resource allocation. Providing differentiated protection services to connections for surviving link failure has been extensively studied in recent years. However, the differentiated protection services for workflow-based applications, which consist of many interdependent tasks, have scarcely been studied. This paper investigates the problem of providing differentiated services for workflow-based applications in optical grid. In this paper, we develop three differentiated protection services provisioning strategies which can provide security level guarantee and network-resource optimization for workflow-based applications. The simulation demonstrates that these heuristic algorithms provide protection cost-effectively while satisfying the applications' failure probability requirements.

Analysis of acute brain slices by electron microscopy: a correlative light-electron microscopy workflow based on Tokuyasu cryo-sectioning.

PubMed

Loussert Fonta, Celine; Leis, Andrew; Mathisen, Cliff; Bouvier, David S; Blanchard, Willy; Volterra, Andrea; Lich, Ben; Humbel, Bruno M

2015-01-01

Acute brain slices are slices of brain tissue that are kept vital in vitro for further recordings and analyses. This tool is of major importance in neurobiology and allows the study of brain cells such as microglia, astrocytes, neurons and their inter/intracellular communications via ion channels or transporters. In combination with light/fluorescence microscopies, acute brain slices enable the ex vivo analysis of specific cells or groups of cells inside the slice, e.g. astrocytes. To bridge ex vivo knowledge of a cell with its ultrastructure, we developed a correlative microscopy approach for acute brain slices. The workflow begins with sampling of the tissue and precise trimming of a region of interest, which contains GFP-tagged astrocytes that can be visualised by fluorescence microscopy of ultrathin sections. The astrocytes and their surroundings are then analysed by high resolution scanning transmission electron microscopy (STEM). An important aspect of this workflow is the modification of a commercial cryo-ultramicrotome to observe the fluorescent GFP signal during the trimming process. It ensured that sections contained at least one GFP astrocyte. After cryo-sectioning, a map of the GFP-expressing astrocytes is established and transferred to correlation software installed on a focused ion beam scanning electron microscope equipped with a STEM detector. Next, the areas displaying fluorescence are selected for high resolution STEM imaging. An overview area (e.g. a whole mesh of the grid) is imaged with an automated tiling and stitching process. In the final stitched image, the local organisation of the brain tissue can be surveyed or areas of interest can be magnified to observe fine details, e.g. vesicles or gold labels on specific proteins. The robustness of this workflow is contingent on the quality of sample preparation, based on Tokuyasu's protocol. This method results in a reasonable compromise between preservation of morphology and maintenance of

Automated quality control in a file-based broadcasting workflow

NASA Astrophysics Data System (ADS)

Zhang, Lina

2014-04-01

Benefit from the development of information and internet technologies, television broadcasting is transforming from inefficient tape-based production and distribution to integrated file-based workflows. However, no matter how many changes have took place, successful broadcasting still depends on the ability to deliver a consistent high quality signal to the audiences. After the transition from tape to file, traditional methods of manual quality control (QC) become inadequate, subjective, and inefficient. Based on China Central Television's full file-based workflow in the new site, this paper introduces an automated quality control test system for accurate detection of hidden troubles in media contents. It discusses the system framework and workflow control when the automated QC is added. It puts forward a QC criterion and brings forth a QC software followed this criterion. It also does some experiments on QC speed by adopting parallel processing and distributed computing. The performance of the test system shows that the adoption of automated QC can make the production effective and efficient, and help the station to achieve a competitive advantage in the media market.

IT-benchmarking of clinical workflows: concept, implementation, and evaluation.

PubMed

Thye, Johannes; Straede, Matthias-Christopher; Liebe, Jan-David; Hübner, Ursula

2014-01-01

Due to the emerging evidence of health IT as opportunity and risk for clinical workflows, health IT must undergo a continuous measurement of its efficacy and efficiency. IT-benchmarks are a proven means for providing this information. The aim of this study was to enhance the methodology of an existing benchmarking procedure by including, in particular, new indicators of clinical workflows and by proposing new types of visualisation. Drawing on the concept of information logistics, we propose four workflow descriptors that were applied to four clinical processes. General and specific indicators were derived from these descriptors and processes. 199 chief information officers (CIOs) took part in the benchmarking. These hospitals were assigned to reference groups of a similar size and ownership from a total of 259 hospitals. Stepwise and comprehensive feedback was given to the CIOs. Most participants who evaluated the benchmark rated the procedure as very good, good, or rather good (98.4%). Benchmark information was used by CIOs for getting a general overview, advancing IT, preparing negotiations with board members, and arguing for a new IT project.

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

A comprehensive quality control workflow for paired tumor-normal NGS experiments.

PubMed

Schroeder, Christopher M; Hilke, Franz J; Löffler, Markus W; Bitzer, Michael; Lenz, Florian; Sturm, Marc

2017-06-01

Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additional metrics specific for tumor-normal pairs can be calculated. The segmentation into different tools offers a high flexibility and allows reuse for other purposes. All tools produce qcML, a generic XML format for QC of -omics experiments. qcML uses quality metrics defined in an ontology, which was adapted for NGS. All QC tools are implemented in C ++ and run both under Linux and Windows. Plotting requires python 2.7 and matplotlib. The software is available under the 'GNU General Public License version 2' as part of the ngs-bits project: https://github.com/imgag/ngs-bits. christopher.schroeder@med.uni-tuebingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

CMS Data Processing Workflows during an Extended Cosmic Ray Run

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

Not Available

2009-11-01

The CMS Collaboration conducted a month-long data taking exercise, the Cosmic Run At Four Tesla, during October-November 2008, with the goal of commissioning the experiment for extended operation. With all installed detector systems participating, CMS recorded 270 million cosmic ray events with the solenoid at a magnetic field strength of 3.8 T. This paper describes the data flow from the detector through the various online and offline computing systems, as well as the workflows used for recording the data, for aligning and calibrating the detector, and for analysis of the data.

