Visualization, documentation, analysis, and communication of large scale gene regulatory networks

PubMed Central

Longabaugh, William J.R.; Davidson, Eric H.; Bolouri, Hamid

2009-01-01

Summary Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on computational GRN modeling tools, and there is a need for custom modeling tools. In this paper, we report on our ongoing development of BioTapestry, an open source, freely available computational tool designed specifically for GRN modeling. We also outline our future development plans, and give some examples of current applications of BioTapestry. PMID:18757046

The challenge of big data in public health: an opportunity for visual analytics.

PubMed

Ola, Oluwakemi; Sedig, Kamran

2014-01-01

Public health (PH) data can generally be characterized as big data. The efficient and effective use of this data determines the extent to which PH stakeholders can sufficiently address societal health concerns as they engage in a variety of work activities. As stakeholders interact with data, they engage in various cognitive activities such as analytical reasoning, decision-making, interpreting, and problem solving. Performing these activities with big data is a challenge for the unaided mind as stakeholders encounter obstacles relating to the data's volume, variety, velocity, and veracity. Such being the case, computer-based information tools are needed to support PH stakeholders. Unfortunately, while existing computational tools are beneficial in addressing certain work activities, they fall short in supporting cognitive activities that involve working with large, heterogeneous, and complex bodies of data. This paper presents visual analytics (VA) tools, a nascent category of computational tools that integrate data analytics with interactive visualizations, to facilitate the performance of cognitive activities involving big data. Historically, PH has lagged behind other sectors in embracing new computational technology. In this paper, we discuss the role that VA tools can play in addressing the challenges presented by big data. In doing so, we demonstrate the potential benefit of incorporating VA tools into PH practice, in addition to highlighting the need for further systematic and focused research.

The Challenge of Big Data in Public Health: An Opportunity for Visual Analytics

PubMed Central

Ola, Oluwakemi; Sedig, Kamran

2014-01-01

Public health (PH) data can generally be characterized as big data. The efficient and effective use of this data determines the extent to which PH stakeholders can sufficiently address societal health concerns as they engage in a variety of work activities. As stakeholders interact with data, they engage in various cognitive activities such as analytical reasoning, decision-making, interpreting, and problem solving. Performing these activities with big data is a challenge for the unaided mind as stakeholders encounter obstacles relating to the data’s volume, variety, velocity, and veracity. Such being the case, computer-based information tools are needed to support PH stakeholders. Unfortunately, while existing computational tools are beneficial in addressing certain work activities, they fall short in supporting cognitive activities that involve working with large, heterogeneous, and complex bodies of data. This paper presents visual analytics (VA) tools, a nascent category of computational tools that integrate data analytics with interactive visualizations, to facilitate the performance of cognitive activities involving big data. Historically, PH has lagged behind other sectors in embracing new computational technology. In this paper, we discuss the role that VA tools can play in addressing the challenges presented by big data. In doing so, we demonstrate the potential benefit of incorporating VA tools into PH practice, in addition to highlighting the need for further systematic and focused research. PMID:24678376

Web Tools: The Second Generation

ERIC Educational Resources Information Center

Pascopella, Angela

2008-01-01

Web 2.0 tools and technologies, or second generation tools, help districts to save time and money, and eliminate the need to transfer or move files back and forth across computers. Many Web 2.0 tools help students think critically and solve problems, which falls under the 21st-century skills. The second-generation tools are growing in popularity…

What Chemists (or Chemistry Students) Need to Know about Computing.

ERIC Educational Resources Information Center

Swift, Mary L.; Zielinski, Theresa Julia

1995-01-01

Presents key points of an on-line conference discussion and integrates them with information from the literature. Key points included: computer as a tool for learning, study, research, and communication; hardware, software, computing concepts, and other teaching concerns; and the appropriate place for chemistry computer-usage instruction. (45…

Health impact assessment – A survey on quantifying tools

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

Fehr, Rainer, E-mail: rainer.fehr@uni-bielefeld.de; Mekel, Odile C.L., E-mail: odile.mekel@lzg.nrw.de; Fintan Hurley, J., E-mail: fintan.hurley@iom-world.org

Integrating human health into prospective impact assessments is known to be challenging. This is true for both approaches: dedicated health impact assessments (HIA) as well as inclusion of health into more general impact assessments. Acknowledging the full range of participatory, qualitative, and quantitative approaches, this study focuses on the latter, especially on computational tools for quantitative health modelling. We conducted a survey among tool developers concerning the status quo of development and availability of such tools; experiences made with model usage in real-life situations; and priorities for further development. Responding toolmaker groups described 17 such tools, most of them beingmore » maintained and reported as ready for use and covering a wide range of topics, including risk & protective factors, exposures, policies, and health outcomes. In recent years, existing models have been improved and were applied in new ways, and completely new models emerged. There was high agreement among respondents on the need to further develop methods for assessment of inequalities and uncertainty. The contribution of quantitative modeling to health foresight would benefit from building joint strategies of further tool development, improving the visibility of quantitative tools and methods, and engaging continuously with actual and potential users. - Highlights: • A survey investigated computational tools for health impact quantification. • Formal evaluation of such tools has been rare. • Handling inequalities and uncertainties are priority areas for further development. • Health foresight would benefit from tool developers and users forming a community. • Joint development strategies across computational tools are needed.« less

SABrE User's Guide

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

Brown, S.A.

In computing landscape which has a plethora of different hardware architectures and supporting software systems ranging from compilers to operating systems, there is an obvious and strong need for a philosophy of software development that lends itself to the design and construction of portable code systems. The current efforts to standardize software bear witness to this need. SABrE is an effort to implement a software development environment which is itself portable and promotes the design and construction of portable applications. SABrE does not include such important tools as editors and compilers. Well built tools of that kind are readily availablemore » across virtually all computer platforms. The areas that SABrE addresses are at a higher level involving issues such as data portability, portable inter-process communication, and graphics. These blocks of functionality have particular significance to the kind of code development done at LLNL. That is partly why the general computing community has not supplied us with these tools already. This is another key feature of the software development environments which we must recognize. The general computing community cannot and should not be expected to produce all of the tools which we require.« less

SABrE User`s Guide

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

Brown, S.A.

In computing landscape which has a plethora of different hardware architectures and supporting software systems ranging from compilers to operating systems, there is an obvious and strong need for a philosophy of software development that lends itself to the design and construction of portable code systems. The current efforts to standardize software bear witness to this need. SABrE is an effort to implement a software development environment which is itself portable and promotes the design and construction of portable applications. SABrE does not include such important tools as editors and compilers. Well built tools of that kind are readily availablemore » across virtually all computer platforms. The areas that SABrE addresses are at a higher level involving issues such as data portability, portable inter-process communication, and graphics. These blocks of functionality have particular significance to the kind of code development done at LLNL. That is partly why the general computing community has not supplied us with these tools already. This is another key feature of the software development environments which we must recognize. The general computing community cannot and should not be expected to produce all of the tools which we require.« less

Investigating the need for clinicians to use tablet computers with a newly envisioned electronic health record.

PubMed

Saleem, Jason J; Savoy, April; Etherton, Gale; Herout, Jennifer

2018-02-01

The Veterans Health Administration (VHA) has deployed a large number of tablet computers in the last several years. However, little is known about how clinicians may use these devices with a newly planned Web-based electronic health record (EHR), as well as other clinical tools. The objective of this study was to understand the types of use that can be expected of tablet computers versus desktops. Semi-structured interviews were conducted with 24 clinicians at a Veterans Health Administration (VHA) Medical Center. An inductive qualitative analysis resulted in findings organized around recurrent themes of: (1) Barriers, (2) Facilitators, (3) Current Use, (4) Anticipated Use, (5) Patient Interaction, and (6) Connection. Our study generated several recommendations for the use of tablet computers with new health information technology tools being developed. Continuous connectivity for the mobile device is essential to avoid interruptions and clinician frustration. Also, making a physical keyboard available as an option for the tablet was a clear desire from the clinicians. Larger tablets (e.g., regular size iPad as compared to an iPad mini) were preferred. Being able to use secure messaging tools with the tablet computer was another consistent finding. Finally, more simplicity is needed for accessing patient data on mobile devices, while balancing the important need for adequate security. Published by Elsevier B.V.

A Complete Interactive Graphical Computer-Aided Instruction System.

ERIC Educational Resources Information Center

Abrams, Steven Selby

The use of interactive graphics in computer-aided instruction systems is discussed with emphasis placed on two requirements of such a system. The first is the need to provide the teacher with a useful tool with which to design and modify teaching sessions tailored to the individual needs and capabilities of the students. The second is the…

Computer programing for geosciences: Teach your students how to make tools

NASA Astrophysics Data System (ADS)

Grapenthin, Ronni

2011-12-01

When I announced my intention to pursue a Ph.D. in geophysics, some people gave me confused looks, because I was working on a master's degree in computer science at the time. My friends, like many incoming geoscience graduate students, have trouble linking these two fields. From my perspective, it is pretty straightforward: Much of geoscience evolves around novel analyses of large data sets that require custom tools—computer programs—to minimize the drudgery of manual data handling; other disciplines share this characteristic. While most faculty adapted to the need for tool development quite naturally, as they grew up around computer terminal interfaces, incoming graduate students lack intuitive understanding of programing concepts such as generalization and automation. I believe the major cause is the intuitive graphical user interfaces of modern operating systems and applications, which isolate the user from all technical details. Generally, current curricula do not recognize this gap between user and machine. For students to operate effectively, they require specialized courses teaching them the skills they need to make tools that operate on particular data sets and solve their specific problems. Courses in computer science departments are aimed at a different audience and are of limited help.

RE-PLAN: An Extensible Software Architecture to Facilitate Disaster Response Planning

PubMed Central

O’Neill, Martin; Mikler, Armin R.; Indrakanti, Saratchandra; Tiwari, Chetan; Jimenez, Tamara

2014-01-01

Computational tools are needed to make data-driven disaster mitigation planning accessible to planners and policymakers without the need for programming or GIS expertise. To address this problem, we have created modules to facilitate quantitative analyses pertinent to a variety of different disaster scenarios. These modules, which comprise the REsponse PLan ANalyzer (RE-PLAN) framework, may be used to create tools for specific disaster scenarios that allow planners to harness large amounts of disparate data and execute computational models through a point-and-click interface. Bio-E, a user-friendly tool built using this framework, was designed to develop and analyze the feasibility of ad hoc clinics for treating populations following a biological emergency event. In this article, the design and implementation of the RE-PLAN framework are described, and the functionality of the modules used in the Bio-E biological emergency mitigation tool are demonstrated. PMID:25419503

Assessing mouse alternatives to access to computer: a case study of a user with cerebral palsy.

PubMed

Pousada, Thais; Pareira, Javier; Groba, Betania; Nieto, Laura; Pazos, Alejandro

2014-01-01

The purpose of this study is to describe the process of assessment of three assistive devices to meet the needs of a woman with cerebral palsy (CP) in order to provide her with computer access and use. The user has quadriplegic CP, with anarthria, using a syllabic keyboard. Devices were evaluated through a three-step approach: (a) use of a questionnaire to preselect potential assistive technologies, (b) use of an eTAO tool to determine the effectiveness of each devised, and (c) a conducting semi-structured interview to obtain qualitative data. Touch screen, joystick, and trackball were the preselected devices. The best device that met the user's needs and priorities was joystick. The finding was corroborated by both the eTAO tool and the semi-structured interview. Computers are a basic form of social participation. It is important to consider the special needs and priorities of users and to try different devices when undertaking a device-selection process. Environmental and personal factors have to be considered, as well. This leads to a need to evaluate new tools in order to provide the appropriate support. The eTAO could be a suitable instrument for this purpose. Additional research is also needed to understand how to better match devices with different user populations and how to comprehensively evaluate emerging technologies relative to users with disabilities.

Computing at h1 - Experience and Future

NASA Astrophysics Data System (ADS)

Eckerlin, G.; Gerhards, R.; Kleinwort, C.; KrÜNer-Marquis, U.; Egli, S.; Niebergall, F.

The H1 experiment has now been successfully operating at the electron proton collider HERA at DESY for three years. During this time the computing environment has gradually shifted from a mainframe oriented environment to the distributed server/client Unix world. This transition is now almost complete. Computing needs are largely determined by the present amount of 1.5 TB of reconstructed data per year (1994), corresponding to 1.2 × 107 accepted events. All data are centrally available at DESY. In addition to data analysis, which is done in all collaborating institutes, most of the centrally organized Monte Carlo production is performed outside of DESY. New software tools to cope with offline computing needs include CENTIPEDE, a tool for the use of distributed batch and interactive resources for Monte Carlo production, and H1 UNIX, a software package for automatic updates of H1 software on all UNIX platforms.

Introduction to the Use of Computers in Libraries: A Textbook for the Non-Technical Student.

ERIC Educational Resources Information Center

Ogg, Harold C.

This book outlines computing and information science from the perspective of what librarians and educators need to do with computer technology and how it can help them perform their jobs more efficiently. It provides practical explanations and library applications for non-technical users of desktop computers and other library automation tools.…

A graph algebra for scalable visual analytics.