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.

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

The Complete Exosome Workflow Solution: From Isolation to Characterization of RNA Cargo

PubMed Central

Schageman, Jeoffrey; Li, Mu; Barta, Tim; Lea, Kristi; Gu, Jian; Magdaleno, Susan; Setterquist, Robert; Vlassov, Alexander V.

2013-01-01

Exosomes are small (30–150 nm) vesicles containing unique RNA and protein cargo, secreted by all cell types in culture. They are also found in abundance in body fluids including blood, saliva, and urine. At the moment, the mechanism of exosome formation, the makeup of the cargo, biological pathways, and resulting functions are incompletely understood. One of their most intriguing roles is intercellular communication—exosomes function as the messengers, delivering various effector or signaling macromolecules between specific cells. There is an exponentially growing need to dissect structure and the function of exosomes and utilize them for development of minimally invasive diagnostics and therapeutics. Critical to further our understanding of exosomes is the development of reagents, tools, and protocols for their isolation, characterization, and analysis of their RNA and protein contents. Here we describe a complete exosome workflow solution, starting from fast and efficient extraction of exosomes from cell culture media and serum to isolation of RNA followed by characterization of exosomal RNA content using qRT-PCR and next-generation sequencing techniques. Effectiveness of this workflow is exemplified by analysis of the RNA content of exosomes derived from HeLa cell culture media and human serum, using Ion Torrent PGM as a sequencing platform. PMID:24205503

Widening the adoption of workflows to include human and human-machine scientific processes

NASA Astrophysics Data System (ADS)

Salayandia, L.; Pinheiro da Silva, P.; Gates, A. Q.

2010-12-01

Scientific workflows capture knowledge in the form of technical recipes to access and manipulate data that help scientists manage and reuse established expertise to conduct their work. Libraries of scientific workflows are being created in particular fields, e.g., Bioinformatics, where combined with cyber-infrastructure environments that provide on-demand access to data and tools, result in powerful workbenches for scientists of those communities. The focus in these particular fields, however, has been more on automating rather than documenting scientific processes. As a result, technical barriers have impeded a wider adoption of scientific workflows by scientific communities that do not rely as heavily on cyber-infrastructure and computing environments. Semantic Abstract Workflows (SAWs) are introduced to widen the applicability of workflows as a tool to document scientific recipes or processes. SAWs intend to capture a scientists’ perspective about the process of how she or he would collect, filter, curate, and manipulate data to create the artifacts that are relevant to her/his work. In contrast, scientific workflows describe the process from the point of view of how technical methods and tools are used to conduct the work. By focusing on a higher level of abstraction that is closer to a scientist’s understanding, SAWs effectively capture the controlled vocabularies that reflect a particular scientific community, as well as the types of datasets and methods used in a particular domain. From there on, SAWs provide the flexibility to adapt to different environments to carry out the recipes or processes. These environments range from manual fieldwork to highly technical cyber-infrastructure environments, i.e., such as those already supported by scientific workflows. Two cases, one from Environmental Science and another from Geophysics, are presented as illustrative examples.

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

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

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

PubMed

Li, Peter; Castrillo, Juan I; Velarde, Giles; Wassink, Ingo; Soiland-Reyes, Stian; Owen, Stuart; Withers, David; Oinn, Tom; Pocock, Matthew R; Goble, Carole A; Oliver, Stephen G; Kell, Douglas B

2008-08-07

There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. Taverna can be used by data analysis

Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data

PubMed Central

Li, Peter; Castrillo, Juan I; Velarde, Giles; Wassink, Ingo; Soiland-Reyes, Stian; Owen, Stuart; Withers, David; Oinn, Tom; Pocock, Matthew R; Goble, Carole A; Oliver, Stephen G; Kell, Douglas B

2008-01-01

Background There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. Results Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. Conclusion Taverna can

Workflows for ingest of research data into digital archives - tests with Archivematica

NASA Astrophysics Data System (ADS)

Kirchner, I.; Bertelmann, R.; Gebauer, P.; Hasler, T.; Hirt, M.; Klump, J. F.; Peters-Kotting, W.; Rusch, B.; Ulbricht, D.

2013-12-01

Publication of research data and future re-use of measured data require the long-term preservation of digital objects. The ISO OAIS reference model defines responsibilities for long-term preservation of digital objects and although there is software available to support preservation of digital data, there are still problems remaining to be solved. A key task in preservation is to make the datasets ready for ingest into the archive, which is called the creation of Submission Information Packages (SIPs) in the OAIS model. This includes the creation of appropriate preservation metadata. Scientists need to be trained to deal with different types of data and to heighten their awareness for quality metadata. Other problems arise during the assembly of SIPs and during ingest into the archive because file format validators may produce conflicting output for identical data files and these conflicts are difficult to resolve automatically. Also, validation and identification tools are notorious for their poor performance. In the project EWIG Zuse-Institute Berlin acts as an infrastructure facility, while the Institute for Meteorology at FU Berlin and the German research Centre for Geosciences GFZ act as two different data producers. The aim of the project is to develop workflows for the transfer of research data into digital archives and the future re-use of data from long-term archives with emphasis on data from the geosciences. The technical work is supplemented by interviews with data practitioners at several institutions to identify problems in digital preservation workflows and by the development of university teaching materials to train students in the curation of research data and metadata. The free and open-source software Archivematica [1] is used as digital preservation system. The creation and ingest of SIPs has to meet several archival standards and be compatible to the Metadata Encoding and Transmission Standard (METS). The two data producers use different

Data Intensive Scientific Workflows on a Federated Cloud: CRADA Final Report

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

Garzoglio, Gabriele

The Fermilab Scientific Computing Division and the KISTI Global Science Experimental Data Hub Center have built a prototypical large-scale infrastructure to handle scientific workflows of stakeholders to run on multiple cloud resources. The demonstrations have been in the areas of (a) Data-Intensive Scientific Workflows on Federated Clouds, (b) Interoperability and Federation of Cloud Resources, and (c) Virtual Infrastructure Automation to enable On-Demand Services.

Aaron's Solution, Instructor's Problem: Teaching Surface Analysis Using GIS

ERIC Educational Resources Information Center

Koch, Tom; Denike, Ken

2007-01-01

Teaching GIS is relatively simple, a matter of helping students develop familiarity with the software. Mapping as an aid to thinking is harder to instruct. This article presents a laboratory and lecture package developed to teach the utility of mapping in a course on spatial data analysis. Following a historical review of the use of surface…

Teaching Data Analysis with Interactive Visual Narratives

ERIC Educational Resources Information Center

Saundage, Dilal; Cybulski, Jacob L.; Keller, Susan; Dharmasena, Lasitha

2016-01-01

Data analysis is a major part of business analytics (BA), which refers to the skills, methods, and technologies that enable managers to make swift, quality decisions based on large amounts of data. BA has become a major component of Information Systems (IS) courses all over the world. The challenge for IS educators is to teach data analysis--the…

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.

The medical simulation markup language - simplifying the biomechanical modeling workflow.

PubMed

Suwelack, Stefan; Stoll, Markus; Schalck, Sebastian; Schoch, Nicolai; Dillmann, Rüdiger; Bendl, Rolf; Heuveline, Vincent; Speidel, Stefanie

2014-01-01

Modeling and simulation of the human body by means of continuum mechanics has become an important tool in diagnostics, computer-assisted interventions and training. This modeling approach seeks to construct patient-specific biomechanical models from tomographic data. Usually many different tools such as segmentation and meshing algorithms are involved in this workflow. In this paper we present a generalized and flexible description for biomechanical models. The unique feature of the new modeling language is that it not only describes the final biomechanical simulation, but also the workflow how the biomechanical model is constructed from tomographic data. In this way, the MSML can act as a middleware between all tools used in the modeling pipeline. The MSML thus greatly facilitates the prototyping of medical simulation workflows for clinical and research purposes. In this paper, we not only detail the XML-based modeling scheme, but also present a concrete implementation. Different examples highlight the flexibility, robustness and ease-of-use of the approach.

A Flexible Workflow for Automated Bioluminescent Kinase Selectivity Profiling.

PubMed

Worzella, Tracy; Butzler, Matt; Hennek, Jacquelyn; Hanson, Seth; Simdon, Laura; Goueli, Said; Cowan, Cris; Zegzouti, Hicham

2017-04-01

Kinase profiling during drug discovery is a necessary process to confirm inhibitor selectivity and assess off-target activities. However, cost and logistical limitations prevent profiling activities from being performed in-house. We describe the development of an automated and flexible kinase profiling workflow that combines ready-to-use kinase enzymes and substrates in convenient eight-tube strips, a bench-top liquid handling device, ADP-Glo Kinase Assay (Promega, Madison, WI) technology to quantify enzyme activity, and a multimode detection instrument. Automated methods were developed for kinase reactions and quantification reactions to be assembled on a Gilson (Middleton, WI) PIPETMAX, following standardized plate layouts for single- and multidose compound profiling. Pipetting protocols were customized at runtime based on user-provided information, including compound number, increment for compound titrations, and number of kinase families to use. After the automated liquid handling procedures, a GloMax Discover (Promega) microplate reader preloaded with SMART protocols was used for luminescence detection and automatic data analysis. The functionality of the automated workflow was evaluated with several compound-kinase combinations in single-dose or dose-response profiling formats. Known target-specific inhibitions were confirmed. Novel small molecule-kinase interactions, including off-target inhibitions, were identified and confirmed in secondary studies. By adopting this streamlined profiling process, researchers can quickly and efficiently profile compounds of interest on site.

Stylistic Patterns in Language Teaching Research Articles: A Multidimensional Analysis

ERIC Educational Resources Information Center

Kitjaroenpaiboon, Woravit; Getkham, Kanyarat

2016-01-01

This paper presents the results of a multidimensional analysis to investigate stylistic patterns and their communicative functions in language teaching research articles. The findings were that language teaching research articles contained six stylistic patterns and communicative functions. Pattern I consisted of seven salient positive features…

Health information exchange technology on the front lines of healthcare: workflow factors and patterns of use

PubMed Central

Johnson, Kevin B; Lorenzi, Nancy M

2011-01-01

Objective The goal of this study was to develop an in-depth understanding of how a health information exchange (HIE) fits into clinical workflow at multiple clinical sites. Materials and Methods The ethnographic qualitative study was conducted over a 9-month period in six emergency departments (ED) and eight ambulatory clinics in Memphis, Tennessee, USA. Data were collected using direct observation, informal interviews during observation, and formal semi-structured interviews. The authors observed for over 180 h, during which providers used the exchange 130 times. Results HIE-related workflow was modeled for each ED site and ambulatory clinic group and substantial site-to-site workflow differences were identified. Common patterns in HIE-related workflow were also identified across all sites, leading to the development of two role-based workflow models: nurse based and physician based. The workflow elements framework was applied to the two role-based patterns. An in-depth description was developed of how providers integrated HIE into existing clinical workflow, including prompts for HIE use. Discussion Workflow differed substantially among sites, but two general role-based HIE usage models were identified. Although providers used HIE to improve continuity of patient care, patient–provider trust played a significant role. Types of information retrieved related to roles, with nurses seeking to retrieve recent hospitalization data and more open-ended usage by nurse practitioners and physicians. User and role-specific customization to accommodate differences in workflow and information needs may increase the adoption and use of HIE. Conclusion Understanding end users' perspectives towards HIE technology is crucial to the long-term success of HIE. By applying qualitative methods, an in-depth understanding of HIE usage was developed. PMID:22003156