PubMed

Shaverdian, Anna A; Zhou, Hao; Michailidis, George; Jagadish, Hosagrahar V

2012-01-01

Visual analytics (VA), which combines analytical techniques with advanced visualization features, is fast becoming a standard tool for extracting information from graph data. Researchers have developed many tools for this purpose, suggesting a need for formal methods to guide these tools' creation. Increased data demands on computing requires redesigning VA tools to consider performance and reliability in the context of analysis of exascale datasets. Furthermore, visual analysts need a way to document their analyses for reuse and results justification. A VA graph framework encapsulated in a graph algebra helps address these needs. Its atomic operators include selection and aggregation. The framework employs a visual operator and supports dynamic attributes of data to enable scalable visual exploration of data.

TethysCluster: A comprehensive approach for harnessing cloud resources for hydrologic modeling

NASA Astrophysics Data System (ADS)

Nelson, J.; Jones, N.; Ames, D. P.

2015-12-01

Advances in water resources modeling are improving the information that can be supplied to support decisions affecting the safety and sustainability of society. However, as water resources models become more sophisticated and data-intensive they require more computational power to run. Purchasing and maintaining the computing facilities needed to support certain modeling tasks has been cost-prohibitive for many organizations. With the advent of the cloud, the computing resources needed to address this challenge are now available and cost-effective, yet there still remains a significant technical barrier to leverage these resources. This barrier inhibits many decision makers and even trained engineers from taking advantage of the best science and tools available. Here we present the Python tools TethysCluster and CondorPy, that have been developed to lower the barrier to model computation in the cloud by providing (1) programmatic access to dynamically scalable computing resources, (2) a batch scheduling system to queue and dispatch the jobs to the computing resources, (3) data management for job inputs and outputs, and (4) the ability to dynamically create, submit, and monitor computing jobs. These Python tools leverage the open source, computing-resource management, and job management software, HTCondor, to offer a flexible and scalable distributed-computing environment. While TethysCluster and CondorPy can be used independently to provision computing resources and perform large modeling tasks, they have also been integrated into Tethys Platform, a development platform for water resources web apps, to enable computing support for modeling workflows and decision-support systems deployed as web apps.

Prediction of miRNA targets.

PubMed

Oulas, Anastasis; Karathanasis, Nestoras; Louloupi, Annita; Pavlopoulos, Georgios A; Poirazi, Panayiota; Kalantidis, Kriton; Iliopoulos, Ioannis

2015-01-01

Computational methods for miRNA target prediction are currently undergoing extensive review and evaluation. There is still a great need for improvement of these tools and bioinformatics approaches are looking towards high-throughput experiments in order to validate predictions. The combination of large-scale techniques with computational tools will not only provide greater credence to computational predictions but also lead to the better understanding of specific biological questions. Current miRNA target prediction tools utilize probabilistic learning algorithms, machine learning methods and even empirical biologically defined rules in order to build models based on experimentally verified miRNA targets. Large-scale protein downregulation assays and next-generation sequencing (NGS) are now being used to validate methodologies and compare the performance of existing tools. Tools that exhibit greater correlation between computational predictions and protein downregulation or RNA downregulation are considered the state of the art. Moreover, efficiency in prediction of miRNA targets that are concurrently verified experimentally provides additional validity to computational predictions and further highlights the competitive advantage of specific tools and their efficacy in extracting biologically significant results. In this review paper, we discuss the computational methods for miRNA target prediction and provide a detailed comparison of methodologies and features utilized by each specific tool. Moreover, we provide an overview of current state-of-the-art high-throughput methods used in miRNA target prediction.

Using Open Source Software in Visual Simulation Development

DTIC Science & Technology

2005-09-01

increased the use of the technology in training activities. Using open source/free software tools in the process can expand these possibilities...resulting in even greater cost reduction and allowing the flexibility needed in a training environment. This thesis presents a configuration and architecture...to be used when developing training visual simulations using both personal computers and open source tools. Aspects of the requirements needed in a

Factors influencing exemplary science teachers' levels of computer use

NASA Astrophysics Data System (ADS)

Hakverdi, Meral

This study examines exemplary science teachers' use of technology in science instruction, factors influencing their level of computer use, their level of knowledge/skills in using specific computer applications for science instruction, their use of computer-related applications/tools during their instruction, and their students' use of computer applications/tools in or for their science class. After a relevant review of the literature certain variables were selected for analysis. These variables included personal self-efficacy in teaching with computers, outcome expectancy, pupil-control ideology, level of computer use, age, gender, teaching experience, personal computer use, professional computer use and science teachers' level of knowledge/skills in using specific computer applications for science instruction. The sample for this study includes middle and high school science teachers who received the Presidential Award for Excellence in Science Teaching Award (sponsored by the White House and the National Science Foundation) between the years 1997 and 2003 from all 50 states and U.S. territories. Award-winning science teachers were contacted about the survey via e-mail or letter with an enclosed return envelope. Of the 334 award-winning science teachers, usable responses were received from 92 science teachers, which made a response rate of 27.5%. Analysis of the survey responses indicated that exemplary science teachers have a variety of knowledge/skills in using computer related applications/tools. The most commonly used computer applications/tools are information retrieval via the Internet, presentation tools, online communication, digital cameras, and data collection probes. Results of the study revealed that students' use of technology in their science classroom is highly correlated with the frequency of their science teachers' use of computer applications/tools. The results of the multiple regression analysis revealed that personal self-efficacy related to the exemplary science teachers' level of computer use suggesting that computer use is dependent on perceived abilities at using computers. The teachers' use of computer-related applications/tools during class, and their personal self-efficacy, age, and gender are highly related with their level of knowledge/skills in using specific computer applications for science instruction. The teachers' level of knowledge/skills in using specific computer applications for science instruction and gender related to their use of computer-related applications/tools during class and the students' use of computer-related applications/tools in or for their science class. In conclusion, exemplary science teachers need assistance in learning and using computer-related applications/tool in their science class.

Fermilab computing at the Intensity Frontier

DOE PAGES

Group, Craig; Fuess, S.; Gutsche, O.; ...

2015-12-23

The Intensity Frontier refers to a diverse set of particle physics experiments using high- intensity beams. In this paper I will focus the discussion on the computing requirements and solutions of a set of neutrino and muon experiments in progress or planned to take place at the Fermi National Accelerator Laboratory located near Chicago, Illinois. In addition, the experiments face unique challenges, but also have overlapping computational needs. In principle, by exploiting the commonality and utilizing centralized computing tools and resources, requirements can be satisfied efficiently and scientists of individual experiments can focus more on the science and less onmore » the development of tools and infrastructure.« less

Three varieties of realism in computer graphics

NASA Astrophysics Data System (ADS)

Ferwerda, James A.

2003-06-01

This paper describes three varieties of realism that need to be considered in evaluating computer graphics images and defines the criteria that need to be met if each kind of realism is to be achieved. The paper introduces a conceptual framework for thinking about realism in images, and describes a set of research tools for measuring image realism and assessing its value in graphics applications.

Chimera grids in the simulation of three-dimensional flowfields in turbine-blade-coolant passages

NASA Technical Reports Server (NTRS)

Stephens, M. A.; Rimlinger, M. J.; Shih, T. I.-P.; Civinskas, K. C.

1993-01-01

When computing flows inside geometrically complex turbine-blade coolant passages, the structure of the grid system used can affect significantly the overall time and cost required to obtain solutions. This paper addresses this issue while evaluating and developing computational tools for the design and analysis of coolant-passages, and is divided into two parts. In the first part, the various types of structured and unstructured grids are compared in relation to their ability to provide solutions in a timely and cost-effective manner. This comparison shows that the overlapping structured grids, known as Chimera grids, can rival and in some instances exceed the cost-effectiveness of unstructured grids in terms of both the man hours needed to generate grids and the amount of computer memory and CPU time needed to obtain solutions. In the second part, a computational tool utilizing Chimera grids was used to compute the flow and heat transfer in two different turbine-blade coolant passages that contain baffles and numerous pin fins. These computations showed the versatility and flexibility offered by Chimera grids.

Towards early software reliability prediction for computer forensic tools (case study).

PubMed

Abu Talib, Manar

2016-01-01

Versatility, flexibility and robustness are essential requirements for software forensic tools. Researchers and practitioners need to put more effort into assessing this type of tool. A Markov model is a robust means for analyzing and anticipating the functioning of an advanced component based system. It is used, for instance, to analyze the reliability of the state machines of real time reactive systems. This research extends the architecture-based software reliability prediction model for computer forensic tools, which is based on Markov chains and COSMIC-FFP. Basically, every part of the computer forensic tool is linked to a discrete time Markov chain. If this can be done, then a probabilistic analysis by Markov chains can be performed to analyze the reliability of the components and of the whole tool. The purposes of the proposed reliability assessment method are to evaluate the tool's reliability in the early phases of its development, to improve the reliability assessment process for large computer forensic tools over time, and to compare alternative tool designs. The reliability analysis can assist designers in choosing the most reliable topology for the components, which can maximize the reliability of the tool and meet the expected reliability level specified by the end-user. The approach of assessing component-based tool reliability in the COSMIC-FFP context is illustrated with the Forensic Toolkit Imager case study.

20180129 - Computational Embryology: Translational Tools for Modeling in vitro Data (Toxicology Forum)

EPA Science Inventory

Integrative models are needed to "decode the toxicological blueprint of active substances that interact with living systems" (Systems toxicology). Computational biology is uniquely positioned to capture this connectivity and help shift decision-making to mechanistic pre...

Galaxy CloudMan: delivering cloud compute clusters.

PubMed

Afgan, Enis; Baker, Dannon; Coraor, Nate; Chapman, Brad; Nekrutenko, Anton; Taylor, James

2010-12-21

Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is "cloud computing", which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate "as is" use by experimental biologists. We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon's EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge.

Northwest Trajectory Analysis Capability: A Platform for Enhancing Computational Biophysics Analysis

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

Peterson, Elena S.; Stephan, Eric G.; Corrigan, Abigail L.

2008-07-30

As computational resources continue to increase, the ability of computational simulations to effectively complement, and in some cases replace, experimentation in scientific exploration also increases. Today, large-scale simulations are recognized as an effective tool for scientific exploration in many disciplines including chemistry and biology. A natural side effect of this trend has been the need for an increasingly complex analytical environment. In this paper, we describe Northwest Trajectory Analysis Capability (NTRAC), an analytical software suite developed to enhance the efficiency of computational biophysics analyses. Our strategy is to layer higher-level services and introduce improved tools within the user’s familiar environmentmore » without preventing researchers from using traditional tools and methods. Our desire is to share these experiences to serve as an example for effectively analyzing data intensive large scale simulation data.« less

Water System Adaptation To Hydrological Changes: Module 11, Methods and Tools: Computational Models

EPA Science Inventory

This course will introduce students to the fundamental principles of water system adaptation to hydrological changes, with emphasis on data analysis and interpretation, technical planning, and computational modeling. Starting with real-world scenarios and adaptation needs, the co...

Modeling Electrostatic Fields Generated by Internal Charging of Materials in Space Radiation Environments

NASA Technical Reports Server (NTRS)

Minow, Joseph I.

2011-01-01

Internal charging is a risk to spacecraft in energetic electron environments. DICTAT, NU MIT computational codes are the most widely used engineering tools for evaluating internal charging of insulator materials exposed to these environments. Engineering tools are designed for rapid evaluation of ESD threats, but there is a need for more physics based models for investigating the science of materials interactions with energetic electron environments. Current tools are limited by the physics included in the models and ease of user implementation .... additional development work is needed to improve models.

Cosmic Strings Stabilized by Quantum Fluctuations

NASA Astrophysics Data System (ADS)

Weigel, H.

2017-03-01

Fermion quantum corrections to the energy of cosmic strings are computed. A number of rather technical tools are needed to formulate this correction, and isospin and gauge invariance are employed to verify consistency of these tools. These corrections must also be included when computing the energy of strings that are charged by populating fermion bound states in its background. It is found that charged strings are dynamically stabilized in theories similar to the standard model of particle physics.

Short-term forecasting tools for agricultural nutrient management

USDA-ARS?s Scientific Manuscript database

The advent of real time/short term farm management tools is motivated by the need to protect water quality above and beyond the general guidance offered by existing nutrient management plans. Advances in high performance computing and hydrologic/climate modeling have enabled rapid dissemination of ...

Grasping Reality Through Illusion: Interactive Graphics Serving Science

DTIC Science & Technology

1988-03-01

SIGGRAPH, or riding techniques to the enhancement of scientific computing. StarTours at Disneyland shows how stunningly far we ........ have come. We need...supercomputer References matching and steering tools. Such tools must be Bergman, L., Fuchs, H., Grant , E., Spach, S. [1986] universal and application

A tool for modeling concurrent real-time computation

NASA Technical Reports Server (NTRS)

Sharma, D. D.; Huang, Shie-Rei; Bhatt, Rahul; Sridharan, N. S.

1990-01-01

Real-time computation is a significant area of research in general, and in AI in particular. The complexity of practical real-time problems demands use of knowledge-based problem solving techniques while satisfying real-time performance constraints. Since the demands of a complex real-time problem cannot be predicted (owing to the dynamic nature of the environment) powerful dynamic resource control techniques are needed to monitor and control the performance. A real-time computation model for a real-time tool, an implementation of the QP-Net simulator on a Symbolics machine, and an implementation on a Butterfly multiprocessor machine are briefly described.

Galaxy CloudMan: delivering cloud compute clusters

PubMed Central

2010-01-01

Background Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is “cloud computing”, which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate “as is” use by experimental biologists. Results We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon’s EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. Conclusions The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge. PMID:21210983

Using an Interactive Computer Program to Communicate With the Wilderness Visitor

Treesearch

David W. Harmon

1992-01-01

The Bureau of Land Management, Oregon State Office, identified a need for a tool to communicate with wilderness visitors, managers, and decisionmakers regarding wilderness values and existing resource information in 87 wilderness study areas. An interactive computer program was developed using a portable Macintosh computer, a touch screen monitor, and laser disk player...

Interface between a printed circuit board computer aided design tool (Tektronix 4051 based) and a numerical paper tape controlled drill press (Slo-Syn 530: 100 w/ Dumore Automatic Head Number 8391)

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

Heckman, B.K.; Chinn, V.K.

1981-01-01

The development and use of computer programs written to produce the paper tape needed for the automation, or numeric control, of drill presses employed to fabricate computed-designed printed circuit boards are described. (LCL)

Decision tools in health care: focus on the problem, not the solution.

PubMed

Liu, Joseph; Wyatt, Jeremy C; Altman, Douglas G

2006-01-20

Systematic reviews or randomised-controlled trials usually help to establish the effectiveness of drugs and other health technologies, but are rarely sufficient by themselves to ensure actual clinical use of the technology. The process from innovation to routine clinical use is complex. Numerous computerised decision support systems (DSS) have been developed, but many fail to be taken up into actual use. Some developers construct technologically advanced systems with little relevance to the real world. Others did not determine whether a clinical need exists. With NHS investing 5 billion pounds sterling in computer systems, also occurring in other countries, there is an urgent need to shift from a technology-driven approach to one that identifies and employs the most cost-effective method to manage knowledge, regardless of the technology. The generic term, 'decision tool' (DT), is therefore suggested to demonstrate that these aids, which seem different technically, are conceptually the same from a clinical viewpoint. Many computerised DSSs failed for various reasons, for example, they were not based on best available knowledge; there was insufficient emphasis on their need for high quality clinical data; their development was technology-led; or evaluation methods were misapplied. We argue that DSSs and other computer-based, paper-based and even mechanical decision aids are members of a wider family of decision tools. A DT is an active knowledge resource that uses patient data to generate case specific advice, which supports decision making about individual patients by health professionals, the patients themselves or others concerned about them. The identification of DTs as a consistent and important category of health technology should encourage the sharing of lessons between DT developers and users and reduce the frequency of decision tool projects focusing only on technology. The focus of evaluation should become more clinical, with the impact of computer-based DTs being evaluated against other computer, paper- or mechanical tools, to identify the most cost effective tool for each clinical problem. We suggested the generic term 'decision tool' to demonstrate that decision-making aids, such as computerised DSSs, paper algorithms, and reminders are conceptually the same, so the methods to evaluate them should be the same.

TSUNAMI Primer: A Primer for Sensitivity/Uncertainty Calculations with SCALE

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

Rearden, Bradley T; Mueller, Don; Bowman, Stephen M

2009-01-01

This primer presents examples in the application of the SCALE/TSUNAMI tools to generate k{sub eff} sensitivity data for one- and three-dimensional models using TSUNAMI-1D and -3D and to examine uncertainties in the computed k{sub eff} values due to uncertainties in the cross-section data used in their calculation. The proper use of unit cell data and need for confirming the appropriate selection of input parameters through direct perturbations are described. The uses of sensitivity and uncertainty data to identify and rank potential sources of computational bias in an application system and TSUNAMI tools for assessment of system similarity using sensitivity andmore » uncertainty criteria are demonstrated. Uses of these criteria in trending analyses to assess computational biases, bias uncertainties, and gap analyses are also described. Additionally, an application of the data adjustment tool TSURFER is provided, including identification of specific details of sources of computational bias.« less

Light-weight Parallel Python Tools for Earth System Modeling Workflows

NASA Astrophysics Data System (ADS)

Mickelson, S. A.; Paul, K.; Xu, H.; Dennis, J.; Brown, D. I.

2015-12-01

With the growth in computing power over the last 30 years, earth system modeling codes have become increasingly data-intensive. As an example, it is expected that the data required for the next Intergovernmental Panel on Climate Change (IPCC) Assessment Report (AR6) will increase by more than 10x to an expected 25PB per climate model. Faced with this daunting challenge, developers of the Community Earth System Model (CESM) have chosen to change the format of their data for long-term storage from time-slice to time-series, in order to reduce the required download bandwidth needed for later analysis and post-processing by climate scientists. Hence, efficient tools are required to (1) perform the transformation of the data from time-slice to time-series format and to (2) compute climatology statistics, needed for many diagnostic computations, on the resulting time-series data. To address the first of these two challenges, we have developed a parallel Python tool for converting time-slice model output to time-series format. To address the second of these challenges, we have developed a parallel Python tool to perform fast time-averaging of time-series data. These tools are designed to be light-weight, be easy to install, have very few dependencies, and can be easily inserted into the Earth system modeling workflow with negligible disruption. In this work, we present the motivation, approach, and testing results of these two light-weight parallel Python tools, as well as our plans for future research and development.

PlantCV v2: Image analysis software for high-throughput plant phenotyping

PubMed Central

Abbasi, Arash; Berry, Jeffrey C.; Callen, Steven T.; Chavez, Leonardo; Doust, Andrew N.; Feldman, Max J.; Gilbert, Kerrigan B.; Hodge, John G.; Hoyer, J. Steen; Lin, Andy; Liu, Suxing; Lizárraga, César; Lorence, Argelia; Miller, Michael; Platon, Eric; Tessman, Monica; Sax, Tony

2017-01-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning. PMID:29209576

PlantCV v2: Image analysis software for high-throughput plant phenotyping.

PubMed

Gehan, Malia A; Fahlgren, Noah; Abbasi, Arash; Berry, Jeffrey C; Callen, Steven T; Chavez, Leonardo; Doust, Andrew N; Feldman, Max J; Gilbert, Kerrigan B; Hodge, John G; Hoyer, J Steen; Lin, Andy; Liu, Suxing; Lizárraga, César; Lorence, Argelia; Miller, Michael; Platon, Eric; Tessman, Monica; Sax, Tony

2017-01-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

PlantCV v2: Image analysis software for high-throughput plant phenotyping

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

Gehan, Malia A.; Fahlgren, Noah; Abbasi, Arash

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here in this paper we present the details andmore » rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.« less

PlantCV v2: Image analysis software for high-throughput plant phenotyping

DOE PAGES

Gehan, Malia A.; Fahlgren, Noah; Abbasi, Arash; ...

2017-12-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here in this paper we present the details andmore » rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.« less

Computer assisted audit techniques for UNIX (UNIX-CAATS)

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

Polk, W.T.

1991-12-31

Federal and DOE regulations impose specific requirements for internal controls of computer systems. These controls include adequate separation of duties and sufficient controls for access of system and data. The DOE Inspector General`s Office has the responsibility to examine internal controls, as well as efficient use of computer system resources. As a result, DOE supported NIST development of computer assisted audit techniques to examine BSD UNIX computers (UNIX-CAATS). These systems were selected due to the increasing number of UNIX workstations in use within DOE. This paper describes the design and development of these techniques, as well as the results ofmore » testing at NIST and the first audit at a DOE site. UNIX-CAATS consists of tools which examine security of passwords, file systems, and network access. In addition, a tool was developed to examine efficiency of disk utilization. Test results at NIST indicated inadequate password management, as well as weak network resource controls. File system security was considered adequate. Audit results at a DOE site indicated weak password management and inefficient disk utilization. During the audit, we also found improvements to UNIX-CAATS were needed when applied to large systems. NIST plans to enhance the techniques developed for DOE/IG in future work. This future work would leverage currently available tools, along with needed enhancements. These enhancements would enable DOE/IG to audit large systems, such as supercomputers.« less

Computer assisted audit techniques for UNIX (UNIX-CAATS)

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

Polk, W.T.

1991-01-01

Federal and DOE regulations impose specific requirements for internal controls of computer systems. These controls include adequate separation of duties and sufficient controls for access of system and data. The DOE Inspector General's Office has the responsibility to examine internal controls, as well as efficient use of computer system resources. As a result, DOE supported NIST development of computer assisted audit techniques to examine BSD UNIX computers (UNIX-CAATS). These systems were selected due to the increasing number of UNIX workstations in use within DOE. This paper describes the design and development of these techniques, as well as the results ofmore » testing at NIST and the first audit at a DOE site. UNIX-CAATS consists of tools which examine security of passwords, file systems, and network access. In addition, a tool was developed to examine efficiency of disk utilization. Test results at NIST indicated inadequate password management, as well as weak network resource controls. File system security was considered adequate. Audit results at a DOE site indicated weak password management and inefficient disk utilization. During the audit, we also found improvements to UNIX-CAATS were needed when applied to large systems. NIST plans to enhance the techniques developed for DOE/IG in future work. This future work would leverage currently available tools, along with needed enhancements. These enhancements would enable DOE/IG to audit large systems, such as supercomputers.« less

Network-Centric Data Mining for Medical Applications

ERIC Educational Resources Information Center

Davis, Darcy A.

2012-01-01

Faced with unsustainable costs and enormous amounts of under-utilized data, health care needs more efficient practices, research, and tools to harness the benefits of data. These methods create a feedback loop where computational tools guide and facilitate research, leading to improved biological knowledge and clinical standards, which will in…

Computational Modeling in Liver Surgery

PubMed Central

Christ, Bruno; Dahmen, Uta; Herrmann, Karl-Heinz; König, Matthias; Reichenbach, Jürgen R.; Ricken, Tim; Schleicher, Jana; Ole Schwen, Lars; Vlaic, Sebastian; Waschinsky, Navina

2017-01-01

The need for extended liver resection is increasing due to the growing incidence of liver tumors in aging societies. Individualized surgical planning is the key for identifying the optimal resection strategy and to minimize the risk of postoperative liver failure and tumor recurrence. Current computational tools provide virtual planning of liver resection by taking into account the spatial relationship between the tumor and the hepatic vascular trees, as well as the size of the future liver remnant. However, size and function of the liver are not necessarily equivalent. Hence, determining the future liver volume might misestimate the future liver function, especially in cases of hepatic comorbidities such as hepatic steatosis. A systems medicine approach could be applied, including biological, medical, and surgical aspects, by integrating all available anatomical and functional information of the individual patient. Such an approach holds promise for better prediction of postoperative liver function and hence improved risk assessment. This review provides an overview of mathematical models related to the liver and its function and explores their potential relevance for computational liver surgery. We first summarize key facts of hepatic anatomy, physiology, and pathology relevant for hepatic surgery, followed by a description of the computational tools currently used in liver surgical planning. Then we present selected state-of-the-art computational liver models potentially useful to support liver surgery. Finally, we discuss the main challenges that will need to be addressed when developing advanced computational planning tools in the context of liver surgery. PMID:29249974

Informed public choices for low-carbon electricity portfolios using a computer decision tool.

PubMed

Mayer, Lauren A Fleishman; Bruine de Bruin, Wändi; Morgan, M Granger

2014-04-01

Reducing CO2 emissions from the electricity sector will likely require policies that encourage the widespread deployment of a diverse mix of low-carbon electricity generation technologies. Public discourse informs such policies. To make informed decisions and to productively engage in public discourse, citizens need to understand the trade-offs between electricity technologies proposed for widespread deployment. Building on previous paper-and-pencil studies, we developed a computer tool that aimed to help nonexperts make informed decisions about the challenges faced in achieving a low-carbon energy future. We report on an initial usability study of this interactive computer tool. After providing participants with comparative and balanced information about 10 electricity technologies, we asked them to design a low-carbon electricity portfolio. Participants used the interactive computer tool, which constrained portfolio designs to be realistic and yield low CO2 emissions. As they changed their portfolios, the tool updated information about projected CO2 emissions, electricity costs, and specific environmental impacts. As in the previous paper-and-pencil studies, most participants designed diverse portfolios that included energy efficiency, nuclear, coal with carbon capture and sequestration, natural gas, and wind. Our results suggest that participants understood the tool and used it consistently. The tool may be downloaded from http://cedmcenter.org/tools-for-cedm/informing-the-public-about-low-carbon-technologies/ .