Workflow Optimization in Vertebrobasilar Occlusion

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

Kamper, Lars, E-mail: lars.kamper@helios-kliniken.de; Meyn, Hannes; Rybacki, Konrad

2012-06-15

Objective: In vertebrobasilar occlusion, rapid recanalization is the only substantial means to improve the prognosis. We introduced a standard operating procedure (SOP) for interventional therapy to analyze the effects on interdisciplinary time management. Methods: Intrahospital time periods between hospital admission and neuroradiological intervention were retrospectively analyzed, together with the patients' outcome, before (n = 18) and after (n = 20) implementation of the SOP. Results: After implementation of the SOP, we observed statistically significant improvement of postinterventional patient neurological status (p = 0.017). In addition, we found a decrease of 5:33 h for the mean time period from hospital admissionmore » until neuroradiological intervention. The recanalization rate increased from 72.2% to 80% after implementation of the SOP. Conclusion: Our results underscore the relevance of SOP implementation and analysis of time management for clinical workflow optimization. Both may trigger awareness for the need of efficient interdisciplinary time management. This could be an explanation for the decreased time periods and improved postinterventional patient status after SOP implementation.« less

Workflow-Based Software Development Environment

NASA Technical Reports Server (NTRS)

Izygon, Michel E.

2013-01-01

The Software Developer's Assistant (SDA) helps software teams more efficiently and accurately conduct or execute software processes associated with NASA mission-critical software. SDA is a process enactment platform that guides software teams through project-specific standards, processes, and procedures. Software projects are decomposed into all of their required process steps or tasks, and each task is assigned to project personnel. SDA orchestrates the performance of work required to complete all process tasks in the correct sequence. The software then notifies team members when they may begin work on their assigned tasks and provides the tools, instructions, reference materials, and supportive artifacts that allow users to compliantly perform the work. A combination of technology components captures and enacts any software process use to support the software lifecycle. It creates an adaptive workflow environment that can be modified as needed. SDA achieves software process automation through a Business Process Management (BPM) approach to managing the software lifecycle for mission-critical projects. It contains five main parts: TieFlow (workflow engine), Business Rules (rules to alter process flow), Common Repository (storage for project artifacts, versions, history, schedules, etc.), SOA (interface to allow internal, GFE, or COTS tools integration), and the Web Portal Interface (collaborative web environment

Improved workflow modelling using role activity diagram-based modelling with application to a radiology service case study.

PubMed

Shukla, Nagesh; Keast, John E; Ceglarek, Darek

2014-10-01

The modelling of complex workflows is an important problem-solving technique within healthcare settings. However, currently most of the workflow models use a simplified flow chart of patient flow obtained using on-site observations, group-based debates and brainstorming sessions, together with historic patient data. This paper presents a systematic and semi-automatic methodology for knowledge acquisition with detailed process representation using sequential interviews of people in the key roles involved in the service delivery process. The proposed methodology allows the modelling of roles, interactions, actions, and decisions involved in the service delivery process. This approach is based on protocol generation and analysis techniques such as: (i) initial protocol generation based on qualitative interviews of radiology staff, (ii) extraction of key features of the service delivery process, (iii) discovering the relationships among the key features extracted, and, (iv) a graphical representation of the final structured model of the service delivery process. The methodology is demonstrated through a case study of a magnetic resonance (MR) scanning service-delivery process in the radiology department of a large hospital. A set of guidelines is also presented in this paper to visually analyze the resulting process model for identifying process vulnerabilities. A comparative analysis of different workflow models is also conducted. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Clinic Workflow Simulations using Secondary EHR Data

PubMed Central

Hribar, Michelle R.; Biermann, David; Read-Brown, Sarah; Reznick, Leah; Lombardi, Lorinna; Parikh, Mansi; Chamberlain, Winston; Yackel, Thomas R.; Chiang, Michael F.

2016-01-01

Clinicians today face increased patient loads, decreased reimbursements and potential negative productivity impacts of using electronic health records (EHR), but have little guidance on how to improve clinic efficiency. Discrete event simulation models are powerful tools for evaluating clinical workflow and improving efficiency, particularly when they are built from secondary EHR timing data. The purpose of this study is to demonstrate that these simulation models can be used for resource allocation decision making as well as for evaluating novel scheduling strategies in outpatient ophthalmology clinics. Key findings from this study are that: 1) secondary use of EHR timestamp data in simulation models represents clinic workflow, 2) simulations provide insight into the best allocation of resources in a clinic, 3) simulations provide critical information for schedule creation and decision making by clinic managers, and 4) simulation models built from EHR data are potentially generalizable. PMID:28269861

[Digital teaching archive. Concept, implementation, and experiences in a university setting].

PubMed

Trumm, C; Dugas, M; Wirth, S; Treitl, M; Lucke, A; Küttner, B; Pander, E; Clevert, D-A; Glaser, C; Reiser, M

2005-08-01

Film-based teaching files require a substantial investment in human, logistic, and financial resources. The combination of computer and network technology facilitates the workflow integration of distributing radiologic teaching cases within an institution (intranet) or via the World Wide Web (Internet). A digital teaching file (DTF) should include the following basic functions: image import from different sources and of different formats, editing of imported images, uniform case classification, quality control (peer review), a controlled access of different user groups (in-house and external), and an efficient retrieval strategy. The portable network graphics image format (PNG) is especially suitable for DTFs because of several features: pixel support, 2D-interlacing, gamma correction, and lossless compression. The American College of Radiology (ACR) "Index for Radiological Diagnoses" is hierarchically organized and thus an ideal classification system for a DTF. Computer-based training (CBT) in radiology is described in numerous publications, from supplementing traditional learning methods to certified education via the Internet. Attractiveness of a CBT application can be increased by integration of graphical and interactive elements but makes workflow integration of daily case input more difficult. Our DTF was built with established Internet instruments and integrated into a heterogeneous PACS/RIS environment. It facilitates a quick transfer (DICOM_Send) of selected images at the time of interpretation to the DTF and access to the DTF application at any time anywhere within the university hospital intranet employing a standard web browser. A DTF is a small but important building block in an institutional strategy of knowledge management.