Crosscut report: Exascale Requirements Reviews, March 9–10, 2017 – Tysons Corner, Virginia. An Office of Science review sponsored by: Advanced Scientific Computing Research, Basic Energy Sciences, Biological and Environmental Research, Fusion Energy Sciences, High Energy Physics, Nuclear Physics

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

Gerber, Richard; Hack, James; Riley, Katherine

The mission of the U.S. Department of Energy Office of Science (DOE SC) is the delivery of scientific discoveries and major scientific tools to transform our understanding of nature and to advance the energy, economic, and national security missions of the United States. To achieve these goals in today’s world requires investments in not only the traditional scientific endeavors of theory and experiment, but also in computational science and the facilities that support large-scale simulation and data analysis. The Advanced Scientific Computing Research (ASCR) program addresses these challenges in the Office of Science. ASCR’s mission is to discover, develop, andmore » deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to DOE. ASCR supports research in computational science, three high-performance computing (HPC) facilities — the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory and Leadership Computing Facilities at Argonne (ALCF) and Oak Ridge (OLCF) National Laboratories — and the Energy Sciences Network (ESnet) at Berkeley Lab. ASCR is guided by science needs as it develops research programs, computers, and networks at the leading edge of technologies. As we approach the era of exascale computing, technology changes are creating challenges for science programs in SC for those who need to use high performance computing and data systems effectively. Numerous significant modifications to today’s tools and techniques will be needed to realize the full potential of emerging computing systems and other novel computing architectures. To assess these needs and challenges, ASCR held a series of Exascale Requirements Reviews in 2015–2017, one with each of the six SC program offices,1 and a subsequent Crosscut Review that sought to integrate the findings from each. Participants at the reviews were drawn from the communities of leading domain scientists, experts in computer science and applied mathematics, ASCR facility staff, and DOE program managers in ASCR and the respective program offices. The purpose of these reviews was to identify mission-critical scientific problems within the DOE Office of Science (including experimental facilities) and determine the requirements for the exascale ecosystem that would be needed to address those challenges. The exascale ecosystem includes exascale computing systems, high-end data capabilities, efficient software at scale, libraries, tools, and other capabilities. This effort will contribute to the development of a strategic roadmap for ASCR compute and data facility investments and will help the ASCR Facility Division establish partnerships with Office of Science stakeholders. It will also inform the Office of Science research needs and agenda. The results of the six reviews have been published in reports available on the web at http://exascaleage.org/. This report presents a summary of the individual reports and of common and crosscutting findings, and it identifies opportunities for productive collaborations among the DOE SC program offices.« less

Advanced Simulation & Computing FY15 Implementation Plan Volume 2, Rev. 0.5

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

McCoy, Michel; Archer, Bill; Matzen, M. Keith

2014-09-16

The Stockpile Stewardship Program (SSP) is a single, highly integrated technical program for maintaining the surety and reliability of the U.S. nuclear stockpile. The SSP uses nuclear test data, computational modeling and simulation, and experimental facilities to advance understanding of nuclear weapons. It includes stockpile surveillance, experimental research, development and engineering programs, and an appropriately scaled production capability to support stockpile requirements. This integrated national program requires the continued use of experimental facilities and programs, and the computational enhancements to support these programs. The Advanced Simulation and Computing Program (ASC) is a cornerstone of the SSP, providing simulation capabilities andmore » computational resources that support annual stockpile assessment and certification, study advanced nuclear weapons design and manufacturing processes, analyze accident scenarios and weapons aging, and provide the tools to enable stockpile Life Extension Programs (LEPs) and the resolution of Significant Finding Investigations (SFIs). This requires a balance of resource, including technical staff, hardware, simulation software, and computer science solutions. As the program approaches the end of its second decade, ASC is intently focused on increasing predictive capabilities in a three-dimensional (3D) simulation environment while maintaining support to the SSP. The program continues to improve its unique tools for solving progressively more difficult stockpile problems (sufficient resolution, dimensionality, and scientific details), quantify critical margins and uncertainties, and resolve increasingly difficult analyses needed for the SSP. Where possible, the program also enables the use of high-performance simulation and computing tools to address broader national security needs, such as foreign nuclear weapon assessments and counternuclear terrorism.« less

Numerical Uncertainty Quantification for Radiation Analysis Tools

NASA Technical Reports Server (NTRS)

Anderson, Brooke; Blattnig, Steve; Clowdsley, Martha

2007-01-01

Recently a new emphasis has been placed on engineering applications of space radiation analyses and thus a systematic effort of Verification, Validation and Uncertainty Quantification (VV&UQ) of the tools commonly used for radiation analysis for vehicle design and mission planning has begun. There are two sources of uncertainty in geometric discretization addressed in this paper that need to be quantified in order to understand the total uncertainty in estimating space radiation exposures. One source of uncertainty is in ray tracing, as the number of rays increase the associated uncertainty decreases, but the computational expense increases. Thus, a cost benefit analysis optimizing computational time versus uncertainty is needed and is addressed in this paper. The second source of uncertainty results from the interpolation over the dose vs. depth curves that is needed to determine the radiation exposure. The question, then, is what is the number of thicknesses that is needed to get an accurate result. So convergence testing is performed to quantify the uncertainty associated with interpolating over different shield thickness spatial grids.

Planetary Data Workshop, Part 2

NASA Technical Reports Server (NTRS)

1984-01-01

Technical aspects of the Planetary Data System (PDS) are addressed. Methods and tools for maintaining and accessing large, complex sets of data are discussed. The specific software and applications needed for processing imaging and non-imaging science data are reviewed. The need for specific software that provides users with information on the location and geometry of scientific observations is discussed. Computer networks and user interface to the PDS are covered along with Computer hardware available to this data system.

Capstone: A Geometry-Centric Platform to Enable Physics-Based Simulation and Design of Systems

DTIC Science & Technology

2015-10-05

foundation for the air-vehicle early design tool DaVinci being developed by CREATETM-AV project to enable development of associative models of air...CREATETM-AV solvers Kestrel [11] and Helios [16,17]. Furthermore, it is the foundation for the CREATETM-AV’s DaVinci [9] tool that provides a... Tools and Environments (CREATETM) program [6] aimed at developing a suite of high- performance physics-based computational tools addressing the needs

Bringing the CMS distributed computing system into scalable operations

NASA Astrophysics Data System (ADS)

Belforte, S.; Fanfani, A.; Fisk, I.; Flix, J.; Hernández, J. M.; Kress, T.; Letts, J.; Magini, N.; Miccio, V.; Sciabà, A.

2010-04-01

Establishing efficient and scalable operations of the CMS distributed computing system critically relies on the proper integration, commissioning and scale testing of the data and workload management tools, the various computing workflows and the underlying computing infrastructure, located at more than 50 computing centres worldwide and interconnected by the Worldwide LHC Computing Grid. Computing challenges periodically undertaken by CMS in the past years with increasing scale and complexity have revealed the need for a sustained effort on computing integration and commissioning activities. The Processing and Data Access (PADA) Task Force was established at the beginning of 2008 within the CMS Computing Program with the mandate of validating the infrastructure for organized processing and user analysis including the sites and the workload and data management tools, validating the distributed production system by performing functionality, reliability and scale tests, helping sites to commission, configure and optimize the networking and storage through scale testing data transfers and data processing, and improving the efficiency of accessing data across the CMS computing system from global transfers to local access. This contribution reports on the tools and procedures developed by CMS for computing commissioning and scale testing as well as the improvements accomplished towards efficient, reliable and scalable computing operations. The activities include the development and operation of load generators for job submission and data transfers with the aim of stressing the experiment and Grid data management and workload management systems, site commissioning procedures and tools to monitor and improve site availability and reliability, as well as activities targeted to the commissioning of the distributed production, user analysis and monitoring systems.

Current and anticipated uses of the thermal hydraulics codes at the NRC

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

Caruso, R.

1997-07-01

The focus of Thermal-Hydraulic computer code usage in nuclear regulatory organizations has undergone a considerable shift since the codes were originally conceived. Less work is being done in the area of {open_quotes}Design Basis Accidents,{close_quotes}, and much more emphasis is being placed on analysis of operational events, probabalistic risk/safety assessment, and maintenance practices. All of these areas need support from Thermal-Hydraulic computer codes to model the behavior of plant fluid systems, and they all need the ability to perform large numbers of analyses quickly. It is therefore important for the T/H codes of the future to be able to support thesemore » needs, by providing robust, easy-to-use, tools that produce easy-to understand results for a wider community of nuclear professionals. These tools need to take advantage of the great advances that have occurred recently in computer software, by providing users with graphical user interfaces for both input and output. In addition, reduced costs of computer memory and other hardware have removed the need for excessively complex data structures and numerical schemes, which make the codes more difficult and expensive to modify, maintain, and debug, and which increase problem run-times. Future versions of the T/H codes should also be structured in a modular fashion, to allow for the easy incorporation of new correlations, models, or features, and to simplify maintenance and testing. Finally, it is important that future T/H code developers work closely with the code user community, to ensure that the code meet the needs of those users.« less

The Nuclear Energy Advanced Modeling and Simulation Enabling Computational Technologies FY09 Report

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

Diachin, L F; Garaizar, F X; Henson, V E

2009-10-12

In this document we report on the status of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Enabling Computational Technologies (ECT) effort. In particular, we provide the context for ECT In the broader NEAMS program and describe the three pillars of the ECT effort, namely, (1) tools and libraries, (2) software quality assurance, and (3) computational facility (computers, storage, etc) needs. We report on our FY09 deliverables to determine the needs of the integrated performance and safety codes (IPSCs) in these three areas and lay out the general plan for software quality assurance to meet the requirements of DOE andmore » the DOE Advanced Fuel Cycle Initiative (AFCI). We conclude with a brief description of our interactions with the Idaho National Laboratory computer center to determine what is needed to expand their role as a NEAMS user facility.« less

Welding. Module 8 of the Vocational Education Readiness Test (VERT).

ERIC Educational Resources Information Center

Thomas, Edward L., Comp.

Focusing on welding, this module is one of eight included in the Vocational Education Readiness Tests (VERT). The module begins by listing the objectives of the module and describing tools and equipment needed. The remainder of the module contains sections on manipulative skills, trade vocabulary, tool identification, trade computational skills,…

ConMap: Investigating New Computer-Based Approaches to Assessing Conceptual Knowledge Structure in Physics.

ERIC Educational Resources Information Center

Beatty, Ian D.

There is a growing consensus among educational researchers that traditional problem-based assessments are not effective tools for diagnosing a student's knowledge state and for guiding pedagogical intervention, and that new tools grounded in the results of cognitive science research are needed. The ConMap ("Conceptual Mapping") project, described…

Bringing Research Tools into the Classroom

ERIC Educational Resources Information Center

Shubert, Charles; Ceraj, Ivica; Riley, Justin

2009-01-01

The advancement of computer technology used for research is creating the need to change the way classes are taught in higher education. "Bringing Research Tools into the Classroom" has become a major focus of the work of the Office of Educational Innovation and Technology (OEIT) for the Dean of Undergraduate Education (DUE) at the…

Masonry. Module 5 of the Vocational Education Readiness Test (VERT).

ERIC Educational Resources Information Center

Thomas, Edward L., Comp.

Focusing on masonry, this module is one of eight included in the Vocational Education Readiness Tests (VERT). The module begins by listing the objectives of the module and describing tools and equipment needed. The remainder of the module contains sections on manipulative skills, trade vocabulary, tool identification, trade computational skills,…

Advanced Tools for Smartphone-Based Experiments: Phyphox

ERIC Educational Resources Information Center

Staacks, S.; Hütz, S.; Stampfer, C.; Heinke, H.

2018-01-01

The sensors in modern smartphones are a promising and cost-effective tool for experimentation in physics education, but many experiments face practical problems. Often the phone is inaccessible during the experiment and the data usually needs to be analyzed subsequently on a computer. We address both problems by introducing a new app, called…

The Russia Project: Building Digital Bridges and Meeting Adolescent Needs

ERIC Educational Resources Information Center

Beal, Candy; Cuper, Pru; Dalton, Pat

2005-01-01

The intent of good education is to meet the needs of learners. How educators go about meeting those needs varies from one context to the next, and has lately been affected by the advent of technology-enhanced learning tools. Today, computer technology applications enable teachers to accelerate the pace of learning, increase the depth of in-school…

Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy

PubMed Central

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-01-01

Cloud computing has revolutionized availability and access to computing and storage resources; making it possible to provision a large computational infrastructure with only a few clicks in a web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this protocol, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatics analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to setup the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command line interface, and the web-based Galaxy interface. PMID:22700313

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

PubMed

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-06-01

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.

PREFACE: International Conference on Computing in High Energy and Nuclear Physics (CHEP'07)

NASA Astrophysics Data System (ADS)

Sobie, Randall; Tafirout, Reda; Thomson, Jana

2007-07-01

The 2007 International Conference on Computing in High Energy and Nuclear Physics (CHEP) was held on 2-7 September 2007 in Victoria, British Columbia, Canada. CHEP is a major series of international conferences for physicists and computing professionals from the High Energy and Nuclear Physics community, Computer Science and Information Technology. The CHEP conference provides an international forum to exchange information on computing experience and needs for the community, and to review recent, ongoing, and future activities. The CHEP'07 conference had close to 500 attendees with a program that included plenary sessions of invited oral presentations, a number of parallel sessions comprising oral and poster presentations, and an industrial exhibition. Conference tracks covered topics in Online Computing, Event Processing, Software Components, Tools and Databases, Software Tools and Information Systems, Computing Facilities, Production Grids and Networking, Grid Middleware and Tools, Distributed Data Analysis and Information Management and Collaborative Tools. The conference included a successful whale-watching excursion involving over 200 participants and a banquet at the Royal British Columbia Museum. The next CHEP conference will be held in Prague in March 2009. We would like thank the sponsors of the conference and the staff at the TRIUMF Laboratory and the University of Victoria who made the CHEP'07 a success. Randall Sobie and Reda Tafirout CHEP'07 Conference Chairs

Modeling a Wireless Network for International Space Station

NASA Technical Reports Server (NTRS)

Alena, Richard; Yaprak, Ece; Lamouri, Saad

2000-01-01

This paper describes the application of wireless local area network (LAN) simulation modeling methods to the hybrid LAN architecture designed for supporting crew-computing tools aboard the International Space Station (ISS). These crew-computing tools, such as wearable computers and portable advisory systems, will provide crew members with real-time vehicle and payload status information and access to digital technical and scientific libraries, significantly enhancing human capabilities in space. A wireless network, therefore, will provide wearable computer and remote instruments with the high performance computational power needed by next-generation 'intelligent' software applications. Wireless network performance in such simulated environments is characterized by the sustainable throughput of data under different traffic conditions. This data will be used to help plan the addition of more access points supporting new modules and more nodes for increased network capacity as the ISS grows.

Evaluating interactive computer-based scenarios designed for learning medical technology.

PubMed

Persson, Johanna; Dalholm, Elisabeth Hornyánszky; Wallergård, Mattias; Johansson, Gerd

2014-11-01

The use of medical equipment is growing in healthcare, resulting in an increased need for resources to educate users in how to manage the various devices. Learning the practical operation of a device is one thing, but learning how to work with the device in the actual clinical context is more challenging. This paper presents a computer-based simulation prototype for learning medical technology in the context of critical care. Properties from simulation and computer games have been adopted to create a visualization-based, interactive and contextually bound tool for learning. A participatory design process, including three researchers and three practitioners from a clinic for infectious diseases, was adopted to adjust the form and content of the prototype to the needs of the clinical practice and to create a situated learning experience. An evaluation with 18 practitioners showed that practitioners were positive to this type of tool for learning and that it served as a good platform for eliciting and sharing knowledge. Our conclusion is that this type of tools can be a complement to traditional learning resources to situate the learning in a context without requiring advanced technology or being resource-demanding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Component-Based Approach for Educating Students in Bioinformatics

ERIC Educational Resources Information Center

Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

2009-01-01

There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

Open source bioimage informatics for cell biology.

PubMed

Swedlow, Jason R; Eliceiri, Kevin W

2009-11-01

Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery.

An Intelligent Tutoring System for Antibody Identification

PubMed Central

Smith, Philip J.; Miller, Thomas E.; Fraser, Jane M.

1990-01-01

Empirical studies of medical technology students indicate that there is considerable need for additional skill development in performing tasks such as antibody identification. While this need is currently met by on-the-job training after employment, computer-based tutoring systems offer an alternative or supplemental problem-based learning environment that could be more cost effective. We have developed a prototype for such a tutoring system as part of a project to develop educational tools for the field of transfusion medicine. This system provides a microworld in which students can explore and solve cases, receiving assistance and tutoring from the computer as needed.

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

Allan, Benjamin A.

We report on the use and design of a portable, extensible performance data collection tool motivated by modeling needs of the high performance computing systems co-design com- munity. The lightweight performance data collectors with Eiger support is intended to be a tailorable tool, not a shrink-wrapped library product, as pro ling needs vary widely. A single code markup scheme is reported which, based on compilation ags, can send perfor- mance data from parallel applications to CSV les, to an Eiger mysql database, or (in a non-database environment) to at les for later merging and loading on a host with mysqlmore » available. The tool supports C, C++, and Fortran applications.« less

Tempest: Tools for Addressing the Needs of Next-Generation Climate Models

NASA Astrophysics Data System (ADS)

Ullrich, P. A.; Guerra, J. E.; Pinheiro, M. C.; Fong, J.

2015-12-01

Tempest is a comprehensive simulation-to-science infrastructure that tackles the needs of next-generation, high-resolution, data intensive climate modeling activities. This project incorporates three key components: TempestDynamics, a global modeling framework for experimental numerical methods and high-performance computing; TempestRemap, a toolset for arbitrary-order conservative and consistent remapping between unstructured grids; and TempestExtremes, a suite of detection and characterization tools for identifying weather extremes in large climate datasets. In this presentation, the latest advances with the implementation of this framework will be discussed, and a number of projects now utilizing these tools will be featured.

Familiarity with Technology among First-Year Students in Rwandan Tertiary Education

ERIC Educational Resources Information Center

Byungura, Jean Claude; Hansson, Henrik; Muparasi, Mugabe; Ruhinda, Ben

2018-01-01

The more the students get experienced with technologies, the more the need for tertiary education systems to adopt innovative pedagogical strategies for accommodating different learning needs. Depending on students' prior experience with computer-based tools, they may have different degrees of familiarity with new technologies. At University of…

Modeling Criminal Activity in Urban Landscapes

NASA Astrophysics Data System (ADS)

Brantingham, Patricia; Glässer, Uwe; Jackson, Piper; Vajihollahi, Mona

Computational and mathematical methods arguably have an enormous potential for serving practical needs in crime analysis and prevention by offering novel tools for crime investigations and experimental platforms for evidence-based policy making. We present a comprehensive formal framework and tool support for mathematical and computational modeling of criminal behavior to facilitate systematic experimental studies of a wide range of criminal activities in urban environments. The focus is on spatial and temporal aspects of different forms of crime, including opportunistic and serial violent crimes. However, the proposed framework provides a basis to push beyond conventional empirical research and engage the use of computational thinking and social simulations in the analysis of terrorism and counter-terrorism.

TOXCAST, A TOOL FOR CATEGORIZATION AND ...

EPA Pesticide Factsheets

Across several EPA Program Offices (e.g., OPPTS, OW, OAR), there is a clear need to develop strategies and methods to screen large numbers of chemicals for potential toxicity, and to use the resulting information to prioritize the use of testing resources towards those entities and endpoints that present the greatest likelihood of risk to human health and the environment. This need could be addressed using the experience of the pharmaceutical industry in the use of advanced modern molecular biology and computational chemistry tools for the development of new drugs, with appropriate adjustment to the needs and desires of environmental toxicology. A conceptual approach named ToxCast has been developed to address the needs of EPA Program Offices in the area of prioritization and screening. Modern computational chemistry and molecular biology tools bring enabling technologies forward that can provide information about the physical and biological properties of large numbers of chemicals. The essence of the proposal is to conduct a demonstration project based upon a rich toxicological database (e.g., registered pesticides, or the chemicals tested in the NTP bioassay program), select a fairly large number (50-100 or more chemicals) representative of a number of differing structural classes and phenotypic outcomes (e.g., carcinogens, reproductive toxicants, neurotoxicants), and evaluate them across a broad spectrum of information domains that modern technology has pro

Computer-Aided Nodule Assessment and Risk Yield Risk Management of Adenocarcinoma: The Future of Imaging?

PubMed

Foley, Finbar; Rajagopalan, Srinivasan; Raghunath, Sushravya M; Boland, Jennifer M; Karwoski, Ronald A; Maldonado, Fabien; Bartholmai, Brian J; Peikert, Tobias

2016-01-01

Increased clinical use of chest high-resolution computed tomography results in increased identification of lung adenocarcinomas and persistent subsolid opacities. However, these lesions range from very indolent to extremely aggressive tumors. Clinically relevant diagnostic tools to noninvasively risk stratify and guide individualized management of these lesions are lacking. Research efforts investigating semiquantitative measures to decrease interrater and intrarater variability are emerging, and in some cases steps have been taken to automate this process. However, many such methods currently are still suboptimal, require validation and are not yet clinically applicable. The computer-aided nodule assessment and risk yield software application represents a validated tool for the automated, quantitative, and noninvasive tool for risk stratification of adenocarcinoma lung nodules. Computer-aided nodule assessment and risk yield correlates well with consensus histology and postsurgical patient outcomes, and therefore may help to guide individualized patient management, for example, in identification of nodules amenable to radiological surveillance, or in need of adjunctive therapy. Copyright © 2016 Elsevier Inc. All rights reserved.

Managing expectations when publishing tools and methods for computational proteomics.

PubMed

Martens, Lennart; Kohlbacher, Oliver; Weintraub, Susan T

2015-05-01

Computational tools are pivotal in proteomics because they are crucial for identification, quantification, and statistical assessment of data. The gateway to finding the best choice of a tool or approach for a particular problem is frequently journal articles, yet there is often an overwhelming variety of options that makes it hard to decide on the best solution. This is particularly difficult for nonexperts in bioinformatics. The maturity, reliability, and performance of tools can vary widely because publications may appear at different stages of development. A novel idea might merit early publication despite only offering proof-of-principle, while it may take years before a tool can be considered mature, and by that time it might be difficult for a new publication to be accepted because of a perceived lack of novelty. After discussions with members of the computational mass spectrometry community, we describe here proposed recommendations for organization of informatics manuscripts as a way to set the expectations of readers (and reviewers) through three different manuscript types that are based on existing journal designations. Brief Communications are short reports describing novel computational approaches where the implementation is not necessarily production-ready. Research Articles present both a novel idea and mature implementation that has been suitably benchmarked. Application Notes focus on a mature and tested tool or concept and need not be novel but should offer advancement from improved quality, ease of use, and/or implementation. Organizing computational proteomics contributions into these three manuscript types will facilitate the review process and will also enable readers to identify the maturity and applicability of the tool for their own workflows.

Human-Computer Interaction and Information Management Research Needs

DTIC Science & Technology

2003-10-01

Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be...hand-held personal digital assistants, networked sensors and actuators, and low-power computers on satellites. 5 most complex tools that humans have...calculations using data on external media such as tapes evolved into our multi-functional 21st century systems. More ideas came as networks of computing

A regional land use survey based on remote sensing and other data: A report on a LANDSAT and computer mapping project, volume 1. [Arizona, Colorado, Montana, New Mexico, Utah, and Wyoming

NASA Technical Reports Server (NTRS)

Nez, G. (Principal Investigator); Mutter, D.

1977-01-01

The author has identified the following significant results. New LANDSAT analysis software and linkages with other computer mapping software were developed. Significant results were also achieved in training, communication, and identification of needs for developing the LANDSAT/computer mapping technologies into operational tools for use by decision makers.

Efficient utilization of graphics technology for space animation

NASA Technical Reports Server (NTRS)

Panos, Gregory Peter

1989-01-01

Efficient utilization of computer graphics technology has become a major investment in the work of aerospace engineers and mission designers. These new tools are having a significant impact in the development and analysis of complex tasks and procedures which must be prepared prior to actual space flight. Design and implementation of useful methods in applying these tools has evolved into a complex interaction of hardware, software, network, video and various user interfaces. Because few people can understand every aspect of this broad mix of technology, many specialists are required to build, train, maintain and adapt these tools to changing user needs. Researchers have set out to create systems where an engineering designer can easily work to achieve goals with a minimum of technological distraction. This was accomplished with high-performance flight simulation visual systems and supercomputer computational horsepower. Control throughout the creative process is judiciously applied while maintaining generality and ease of use to accommodate a wide variety of engineering needs.

An Examination of How a Teacher's Use of Digital Tools Empowers and Constrains Language Arts Instruction

ERIC Educational Resources Information Center

Hutchison, Amy C.; Woodward, Lindsay

2014-01-01

The Common Core State Standards produce a need to understand how digital tools can support literacy instruction. The purpose of this case study was to explore how a language arts teacher's integration of computers and iPads empowered and constrained her and the resulting classroom instruction. Constraining factors included (a) inadequate…

Web Pages as an Interdisciplinary Tool in English for Architects Classes.

ERIC Educational Resources Information Center

Mansilla, Paloma Ubeda

2002-01-01

Proposes the use of web pages as an interdisciplinary tool in classes of English for professional and academic purposes. Languages and computing are two areas of knowledge that the graduate of the Polytechnic University of Madrid and its School of architecture need to study in order to supplement the education received during their degree with the…

A smarter way to search, share and utilize open-spatial online data for energy R&D - Custom machine learning and GIS tools in U.S. DOE's virtual data library & laboratory, EDX

NASA Astrophysics Data System (ADS)

Rose, K.; Bauer, J.; Baker, D.; Barkhurst, A.; Bean, A.; DiGiulio, J.; Jones, K.; Jones, T.; Justman, D.; Miller, R., III; Romeo, L.; Sabbatino, M.; Tong, A.

2017-12-01

As spatial datasets are increasingly accessible through open, online systems, the opportunity to use these resources to address a range of Earth system questions grows. Simultaneously, there is a need for better infrastructure and tools to find and utilize these resources. We will present examples of advanced online computing capabilities, hosted in the U.S. DOE's Energy Data eXchange (EDX), that address these needs for earth-energy research and development. In one study the computing team developed a custom, machine learning, big data computing tool designed to parse the web and return priority datasets to appropriate servers to develop an open-source global oil and gas infrastructure database. The results of this spatial smart search approach were validated against expert-driven, manual search results which required a team of seven spatial scientists three months to produce. The custom machine learning tool parsed online, open systems, including zip files, ftp sites and other web-hosted resources, in a matter of days. The resulting resources were integrated into a geodatabase now hosted for open access via EDX. Beyond identifying and accessing authoritative, open spatial data resources, there is also a need for more efficient tools to ingest, perform, and visualize multi-variate, spatial data analyses. Within the EDX framework, there is a growing suite of processing, analytical and visualization capabilities that allow multi-user teams to work more efficiently in private, virtual workspaces. An example of these capabilities are a set of 5 custom spatio-temporal models and data tools that form NETL's Offshore Risk Modeling suite that can be used to quantify oil spill risks and impacts. Coupling the data and advanced functions from EDX with these advanced spatio-temporal models has culminated with an integrated web-based decision-support tool. This platform has capabilities to identify and combine data across scales and disciplines, evaluate potential environmental, social, and economic impacts, highlight knowledge or technology gaps, and reduce uncertainty for a range of `what if' scenarios relevant to oil spill prevention efforts. These examples illustrate EDX's growing capabilities for advanced spatial data search and analysis to support geo-data science needs.