Time analysis for optimization of radiology workflow in conventional radiology during RIS-PACS-integration

NASA Astrophysics Data System (ADS)

Falkensammer, Peter; Soegner, Peter I.; zur Nedden, Dieter

2002-05-01

The integration of RIS-PACS systems in radiology units are intended to reduce time consumption in radiology workflow and thus to increase radiologist productivity. Along with the RIS-PACS integration at the University Hospital Innsbruck we analyzed workflow from patient admission to release of final reports before implementation. The follow up study after six months of the implementation is currently in work. In this study we compared chest to skeletal x-ray examinations in 969 patients before the implementation. Drawing the admission-to-release-of-final-report period showed a two-peak diagram with the first peak corresponding to a release of final results on the same day and the second peak to a release on the following day. In the chest x-ray group, 57% were released the same day (mean value 4:02 hours) and 43% the next day (mean value 21:47 hours). Looking at the skeletal x-rays 40% were released the same day (mean value 3:58 hours) and 60% were released the next day (mean value 21:05 hours). Summarizing the results we should say, that the average chest x-ray requires less time than an skeletal x-ray, due to the fact that a greater percentage of reports is released the same day. The most important result is, that the most time consuming workstep is the exchange of data media between radiologist and secretary with at least 5 hours.

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

An automated workflow for patient-specific quality control of contour propagation

NASA Astrophysics Data System (ADS)

Beasley, William J.; McWilliam, Alan; Slevin, Nicholas J.; Mackay, Ranald I.; van Herk, Marcel

2016-12-01

Contour propagation is an essential component of adaptive radiotherapy, but current contour propagation algorithms are not yet sufficiently accurate to be used without manual supervision. Manual review of propagated contours is time-consuming, making routine implementation of real-time adaptive radiotherapy unrealistic. Automated methods of monitoring the performance of contour propagation algorithms are therefore required. We have developed an automated workflow for patient-specific quality control of contour propagation and validated it on a cohort of head and neck patients, on which parotids were outlined by two observers. Two types of error were simulated—mislabelling of contours and introducing noise in the scans before propagation. The ability of the workflow to correctly predict the occurrence of errors was tested, taking both sets of observer contours as ground truth, using receiver operator characteristic analysis. The area under the curve was 0.90 and 0.85 for the observers, indicating good ability to predict the occurrence of errors. This tool could potentially be used to identify propagated contours that are likely to be incorrect, acting as a flag for manual review of these contours. This would make contour propagation more efficient, facilitating the routine implementation of adaptive radiotherapy.

Development of a High-Throughput Ion-Exchange Resin Characterization Workflow.

PubMed

Liu, Chun; Dermody, Daniel; Harris, Keith; Boomgaard, Thomas; Sweeney, Jeff; Gisch, Daryl; Goltz, Bob

2017-06-12

A novel high-throughout (HTR) ion-exchange (IEX) resin workflow has been developed for characterizing ion exchange equilibrium of commercial and experimental IEX resins against a range of different applications where water environment differs from site to site. Because of its much higher throughput, design of experiment (DOE) methodology can be easily applied for studying the effects of multiple factors on resin performance. Two case studies will be presented to illustrate the efficacy of the combined HTR workflow and DOE method. In case study one, a series of anion exchange resins have been screened for selective removal of NO 3 - and NO 2 - in water environments consisting of multiple other anions, varied pH, and ionic strength. The response surface model (RSM) is developed to statistically correlate the resin performance with the water composition and predict the best resin candidate. In case study two, the same HTR workflow and DOE method have been applied for screening different cation exchange resins in terms of the selective removal of Mg 2+ , Ca 2+ , and Ba 2+ from high total dissolved salt (TDS) water. A master DOE model including all of the cation exchange resins is created to predict divalent cation removal by different IEX resins under specific conditions, from which the best resin candidates can be identified. The successful adoption of HTR workflow and DOE method for studying the ion exchange of IEX resins can significantly reduce the resources and time to address industry and application needs.

Structuring research methods and data with the research object model: genomics workflows as a case study.

PubMed

Hettne, Kristina M; Dharuri, Harish; Zhao, Jun; Wolstencroft, Katherine; Belhajjame, Khalid; Soiland-Reyes, Stian; Mina, Eleni; Thompson, Mark; Cruickshank, Don; Verdes-Montenegro, Lourdes; Garrido, Julian; de Roure, David; Corcho, Oscar; Klyne, Graham; van Schouwen, Reinout; 't Hoen, Peter A C; Bechhofer, Sean; Goble, Carole; Roos, Marco

2014-01-01

One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?". Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro.

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.

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

PubMed Central

Powers, Christina M; Mills, Karmann A; Morris, Stephanie A; Klaessig, Fred; Gaheen, Sharon; Lewinski, Nastassja

2015-01-01

Summary There is a critical opportunity in the field of nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics). This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration). Other articles in this series discuss key aspects of nanocuration (temporal metadata, data completeness, database integration), while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1) the rationale and importance of a defined workflow in nanocuration, 2) the influence of organizational goals or purpose on the workflow, 3) established workflow practices in other fields, 4) current workflow practices in nanocuration, 5) key challenges for workflows in emerging fields like nanomaterials, 6) examples to make these challenges more tangible, and 7) recommendations to address the identified challenges. Throughout the article, there is an emphasis on illustrating key concepts and current practices in the field. Data on current practices in the field are from a group of stakeholders active in nanocuration. In general, the development of workflows for nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano). Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research groups) and providing nanocuration resources (e.g., training) will likely prove crucial for the wider application of nanocuration workflows in the scientific community. PMID:26425437

Using Modules in Teaching Complex Analysis

ERIC Educational Resources Information Center

Kinney, William M.