The efficiency of geophysical adjoint codes generated by automatic differentiation tools

NASA Astrophysics Data System (ADS)

Vlasenko, A. V.; Köhl, A.; Stammer, D.

2016-02-01

The accuracy of numerical models that describe complex physical or chemical processes depends on the choice of model parameters. Estimating an optimal set of parameters by optimization algorithms requires knowledge of the sensitivity of the process of interest to model parameters. Typically the sensitivity computation involves differentiation of the model, which can be performed by applying algorithmic differentiation (AD) tools to the underlying numerical code. However, existing AD tools differ substantially in design, legibility and computational efficiency. In this study we show that, for geophysical data assimilation problems of varying complexity, the performance of adjoint codes generated by the existing AD tools (i) Open_AD, (ii) Tapenade, (iii) NAGWare and (iv) Transformation of Algorithms in Fortran (TAF) can be vastly different. Based on simple test problems, we evaluate the efficiency of each AD tool with respect to computational speed, accuracy of the adjoint, the efficiency of memory usage, and the capability of each AD tool to handle modern FORTRAN 90-95 elements such as structures and pointers, which are new elements that either combine groups of variables or provide aliases to memory addresses, respectively. We show that, while operator overloading tools are the only ones suitable for modern codes written in object-oriented programming languages, their computational efficiency lags behind source transformation by orders of magnitude, rendering the application of these modern tools to practical assimilation problems prohibitive. In contrast, the application of source transformation tools appears to be the most efficient choice, allowing handling even large geophysical data assimilation problems. However, they can only be applied to numerical models written in earlier generations of programming languages. Our study indicates that applying existing AD tools to realistic geophysical problems faces limitations that urgently need to be solved to allow the continuous use of AD tools for solving geophysical problems on modern computer architectures.

ADAM: analysis of discrete models of biological systems using computer algebra.

PubMed

Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

2011-07-20

Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web-based tool for several different input formats, and it makes analysis of complex models accessible to a larger community, as it is platform independent as a web-service and does not require understanding of the underlying mathematics.

Searching for SNPs with cloud computing

PubMed Central

2009-01-01

As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/. PMID:19930550

Computational Fluid Dynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Kutler, Paul

1994-01-01

Computational fluid dynamics (CFD) is beginning to play a major role in the aircraft industry of the United States because of the realization that CFD can be a new and effective design tool and thus could provide a company with a competitive advantage. It is also playing a significant role in research institutions, both governmental and academic, as a tool for researching new fluid physics, as well as supplementing and complementing experimental testing. In this presentation, some of the progress made to date in CFD at NASA Ames will be reviewed. The presentation addresses the status of CFD in terms of methods, examples of CFD solutions, and computer technology. In addition, the role CFD will play in supporting the revolutionary goals set forth by the Aeronautical Policy Review Committee established by the Office of Science and Technology Policy is noted. The need for validated CFD tools is also briefly discussed.

CLAST: CUDA implemented large-scale alignment search tool.

PubMed

Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

2014-12-11

Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.

Modeling Biodegradation and Reactive Transport: Analytical and Numerical Models

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

Sun, Y; Glascoe, L

The computational modeling of the biodegradation of contaminated groundwater systems accounting for biochemical reactions coupled to contaminant transport is a valuable tool for both the field engineer/planner with limited computational resources and the expert computational researcher less constrained by time and computer power. There exists several analytical and numerical computer models that have been and are being developed to cover the practical needs put forth by users to fulfill this spectrum of computational demands. Generally, analytical models provide rapid and convenient screening tools running on very limited computational power, while numerical models can provide more detailed information with consequent requirementsmore » of greater computational time and effort. While these analytical and numerical computer models can provide accurate and adequate information to produce defensible remediation strategies, decisions based on inadequate modeling output or on over-analysis can have costly and risky consequences. In this chapter we consider both analytical and numerical modeling approaches to biodegradation and reactive transport. Both approaches are discussed and analyzed in terms of achieving bioremediation goals, recognizing that there is always a tradeoff between computational cost and the resolution of simulated systems.« less

Computational aerodynamics requirements: The future role of the computer and the needs of the aerospace industry

NASA Technical Reports Server (NTRS)

Rubbert, P. E.

1978-01-01

The commercial airplane builder's viewpoint on the important issues involved in the development of improved computational aerodynamics tools such as powerful computers optimized for fluid flow problems is presented. The primary user of computational aerodynamics in a commercial aircraft company is the design engineer who is concerned with solving practical engineering problems. From his viewpoint, the development of program interfaces and pre-and post-processing capability for new computational methods is just as important as the algorithms and machine architecture. As more and more details of the entire flow field are computed, the visibility of the output data becomes a major problem which is then doubled when a design capability is added. The user must be able to see, understand, and interpret the results calculated. Enormous costs are expanded because of the need to work with programs having only primitive user interfaces.

Preschool and Primary School Pedagogy Specialization Students' Opinion about Computers in Education

ERIC Educational Resources Information Center

Zsoldos-Marchis, Iuliana

2017-01-01

Computers became an important tool in most of the working places. Also, children today grow with different technological devices around, they start to use them from very early ages. Thus Education should integrate these technological devices from more purposes: they are attractive for children, they need to learn how to use them properly and…

Comparative Modeling of Proteins: A Method for Engaging Students' Interest in Bioinformatics Tools

ERIC Educational Resources Information Center

Badotti, Fernanda; Barbosa, Alan Sales; Reis, André Luiz Martins; do Valle, Ítalo Faria; Ambrósio, Lara; Bitar, Mainá

2014-01-01

The huge increase in data being produced in the genomic era has produced a need to incorporate computers into the research process. Sequence generation, its subsequent storage, interpretation, and analysis are now entirely computer-dependent tasks. Universities from all over the world have been challenged to seek a way of encouraging students to…

Identifying Key Features, Cutting Edge Cloud Resources, and Artificial Intelligence Tools to Achieve User-Friendly Water Science in the Cloud

NASA Astrophysics Data System (ADS)

Pierce, S. A.

2017-12-01

Decision making for groundwater systems is becoming increasingly important, as shifting water demands increasingly impact aquifers. As buffer systems, aquifers provide room for resilient responses and augment the actual timeframe for hydrological response. Yet the pace impacts, climate shifts, and degradation of water resources is accelerating. To meet these new drivers, groundwater science is transitioning toward the emerging field of Integrated Water Resources Management, or IWRM. IWRM incorporates a broad array of dimensions, methods, and tools to address problems that tend to be complex. Computational tools and accessible cyberinfrastructure (CI) are needed to cross the chasm between science and society. Fortunately cloud computing environments, such as the new Jetstream system, are evolving rapidly. While still targeting scientific user groups systems such as, Jetstream, offer configurable cyberinfrastructure to enable interactive computing and data analysis resources on demand. The web-based interfaces allow researchers to rapidly customize virtual machines, modify computing architecture and increase the usability and access for broader audiences to advanced compute environments. The result enables dexterous configurations and opening up opportunities for IWRM modelers to expand the reach of analyses, number of case studies, and quality of engagement with stakeholders and decision makers. The acute need to identify improved IWRM solutions paired with advanced computational resources refocuses the attention of IWRM researchers on applications, workflows, and intelligent systems that are capable of accelerating progress. IWRM must address key drivers of community concern, implement transdisciplinary methodologies, adapt and apply decision support tools in order to effectively support decisions about groundwater resource management. This presentation will provide an overview of advanced computing services in the cloud using integrated groundwater management case studies to highlight how Cloud CI streamlines the process for setting up an interactive decision support system. Moreover, advances in artificial intelligence offer new techniques for old problems from integrating data to adaptive sensing or from interactive dashboards to optimizing multi-attribute problems. The combination of scientific expertise, flexible cloud computing solutions, and intelligent systems opens new research horizons.

Computational Screening of 2D Materials for Photocatalysis.

PubMed

Singh, Arunima K; Mathew, Kiran; Zhuang, Houlong L; Hennig, Richard G

2015-03-19

Two-dimensional (2D) materials exhibit a range of extraordinary electronic, optical, and mechanical properties different from their bulk counterparts with potential applications for 2D materials emerging in energy storage and conversion technologies. In this Perspective, we summarize the recent developments in the field of solar water splitting using 2D materials and review a computational screening approach to rapidly and efficiently discover more 2D materials that possess properties suitable for solar water splitting. Computational tools based on density-functional theory can predict the intrinsic properties of potential photocatalyst such as their electronic properties, optical absorbance, and solubility in aqueous solutions. Computational tools enable the exploration of possible routes to enhance the photocatalytic activity of 2D materials by use of mechanical strain, bias potential, doping, and pH. We discuss future research directions and needed method developments for the computational design and optimization of 2D materials for photocatalysis.

Grids: The Top Ten Questions

DOE PAGES

Schopf, Jennifer M.; Nitzberg, Bill

2002-01-01

The design and implementation of a national computing system and data grid has become a reachable goal from both the computer science and computational science point of view. A distributed infrastructure capable of sophisticated computational functions can bring many benefits to scientific work, but poses many challenges, both technical and socio-political. Technical challenges include having basic software tools, higher-level services, functioning and pervasive security, and standards, while socio-political issues include building a user community, adding incentives for sites to be part of a user-centric environment, and educating funding sources about the needs of this community. This paper details the areasmore » relating to Grid research that we feel still need to be addressed to fully leverage the advantages of the Grid.« less

Computer-Generated Movies for Mission Planning

NASA Technical Reports Server (NTRS)

Roberts, P. H., Jr.; vanDillen, S. L.

1973-01-01

Computer-generated movies help the viewer to understand mission dynamics and get quantitative details. Sample movie frames demonstrate the uses and effectiveness of movies in mission planning. Tools needed for movie-making include computer programs to generate images on film and film processing to give the desired result. Planning scenes to make an effective product requires some thought and experience. Viewpoints and timing are particularly important. Lessons learned so far and problems still encountered are discussed.

Enseigner l'intonation: L'ordinateur a la rescousse (Teaching Intonation: The Computer to the Rescue).

ERIC Educational Resources Information Center

Canto-Knoerr, Helene

1992-01-01

A discussion of intonation instruction in second-language teaching looks at the role, objectives, and scope of such instruction; the tools teachers need to accomplish it (background in theory, practical guidelines, a method, appropriate research, and equipment); and the need for and possible design of related software. (MSE)

Applying Technology to Unmet Needs. Technology and the American Economy, Appendix, Volume V.

ERIC Educational Resources Information Center

National Commission on Technology, Automation and Economic Progress, Washington, DC.

Twelve studies dealing with the problems of applying technology to unmet human and community needs are presented. "Urban Planning and Metropolitan Development--The Role of Technology," examines the possibilities of the computer and other modern planning tools. "Technology, Automation, and Economic Progress in Housing and Urban Development"…

Vehicle Lightweighting: Challenges and Opportunities with Aluminum

NASA Astrophysics Data System (ADS)

Sachdev, Anil K.; Mishra, Raja K.; Mahato, Anirban; Alpas, Ahmet

Rising energy costs, consumer preferences and regulations drive requirements for fuel economy, performance, comfort, safety and cost of future automobiles. These conflicting situations offer challenges for vehicle lightweighting, for which aluminum applications are key. This paper describes product design needs and materials and process development opportunities driven by theoretical, experimental and modeling tools in the area of sheet and castings. Computational tools and novel experimental techniques used in their development are described. The paper concludes with challenges that lie ahead for pervasive use of aluminum and the necessary fundamental R&D that is still needed.

Open source bioimage informatics for cell biology

PubMed Central

Swedlow, Jason R.; Eliceiri, Kevin W.

2009-01-01

Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery. PMID:19833518

You're a What? Usability Engineer.

ERIC Educational Resources Information Center

Crosby, Olivia

2001-01-01

Describes the work of usability engineers, who improve computer hardware, software, and websites by focusing on how users perceive and manipulate those tools. Discusses education, training, salaries, and talents needed by usability engineers. (Author/JOW)

NREL to Lead New Consortium to Develop Advanced Water Splitting Materials

Science.gov Websites

said. "Our research strategy integrates computational tools and modeling, material synthesis needs, such as high-throughput synthesis techniques and auxiliary component design. HydroGEN is the

A Python tool to set up relative free energy calculations in GROMACS.

PubMed

Klimovich, Pavel V; Mobley, David L

2015-11-01

Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations.

Shifting the Load: A Peer Dialogue Agent That Encourages Its Human Collaborator to Contribute More to Problem Solving

ERIC Educational Resources Information Center

Howard, Cynthia; Jordan, Pamela; Di Eugenio, Barbara; Katz, Sandra

2017-01-01

Despite a growing need for educational tools that support students at the earliest phases of undergraduate Computer Science (CS) curricula, relatively few such tools exist--the majority being Intelligent Tutoring Systems. Since peer interactions more readily give rise to challenges and negotiations, another way in which students can become more…

Modifications in the AA5083 Johnson-Cook Material Model for Use in Friction Stir Welding Computational Analyses

DTIC Science & Technology

2011-12-30

which reduces the need for expensive post-weld machining; and (g) low environmental impact . However, some disadvantages of the FSW process have also...next set to that of AISI- H13 , a hot-worked tool steel, frequently used as the FSW-tool material (Ref 16). The work-piece material is assumed to be

Projected role of advanced computational aerodynamic methods at the Lockheed-Georgia company

NASA Technical Reports Server (NTRS)

Lores, M. E.