2017-01-01

Educational modules can play an important part in revitalizing the teaching and learning of complex analysis. At the Westmont College workshop on the subject in June 2014, time was spent generating ideas and creating structures for module proposals. Sharing some of those ideas and giving a few example modules is the main purpose of this paper. The…

Workflow opportunities using JPEG 2000

NASA Astrophysics Data System (ADS)

Foshee, Scott

2002-11-01

JPEG 2000 is a new image compression standard from ISO/IEC JTC1 SC29 WG1, the Joint Photographic Experts Group (JPEG) committee. Better thought of as a sibling to JPEG rather than descendant, the JPEG 2000 standard offers wavelet based compression as well as companion file formats and related standardized technology. This paper examines the JPEG 2000 standard for features in four specific areas-compression, file formats, client-server, and conformance/compliance that enable image workflows.

An end-to-end workflow for engineering of biological networks from high-level specifications.

PubMed

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; Yaman, Fusun

2012-08-17

We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.

A workflow for improving estimates of microplastic contamination in marine waters: A case study from North-Western Australia.

PubMed

Kroon, Frederieke; Motti, Cherie; Talbot, Sam; Sobral, Paula; Puotinen, Marji

2018-07-01

Plastic pollution is ubiquitous throughout the marine environment, with microplastic (i.e. <5 mm) contamination a global issue of emerging concern. The lack of universally accepted methods for quantifying microplastic contamination, including consistent application of microscopy, photography, an spectroscopy and photography, may result in unrealistic contamination estimates. Here, we present and apply an analysis workflow tailored to quantifying microplastic contamination in marine waters, incorporating stereomicroscopic visual sorting, microscopic photography and attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. The workflow outlines step-by-step processing and associated decision making, thereby reducing bias in plastic identification and improving confidence in contamination estimates. Specific processing steps include (i) the use of a commercial algorithm-based comparison of particle spectra against an extensive commercially curated spectral library, followed by spectral interpretation to establish the chemical composition, (ii) a comparison against a customised contaminant spectral library to eliminate procedural contaminants, and (iii) final assignment of particles as either natural- or anthropogenic-derived materials, based on chemical type, a compare analysis of each particle against other particle spectra, and physical characteristics of particles. Applying this workflow to 54 tow samples collected in marine waters of North-Western Australia visually identified 248 potential anthropogenic particles. Subsequent ATR-FTIR spectroscopy, chemical assignment and visual re-inspection of photographs established 144 (58%) particles to be of anthropogenic origin. Of the original 248 particles, 97 (39%) were ultimately confirmed to be plastics, with 85 of these (34%) classified as microplastics, demonstrating that over 60% of particles may be misidentified as plastics if visual identification is not complemented by spectroscopy

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...

A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine

PubMed Central

Zou, Wei; She, Jianwen; Tolstikov, Vladimir V.

2013-01-01

Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC–LC), reversed-phase liquid chromatography (RP–LC), and gas chromatography (GC). All three techniques are coupled to a mass spectrometer (MS) in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM) and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow. PMID:24958150

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.

Critical care physician cognitive task analysis: an exploratory study

PubMed Central

Fackler, James C; Watts, Charles; Grome, Anna; Miller, Thomas; Crandall, Beth; Pronovost, Peter

2009-01-01

Introduction For better or worse, the imposition of work-hour limitations on house-staff has imperiled continuity and/or improved decision-making. Regardless, the workflow of every physician team in every academic medical centre has been irrevocably altered. We explored the use of cognitive task analysis (CTA) techniques, most commonly used in other high-stress and time-sensitive environments, to analyse key cognitive activities in critical care medicine. The study objective was to assess the usefulness of CTA as an analytical tool in order that physician cognitive tasks may be understood and redistributed within the work-hour limited medical decision-making teams. Methods After approval from each Institutional Review Board, two intensive care units (ICUs) within major university teaching hospitals served as data collection sites for CTA observations and interviews of critical care providers. Results Five broad categories of cognitive activities were identified: pattern recognition; uncertainty management; strategic vs. tactical thinking; team coordination and maintenance of common ground; and creation and transfer of meaning through stories. Conclusions CTA within the framework of Naturalistic Decision Making is a useful tool to understand the critical care process of decision-making and communication. The separation of strategic and tactical thinking has implications for workflow redesign. Given the global push for work-hour limitations, such workflow redesign is occurring. Further work with CTA techniques will provide important insights toward rational, rather than random, workflow changes. PMID:19265517

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

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

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.

High throughput workflow for coacervate formation and characterization in shampoo systems.

PubMed

Kalantar, T H; Tucker, C J; Zalusky, A S; Boomgaard, T A; Wilson, B E; Ladika, M; Jordan, S L; Li, W K; Zhang, X; Goh, C G

2007-01-01

Cationic cellulosic polymers find wide utility as benefit agents in shampoo. Deposition of these polymers onto hair has been shown to mend split-ends, improve appearance and wet combing, as well as provide controlled delivery of insoluble actives. The deposition is thought to be enhanced by the formation of a polymer/surfactant complex that phase-separates from the bulk solution upon dilution. A standard characterization method has been developed to characterize the coacervate formation upon dilution, but the test is time and material prohibitive. We have developed a semi-automated high throughput workflow to characterize the coacervate-forming behavior of different shampoo formulations. A procedure that allows testing of real use shampoo dilutions without first formulating a complete shampoo was identified. This procedure was adapted to a Tecan liquid handler by optimizing the parameters for liquid dispensing as well as for mixing. The high throughput workflow enabled preparation and testing of hundreds of formulations with different types and levels of cationic cellulosic polymers and surfactants, and for each formulation a haze diagram was constructed. Optimal formulations and their dilutions that give substantial coacervate formation (determined by haze measurements) were identified. Results from this high throughput workflow were shown to reproduce standard haze and bench-top turbidity measurements, and this workflow has the advantages of using less material and allowing more variables to be tested with significant time savings.

Workflow interruptions and mental workload in hospital pediatricians: an observational study.

PubMed

Weigl, Matthias; Müller, Andreas; Angerer, Peter; Hoffmann, Florian

2014-09-24

Pediatricians' workload is increasingly thought to affect pediatricians' quality of work life and patient safety. Workflow interruptions are a frequent stressor in clinical work, impeding clinicians' attention and contributing to clinical malpractice. We aimed to investigate prospective associations of workflow interruptions with multiple dimensions of mental workload in pediatricians during clinical day shifts. In an Academic Children's Hospital a prospective study of 28 full shift observations was conducted among pediatricians providing ward coverage. The prevalence of workflow interruptions was based on expert observation using a validated observation instrument. Concurrently, Pediatricians' workload ratings were assessed with three workload dimensions of the well-validated NASA-Task Load Index: mental demands, effort, and frustration. Observed pediatricians were, on average, disrupted 4.7 times per hour. Most frequent were interruptions by colleagues (30.2%), nursing staff (29.7%), and by telephone/beeper calls (16.3%). Interruption measures were correlated with two workload outcomes of interest: frequent workflow interruptions were related to less cognitive demands, but frequent interruptions were associated with increased frustration. With regard to single sources, interruptions by colleagues showed the strongest associations to workload. The findings provide insights into specific pathways between different types of interruptions and pediatricians' mental workload. These findings suggest further research and yield a number of work and organization re-design suggestions for pediatric care.

Teaching Case: Analysis of an Electronic Voting System

ERIC Educational Resources Information Center

Thompson, Nik; Toohey, Danny

2014-01-01

This teaching case discusses the analysis of an electronic voting system. The development of the case was motivated by research into information security and management, but as it includes procedural aspects, organizational structure and personnel, it is a suitable basis for all aspects of systems analysis, planning and design tasks. The material…

Quality Control of Structural MRI Images Applied Using FreeSurfer—A Hands-On Workflow to Rate Motion Artifacts

PubMed Central

Backhausen, Lea L.; Herting, Megan M.; Buse, Judith; Roessner, Veit; Smolka, Michael N.; Vetter, Nora C.

2016-01-01

In structural magnetic resonance imaging motion artifacts are common, especially when not scanning healthy young adults. It has been shown that motion affects the analysis with automated image-processing techniques (e.g., FreeSurfer). This can bias results. Several developmental and adult studies have found reduced volume and thickness of gray matter due to motion artifacts. Thus, quality control is necessary in order to ensure an acceptable level of quality and to define exclusion criteria of images (i.e., determine participants with most severe artifacts). However, information about the quality control workflow and image exclusion procedure is largely lacking in the current literature and the existing rating systems differ. Here, we propose a stringent workflow of quality control steps during and after acquisition of T1-weighted images, which enables researchers dealing with populations that are typically affected by motion artifacts to enhance data quality and maximize sample sizes. As an underlying aim we established a thorough quality control rating system for T1-weighted images and applied it to the analysis of developmental clinical data using the automated processing pipeline FreeSurfer. This hands-on workflow and quality control rating system will aid researchers in minimizing motion artifacts in the final data set, and therefore enhance the quality of structural magnetic resonance imaging studies. PMID:27999528

Mathematical Modeling and Analysis of Mass Spectrometry Data in Workflows for the Discovery of Biomarkets in Breast Cancer

DTIC Science & Technology

2008-07-01

Mass Spectrometry Data in Workflows for the Discovery of Biomarkets in Breast Cancer PRINCIPAL INVESTIGATOR: Vladimir Fokin, Ph.D... Biomarkets in Breast Cancer 5b. GRANT NUMBER W81XWH-07-1-0447 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Vladimir Fokin, Ph.D

A meta-analysis of instructional systems applied in science teaching

NASA Astrophysics Data System (ADS)

Willett, John B.; Yamashita, June J. M.; Anderson, Ronald D.

This article is a report of a meta-analysis on the question: What are the effects of different instructional systems used in science teaching? The studies utilized in this meta-analysis were identified by a process that included a systematic screening of all dissertations completed in the field of science education since 1950, an ERIC search of the literature, a systematic screening of selected research journals, and the standard procedure of identifying potentially relevant studies through examination of the bibliographies of the studies reviewed. In all, the 130 studies coded gave rise to 341 effect sizes. The mean effect size produced over all systems was 0.10 with a standard deviation of 0.41, indicating that, on the average, an innovative teaching system in this sample produced one-tenth of a standard deviation better performance than traditional science teaching. Particular kinds of teaching systems, however, produced results that varied from this overall result. Mean effect sizes were also computed by year of publication, form of publication, grade level, and subject matter.

Provenance for Runtime Workflow Steering and Validation in Computational Seismology

NASA Astrophysics Data System (ADS)

Spinuso, A.; Krischer, L.; Krause, A.; Filgueira, R.; Magnoni, F.; Muraleedharan, V.; David, M.

2014-12-01

Provenance systems may be offered by modern workflow engines to collect metadata about the data transformations at runtime. If combined with effective visualisation and monitoring interfaces, these provenance recordings can speed up the validation process of an experiment, suggesting interactive or automated interventions with immediate effects on the lifecycle of a workflow run. For instance, in the field of computational seismology, if we consider research applications performing long lasting cross correlation analysis and high resolution simulations, the immediate notification of logical errors and the rapid access to intermediate results, can produce reactions which foster a more efficient progress of the research. These applications are often executed in secured and sophisticated HPC and HTC infrastructures, highlighting the need for a comprehensive framework that facilitates the extraction of fine grained provenance and the development of provenance aware components, leveraging the scalability characteristics of the adopted workflow engines, whose enactment can be mapped to different technologies (MPI, Storm clusters, etc). This work looks at the adoption of W3C-PROV concepts and data model within a user driven processing and validation framework for seismic data, supporting also computational and data management steering. Validation needs to balance automation with user intervention, considering the scientist as part of the archiving process. Therefore, the provenance data is enriched with community-specific metadata vocabularies and control messages, making an experiment reproducible and its description consistent with the community understandings. Moreover, it can contain user defined terms and annotations. The current implementation of the system is supported by the EU-Funded VERCE (http://verce.eu). It provides, as well as the provenance generation mechanisms, a prototypal browser-based user interface and a web API built on top of a NoSQL storage

Pedagogical issues for effective teaching of biosignal processing and analysis.