1978-01-01

Experience with advanced computational methods being used at the Lockheed-Georgia Company to aid in the evaluation and design of new and modified aircraft indicates that large and specialized computers will be needed to make advanced three-dimensional viscous aerodynamic computations practical. The Numerical Aerodynamic Simulation Facility should be used to provide a tool for designing better aerospace vehicles while at the same time reducing development costs by performing computations using Navier-Stokes equations solution algorithms and permitting less sophisticated but nevertheless complex calculations to be made efficiently. Configuration definition procedures and data output formats can probably best be defined in cooperation with industry, therefore, the computer should handle many remote terminals efficiently. The capability of transferring data to and from other computers needs to be provided. Because of the significant amount of input and output associated with 3-D viscous flow calculations and because of the exceedingly fast computation speed envisioned for the computer, special attention should be paid to providing rapid, diversified, and efficient input and output.

XS: a FASTQ read simulator.

PubMed

Pratas, Diogo; Pinho, Armando J; Rodrigues, João M O S

2014-01-16

The emerging next-generation sequencing (NGS) is bringing, besides the natural huge amounts of data, an avalanche of new specialized tools (for analysis, compression, alignment, among others) and large public and private network infrastructures. Therefore, a direct necessity of specific simulation tools for testing and benchmarking is rising, such as a flexible and portable FASTQ read simulator, without the need of a reference sequence, yet correctly prepared for producing approximately the same characteristics as real data. We present XS, a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores). XS provides an efficient and convenient method for fast simulation of FASTQ files, such as those from Ion Torrent (currently uncovered by other simulators), Roche-454, Illumina and ABI-SOLiD sequencing machines. This tool is publicly available at http://bioinformatics.ua.pt/software/xs/.

Information Power Grid (IPG) Tutorial 2003

NASA Technical Reports Server (NTRS)

Meyers, George

2003-01-01

For NASA and the general community today Grid middleware: a) provides tools to access/use data sources (databases, instruments, ...); b) provides tools to access computing (unique and generic); c) Is an enabler of large scale collaboration. Dynamically responding to needs is a key selling point of a grid. Independent resources can be joined as appropriate to solve a problem. Provide tools to enable the building of a frameworks for application. Provide value added service to the NASA user base for utilizing resources on the grid in new and more efficient ways. Provides tools for development of Frameworks.

Use of handheld computers in clinical practice: a systematic review.

PubMed

Mickan, Sharon; Atherton, Helen; Roberts, Nia Wyn; Heneghan, Carl; Tilson, Julie K

2014-07-06

Many healthcare professionals use smartphones and tablets to inform patient care. Contemporary research suggests that handheld computers may support aspects of clinical diagnosis and management. This systematic review was designed to synthesise high quality evidence to answer the question; Does healthcare professionals' use of handheld computers improve their access to information and support clinical decision making at the point of care? A detailed search was conducted using Cochrane, MEDLINE, EMBASE, PsycINFO, Science and Social Science Citation Indices since 2001. Interventions promoting healthcare professionals seeking information or making clinical decisions using handheld computers were included. Classroom learning and the use of laptop computers were excluded. Two authors independently selected studies, assessed quality using the Cochrane Risk of Bias tool and extracted data. High levels of data heterogeneity negated statistical synthesis. Instead, evidence for effectiveness was summarised narratively, according to each study's aim for assessing the impact of handheld computer use. We included seven randomised trials investigating medical or nursing staffs' use of Personal Digital Assistants. Effectiveness was demonstrated across three distinct functions that emerged from the data: accessing information for clinical knowledge, adherence to guidelines and diagnostic decision making. When healthcare professionals used handheld computers to access clinical information, their knowledge improved significantly more than peers who used paper resources. When clinical guideline recommendations were presented on handheld computers, clinicians made significantly safer prescribing decisions and adhered more closely to recommendations than peers using paper resources. Finally, healthcare professionals made significantly more appropriate diagnostic decisions using clinical decision making tools on handheld computers compared to colleagues who did not have access to these tools. For these clinical decisions, the numbers need to test/screen were all less than 11. Healthcare professionals' use of handheld computers may improve their information seeking, adherence to guidelines and clinical decision making. Handheld computers can provide real time access to and analysis of clinical information. The integration of clinical decision support systems within handheld computers offers clinicians the highest level of synthesised evidence at the point of care. Future research is needed to replicate these early results and to identify beneficial clinical outcomes.

Use of handheld computers in clinical practice: a systematic review

PubMed Central

2014-01-01

Background Many healthcare professionals use smartphones and tablets to inform patient care. Contemporary research suggests that handheld computers may support aspects of clinical diagnosis and management. This systematic review was designed to synthesise high quality evidence to answer the question; Does healthcare professionals’ use of handheld computers improve their access to information and support clinical decision making at the point of care? Methods A detailed search was conducted using Cochrane, MEDLINE, EMBASE, PsycINFO, Science and Social Science Citation Indices since 2001. Interventions promoting healthcare professionals seeking information or making clinical decisions using handheld computers were included. Classroom learning and the use of laptop computers were excluded. Two authors independently selected studies, assessed quality using the Cochrane Risk of Bias tool and extracted data. High levels of data heterogeneity negated statistical synthesis. Instead, evidence for effectiveness was summarised narratively, according to each study’s aim for assessing the impact of handheld computer use. Results We included seven randomised trials investigating medical or nursing staffs’ use of Personal Digital Assistants. Effectiveness was demonstrated across three distinct functions that emerged from the data: accessing information for clinical knowledge, adherence to guidelines and diagnostic decision making. When healthcare professionals used handheld computers to access clinical information, their knowledge improved significantly more than peers who used paper resources. When clinical guideline recommendations were presented on handheld computers, clinicians made significantly safer prescribing decisions and adhered more closely to recommendations than peers using paper resources. Finally, healthcare professionals made significantly more appropriate diagnostic decisions using clinical decision making tools on handheld computers compared to colleagues who did not have access to these tools. For these clinical decisions, the numbers need to test/screen were all less than 11. Conclusion Healthcare professionals’ use of handheld computers may improve their information seeking, adherence to guidelines and clinical decision making. Handheld computers can provide real time access to and analysis of clinical information. The integration of clinical decision support systems within handheld computers offers clinicians the highest level of synthesised evidence at the point of care. Future research is needed to replicate these early results and to identify beneficial clinical outcomes. PMID:24998515

DOE's Computer Incident Advisory Capability (CIAC)

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

Schultz, E.

1990-09-01

Computer security is essential in maintaining quality in the computing environment. Computer security incidents, however, are becoming more sophisticated. The DOE Computer Incident Advisory Capability (CIAC) team was formed primarily to assist DOE sites in responding to computer security incidents. Among CIAC's other responsibilities are gathering and distributing information to DOE sites, providing training workshops, coordinating with other agencies, response teams, and vendors, creating guidelines for incident handling, and developing software tools. CIAC has already provided considerable assistance to DOE sites faced with virus infections and worm and hacker attacks, has issued over 40 information bulletins, and has developed andmore » presented a workshop on incident handling. CIAC's experience in helping sites has produced several lessons learned, including the need to follow effective procedures to avoid virus infections in small systems and the need for sound password management and system administration in networked systems. CIAC's activity and scope will expand in the future. 4 refs.« less

Applied Linguistics Project: Student-Led Computer Assisted Research in High School EAL/EAP

ERIC Educational Resources Information Center

Bohát, Róbert; Rödlingová, Beata; Horáková, Nina

2015-01-01

The Applied Linguistics Project (ALP) started at the International School of Prague (ISP) in 2013. Every year, Grade 9 English as an Additional Language (EAL) students identify an area of learning in need of improvement and design a research method followed by data collection and analysis using basic computer software tools or online corpora.…

A computer-based specification methodology

NASA Technical Reports Server (NTRS)

Munck, Robert G.

1986-01-01

Standard practices for creating and using system specifications are inadequate for large, advanced-technology systems. A need exists to break away from paper documents in favor of documents that are stored in computers and which are read and otherwise used with the help of computers. An SADT-based system, running on the proposed Space Station data management network, could be a powerful tool for doing much of the required technical work of the Station, including creating and operating the network itself.

A Quantum Computing Approach to Model Checking for Advanced Manufacturing Problems

DTIC Science & Technology

2014-07-01

amount of time. In summary, the tool we developed succeeded in allowing us to produce good solutions for optimization problems that did not fit ...We compared the value of the objective obtained in each run with the known optimal value, and used this information to compute the probability of ...success for each given instance. Then we used this information to compute the expected number of repetitions (or runs) needed to obtain the optimal

Extensible Computational Chemistry Environment

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

2012-08-09

ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. ECCE was conceived as part of the Environmental Molecular Sciences Laboratory construction to solve the problem of researchers being able to effectively utilize complex computational chemistry codes and massively parallel high performance compute resources. Bringing the power of these codes and resources to the desktops of researcher and thus enabling world class research without users needing a detailed understanding of themore » inner workings of either the theoretical codes or the supercomputers needed to run them was a grand challenge problem in the original version of the EMSL. ECCE allows collaboration among researchers using a web-based data repository where the inputs and results for all calculations done within ECCE are organized. ECCE is a first of kind end-to-end problem solving environment for all phases of computational chemistry research: setting up calculations with sophisticated GUI and direct manipulation visualization tools, submitting and monitoring calculations on remote high performance supercomputers without having to be familiar with the details of using these compute resources, and performing results visualization and analysis including creating publication quality images. ECCE is a suite of tightly integrated applications that are employed as the user moves through the modeling process.« less

AMAS: a fast tool for alignment manipulation and computing of summary statistics.

PubMed

Borowiec, Marek L

2016-01-01

The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python's core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License.

CAESY - COMPUTER AIDED ENGINEERING SYSTEM

NASA Technical Reports Server (NTRS)

Wette, M. R.

1994-01-01

Many developers of software and algorithms for control system design have recognized that current tools have limits in both flexibility and efficiency. Many forces drive the development of new tools including the desire to make complex system modeling design and analysis easier and the need for quicker turnaround time in analysis and design. Other considerations include the desire to make use of advanced computer architectures to help in control system design, adopt new methodologies in control, and integrate design processes (e.g., structure, control, optics). CAESY was developed to provide a means to evaluate methods for dealing with user needs in computer-aided control system design. It is an interpreter for performing engineering calculations and incorporates features of both Ada and MATLAB. It is designed to be reasonably flexible and powerful. CAESY includes internally defined functions and procedures, as well as user defined ones. Support for matrix calculations is provided in the same manner as MATLAB. However, the development of CAESY is a research project, and while it provides some features which are not found in commercially sold tools, it does not exhibit the robustness that many commercially developed tools provide. CAESY is written in C-language for use on Sun4 series computers running SunOS 4.1.1 and later. The program is designed to optionally use the LAPACK math library. The LAPACK math routines are available through anonymous ftp from research.att.com. CAESY requires 4Mb of RAM for execution. The standard distribution medium is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. CAESY was developed in 1993 and is a copyrighted work with all copyright vested in NASA.

Toward Interactive Scenario Analysis and Exploration

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

Gayle, Thomas R.; Summers, Kenneth Lee; Jungels, John

2015-01-01

As Modeling and Simulation (M&S) tools have matured, their applicability and importance have increased across many national security challenges. In particular, they provide a way to test how something may behave without the need to do real world testing. However, current and future changes across several factors including capabilities, policy, and funding are driving a need for rapid response or evaluation in ways that many M&S tools cannot address. Issues around large data, computational requirements, delivery mechanisms, and analyst involvement already exist and pose significant challenges. Furthermore, rising expectations, rising input complexity, and increasing depth of analysis will only increasemore » the difficulty of these challenges. In this study we examine whether innovations in M&S software coupled with advances in ''cloud'' computing and ''big-data'' methodologies can overcome many of these challenges. In particular, we propose a simple, horizontally-scalable distributed computing environment that could provide the foundation (i.e. ''cloud'') for next-generation M&S-based applications based on the notion of ''parallel multi-simulation''. In our context, the goal of parallel multi- simulation is to consider as many simultaneous paths of execution as possible. Therefore, with sufficient resources, the complexity is dominated by the cost of single scenario runs as opposed to the number of runs required. We show the feasibility of this architecture through a stable prototype implementation coupled with the Umbra Simulation Framework [6]. Finally, we highlight the utility through multiple novel analysis tools and by showing the performance improvement compared to existing tools.« less

Web-based Tool Suite for Plasmasphere Information Discovery

NASA Astrophysics Data System (ADS)

Newman, T. S.; Wang, C.; Gallagher, D. L.

2005-12-01

A suite of tools that enable discovery of terrestrial plasmasphere characteristics from NASA IMAGE Extreme Ultra Violet (EUV) images is described. The tool suite is web-accessible, allowing easy remote access without the need for any software installation on the user's computer. The features supported by the tool include reconstruction of the plasmasphere plasma density distribution from a short sequence of EUV images, semi-automated selection of the plasmapause boundary in an EUV image, and mapping of the selected boundary to the geomagnetic equatorial plane. EUV image upload and result download is also supported. The tool suite's plasmapause mapping feature is achieved via the Roelof and Skinner (2000) Edge Algorithm. The plasma density reconstruction is achieved through a tomographic technique that exploits physical constraints to allow for a moderate resolution result. The tool suite's software architecture uses Java Server Pages (JSP) and Java Applets on the front side for user-software interaction and Java Servlets on the server side for task execution. The compute-intensive components of the tool suite are implemented in C++ and invoked by the server via Java Native Interface (JNI).