PubMed

Sandham, William A; Hamilton, David J

2010-01-01

Biosignal processing and analysis is generally perceived by many students to be a challenging topic to understand, and to become adept with the necessary analytical skills. This is a direct consequence of the high mathematical content involved, and the many abstract features of the topic. The MATLAB and Mathcad software packages offer an excellent algorithm development environment for teaching biosignal processing and analysis modules, and can also be used effectively in many biosignal, and indeed bioengineering, research areas. In this paper, traditional introductory and advanced biosignal processing (and analysis) syllabi are reviewed, and the use of MATLAB and Mathcad for teaching and research is illustrated with a number of examples.

Scan-layered reconstructions: A pilot study of a nondestructive dental histoanatomical analysis method and digital workflow to create restorations driven by natural dentin and enamel morphology.

PubMed

Malta Barbosa, João; Tovar, Nick; A Tuesta, Pablo; Hirata, Ronaldo; Guimarães, Nuno; Romanini, José C; Moghadam, Marjan; Coelho, Paulo G; Jahangiri, Leila

2017-07-08

This work aims to present a pilot study of a non-destructive dental histo-anatomical analysis technique as well as to push the boundaries of the presently available restorative workflows for the fabrication of highly customized ceramic restorations. An extracted human maxillary central incisor was subject to a micro computed tomography scan and the acquired data was transferred into a workstation, reconstructed, segmented, evaluated and later imported into a Computer-Aided Design/Computer-Aided Manufacturing software for the fabrication of a ceramic resin-bonded prosthesis. The obtained prosthesis presented an encouraging optical behavior and was used clinically as final restoration. The digitally layered restorative replication of natural tooth morphology presents today as a clear possibility. New clinical and laboratory-fabricated, biologically inspired digital restorative protocols are to be expected in the near future. The digitally layered restorative replication of natural tooth morphology presents today as a clear possibility. This pilot study may represent a stimulus for future research and applications of digital imaging as well as digital restorative workflows in service of esthetic dentistry. © 2017 Wiley Periodicals, Inc.

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.

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography.

PubMed

Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M F; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A; Gotz, Andy

2012-08-01

The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

PubMed Central

Laffy, Patrick W.; Wood-Charlson, Elisha M.; Turaev, Dmitrij; Weynberg, Karen D.; Botté, Emmanuelle S.; van Oppen, Madeleine J. H.; Webster, Nicole S.; Rattei, Thomas

2016-01-01

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments. PMID:27375564

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.

PubMed

Välikangas, Tommi; Suomi, Tomi; Elo, Laura L

2017-05-31

Label-free mass spectrometry (MS) has developed into an important tool applied in various fields of biological and life sciences. Several software exist to process the raw MS data into quantified protein abundances, including open source and commercial solutions. Each software includes a set of unique algorithms for different tasks of the MS data processing workflow. While many of these algorithms have been compared separately, a thorough and systematic evaluation of their overall performance is missing. Moreover, systematic information is lacking about the amount of missing values produced by the different proteomics software and the capabilities of different data imputation methods to account for them.In this study, we evaluated the performance of five popular quantitative label-free proteomics software workflows using four different spike-in data sets. Our extensive testing included the number of proteins quantified and the number of missing values produced by each workflow, the accuracy of detecting differential expression and logarithmic fold change and the effect of different imputation and filtering methods on the differential expression results. We found that the Progenesis software performed consistently well in the differential expression analysis and produced few missing values. The missing values produced by the other software decreased their performance, but this difference could be mitigated using proper data filtering or imputation methods. Among the imputation methods, we found that the local least squares (lls) regression imputation consistently increased the performance of the software in the differential expression analysis, and a combination of both data filtering and local least squares imputation increased performance the most in the tested data sets. © The Author 2017. Published by Oxford University Press.

Quantifying nursing workflow in medication administration.

PubMed

Keohane, Carol A; Bane, Anne D; Featherstone, Erica; Hayes, Judy; Woolf, Seth; Hurley, Ann; Bates, David W; Gandhi, Tejal K; Poon, Eric G

2008-01-01

New medication administration systems are showing promise in improving patient safety at the point of care, but adoption of these systems requires significant changes in nursing workflow. To prepare for these changes, the authors report on a time-motion study that measured the proportion of time that nurses spend on various patient care activities, focusing on medication administration-related activities. Implications of their findings are discussed.

Enabling Smart Workflows over Heterogeneous ID-Sensing Technologies

PubMed Central

Giner, Pau; Cetina, Carlos; Lacuesta, Raquel; Palacios, Guillermo

2012-01-01

Sensing technologies in mobile devices play a key role in reducing the gap between the physical and the digital world. The use of automatic identification capabilities can improve user participation in business processes where physical elements are involved (Smart Workflows). However, identifying all objects in the user surroundings does not automatically translate into meaningful services to the user. This work introduces Parkour, an architecture that allows the development of services that match the goals of each of the participants in a smart workflow. Parkour is based on a pluggable architecture that can be extended to provide support for new tasks and technologies. In order to facilitate the development of these plug-ins, tools that automate the development process are also provided. Several Parkour-based systems have been developed in order to validate the applicability of the proposal. PMID:23202193

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