Turbomachinery

NASA Technical Reports Server (NTRS)

Simoneau, Robert J.; Strazisar, Anthony J.; Sockol, Peter M.; Reid, Lonnie; Adamczyk, John J.

1987-01-01

The discipline research in turbomachinery, which is directed toward building the tools needed to understand such a complex flow phenomenon, is based on the fact that flow in turbomachinery is fundamentally unsteady or time dependent. Success in building a reliable inventory of analytic and experimental tools will depend on how the time and time-averages are treated, as well as on who the space and space-averages are treated. The raw tools at disposal (both experimentally and computational) are truly powerful and their numbers are growing at a staggering pace. As a result of this power, a case can be made that a situation exists where information is outstripping understanding. The challenge is to develop a set of computational and experimental tools which genuinely increase understanding of the fluid flow and heat transfer in a turbomachine. Viewgraphs outline a philosophy based on working on a stairstep hierarchy of mathematical and experimental complexity to build a system of tools, which enable one to aggressively design the turbomachinery of the next century. Examples of the types of computational and experimental tools under current development at Lewis, with progress to date, are examined. The examples include work in both the time-resolved and time-averaged domains. Finally, an attempt is made to identify the proper place for Lewis in this continuum of research.

A new approach to the rationale discovery of polymeric biomaterials

PubMed Central

Kohn, Joachim; Welsh, William J.; Knight, Doyle

2007-01-01

This paper attempts to illustrate both the need for new approaches to biomaterials discovery as well as the significant promise inherent in the use of combinatorial and computational design strategies. The key observation of this Leading Opinion Paper is that the biomaterials community has been slow to embrace advanced biomaterials discovery tools such as combinatorial methods, high throughput experimentation, and computational modeling in spite of the significant promise shown by these discovery tools in materials science, medicinal chemistry and the pharmaceutical industry. It seems that the complexity of living cells and their interactions with biomaterials has been a conceptual as well as a practical barrier to the use of advanced discovery tools in biomaterials science. However, with the continued increase in computer power, the goal of predicting the biological response of cells in contact with biomaterials surfaces is within reach. Once combinatorial synthesis, high throughput experimentation, and computational modeling are integrated into the biomaterials discovery process, a significant acceleration is possible in the pace of development of improved medical implants, tissue regeneration scaffolds, and gene/drug delivery systems. PMID:17644176

The Use of Physical and Virtual Manipulatives in an Undergraduate Mechanical Engineering (Dynamics) Course

ERIC Educational Resources Information Center

Pan, Edward A.

2013-01-01

Science, technology, engineering, and mathematics (STEM) education is a national focus. Engineering education, as part of STEM education, needs to adapt to meet the needs of the nation in a rapidly changing world. Using computer-based visualization tools and corresponding 3D printed physical objects may help nontraditional students succeed in…

Dynamic VM Provisioning for TORQUE in a Cloud Environment

NASA Astrophysics Data System (ADS)

Zhang, S.; Boland, L.; Coddington, P.; Sevior, M.

2014-06-01

Cloud computing, also known as an Infrastructure-as-a-Service (IaaS), is attracting more interest from the commercial and educational sectors as a way to provide cost-effective computational infrastructure. It is an ideal platform for researchers who must share common resources but need to be able to scale up to massive computational requirements for specific periods of time. This paper presents the tools and techniques developed to allow the open source TORQUE distributed resource manager and Maui cluster scheduler to dynamically integrate OpenStack cloud resources into existing high throughput computing clusters.

BIRCH: a user-oriented, locally-customizable, bioinformatics system.

PubMed

Fristensky, Brian

2007-02-09

Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

BIRCH: A user-oriented, locally-customizable, bioinformatics system

PubMed Central

Fristensky, Brian

2007-01-01

Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere. PMID:17291351

Extraction and Analysis of Display Data

NASA Technical Reports Server (NTRS)

Land, Chris; Moye, Kathryn

2008-01-01

The Display Audit Suite is an integrated package of software tools that partly automates the detection of Portable Computer System (PCS) Display errors. [PCS is a lap top computer used onboard the International Space Station (ISS).] The need for automation stems from the large quantity of PCS displays (6,000+, with 1,000,000+ lines of command and telemetry data). The Display Audit Suite includes data-extraction tools, automatic error detection tools, and database tools for generating analysis spread sheets. These spread sheets allow engineers to more easily identify many different kinds of possible errors. The Suite supports over 40 independent analyses, 16 NASA Tech Briefs, November 2008 and complements formal testing by being comprehensive (all displays can be checked) and by revealing errors that are difficult to detect via test. In addition, the Suite can be run early in the development cycle to find and correct errors in advance of testing.

Low-cost computer mouse for the elderly or disabled in Taiwan.

PubMed

Chen, C-C; Chen, W-L; Chen, B-N; Shih, Y-Y; Lai, J-S; Chen, Y-L

2014-01-01

A mouse is an important communication interface between a human and a computer, but it is still difficult to use for the elderly or disabled. To develop a low-cost computer mouse auxiliary tool. The principal structure of the low-cost mouse auxiliary tool is the IR (infrared ray) array module and the Wii icon sensor module, which combine with reflective tape and the SQL Server database. This has several benefits including cheap hardware cost, fluent control, prompt response, adaptive adjustment and portability. Also, it carries the game module with the function of training and evaluation; to the trainee, it is really helpful to upgrade the sensitivity of consciousness/sense and the centralization of attention. The intervention phase/maintenance phase, with regard to clicking accuracy and use of time, p value (p< 0.05) reach the level of significance. The development of the low cost adaptive computer mouse auxiliary tool was completed during the study and was also verified as having the characteristics of low cost, easy operation and the adaptability. To patients with physical disabilities, if they have independent control action parts of their limbs, the mouse auxiliary tool is suitable for them to use, i.e. the user only needs to paste the reflective tape by the independent control action parts of the body to operate the mouse auxiliary tool.

The Hico Image Processing System: A Web-Accessible Hyperspectral Remote Sensing Toolbox

NASA Astrophysics Data System (ADS)

Harris, A. T., III; Goodman, J.; Justice, B.

2014-12-01

As the quantity of Earth-observation data increases, the use-case for hosting analytical tools in geospatial data centers becomes increasingly attractive. To address this need, HySpeed Computing and Exelis VIS have developed the HICO Image Processing System, a prototype cloud computing system that provides online, on-demand, scalable remote sensing image processing capabilities. The system provides a mechanism for delivering sophisticated image processing analytics and data visualization tools into the hands of a global user community, who will only need a browser and internet connection to perform analysis. Functionality of the HICO Image Processing System is demonstrated using imagery from the Hyperspectral Imager for the Coastal Ocean (HICO), an imaging spectrometer located on the International Space Station (ISS) that is optimized for acquisition of aquatic targets. Example applications include a collection of coastal remote sensing algorithms that are directed at deriving critical information on water and habitat characteristics of our vulnerable coastal environment. The project leverages the ENVI Services Engine as the framework for all image processing tasks, and can readily accommodate the rapid integration of new algorithms, datasets and processing tools.

NREL Discovers Enzyme Domains that Dramatically Improve Performance | News

Science.gov Websites

seven years of thorough experimental work to develop the tools needed to ascertain that there are a . It was the melding of experimental biochemistry and computational science that brought this study to

Usability of Low-Cost Android Data Collection System for Community-Based Participatory Research.

PubMed

Salihu, Hamisu M; Salinas-Miranda, Abraham; Turner, DeAnne; King, Lindsey; Paothong, Arnut; Austin, Deborah; Berry, Estrellita Lo

2016-01-01

Android tablet computers can be valuable tools for data collection, but their usability has not been evaluated in community-based participatory research (CBPR). This article examines the usability of a low-cost bilingual touchscreen computerized survey system using Android tablets, piloted with a sample of 201 community residents in Tampa, Florida, from November 2013 to March 2014. Needs assessment questions were designed with the droidSURVEY software, and deployed using Android tablet computers. In addition, participants were asked questions about system usability. The mean system usability was 77.57 ± 17.66 (range, 0-100). The mean completion time for taking the 63 survey questions in the needs assessment was 23.11 ± 9.62 minutes. The survey completion rate was optimal (100%), with only 6.34% missingness per variable. We found no sociodemographic differences in usability scores. Our findings indicate that Android tablets could serve as useful tools in CBPR studies.

Centralized Authentication with Kerberos 5, Part I

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

Wachsmann, A

Account administration in a distributed Unix/Linux environment can become very complicated and messy if done by hand. Large sites use special tools to deal with this problem. I will describe how even very small installations like your three computer network at home can take advantage of the very same tools. The problem in a distributed environment is that password and shadow files need to be changed individually on each machine if an account change occurs. Account changes include: password change, addition/removal of accounts, name change of an account (UID/GID changes are a big problem in any case), additional or removedmore » login privileges to a (group of) computer(s), etc. In this article, I will show how Kerberos 5 solves the authentication problem in a distributed computing environment. A second article will describe a solution for the authorization problem.« less

Using the iPlant collaborative discovery environment.

PubMed

Oliver, Shannon L; Lenards, Andrew J; Barthelson, Roger A; Merchant, Nirav; McKay, Sheldon J

2013-06-01

The iPlant Collaborative is an academic consortium whose mission is to develop an informatics and social infrastructure to address the "grand challenges" in plant biology. Its cyberinfrastructure supports the computational needs of the research community and facilitates solving major challenges in plant science. The Discovery Environment provides a powerful and rich graphical interface to the iPlant Collaborative cyberinfrastructure by creating an accessible virtual workbench that enables all levels of expertise, ranging from students to traditional biology researchers and computational experts, to explore, analyze, and share their data. By providing access to iPlant's robust data-management system and high-performance computing resources, the Discovery Environment also creates a unified space in which researchers can access scalable tools. Researchers can use available Applications (Apps) to execute analyses on their data, as well as customize or integrate their own tools to better meet the specific needs of their research. These Apps can also be used in workflows that automate more complicated analyses. This module describes how to use the main features of the Discovery Environment, using bioinformatics workflows for high-throughput sequence data as examples. © 2013 by John Wiley & Sons, Inc.

Overview of the Aeroelastic Prediction Workshop

NASA Technical Reports Server (NTRS)

Heeg, Jennifer; Chwalowski, Pawel; Schuster, David M.; Dalenbring, Mats

2013-01-01

The AIAA Aeroelastic Prediction Workshop (AePW) was held in April, 2012, bringing together communities of aeroelasticians and computational fluid dynamicists. The objective in conducting this workshop on aeroelastic prediction was to assess state-of-the-art computational aeroelasticity methods as practical tools for the prediction of static and dynamic aeroelastic phenomena. No comprehensive aeroelastic benchmarking validation standard currently exists, greatly hindering validation and state-of-the-art assessment objectives. The workshop was a step towards assessing the state of the art in computational aeroelasticity. This was an opportunity to discuss and evaluate the effectiveness of existing computer codes and modeling techniques for unsteady flow, and to identify computational and experimental areas needing additional research and development. Three configurations served as the basis for the workshop, providing different levels of geometric and flow field complexity. All cases considered involved supercritical airfoils at transonic conditions. The flow fields contained oscillating shocks and in some cases, regions of separation. The computational tools principally employed Reynolds-Averaged Navier Stokes solutions. The successes and failures of the computations and the experiments are examined in this paper.

The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

PubMed

Harb, Omar S; Roos, David S

2015-01-01

Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

Human-Centered Design of Human-Computer-Human Dialogs in Aerospace Systems

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.

1998-01-01

A series of ongoing research programs at Georgia Tech established a need for a simulation support tool for aircraft computer-based aids. This led to the design and development of the Georgia Tech Electronic Flight Instrument Research Tool (GT-EFIRT). GT-EFIRT is a part-task flight simulator specifically designed to study aircraft display design and single pilot interaction. ne simulator, using commercially available graphics and Unix workstations, replicates to a high level of fidelity the Electronic Flight Instrument Systems (EFIS), Flight Management Computer (FMC) and Auto Flight Director System (AFDS) of the Boeing 757/767 aircraft. The simulator can be configured to present information using conventional looking B757n67 displays or next generation Primary Flight Displays (PFD) such as found on the Beech Starship and MD-11.

"Tennis elbow". A challenging call for computation and medicine

NASA Astrophysics Data System (ADS)

Sfetsioris, D.; Bontioti, E. N.

2014-10-01

An attempt to give an insight on the features composing this musculotendinous disorder. We address the issues of definition, pathophysiology and the mechanism underlying the onset and the occurrence of the disease, diagnosis and diagnostic tools as well as the methods of treatment. We focus mostly on conservative treatment protocols and we recognize the need for a more thorough investigation with the aid of computation.

What Can Technology Offer to Linguistically Diverse Classrooms? Using Multilingual Content in a Computer-Based Learning Environment for Primary Education

ERIC Educational Resources Information Center

Van Laere, Evelien; Rosiers, Kirsten; Van Avermaet, Piet; Slembrouck, Stef; van Braak, Johan

2017-01-01

Computer-based learning environments (CBLEs) have the potential to integrate the linguistic diversity present in classrooms as a resourceful tool in pupils' learning process. Particularly for pupils who speak a language at home other than the language which is used at school, more understanding is needed on how CBLEs offering multilingual content…

Combining qualitative and quantitative methods to analyze serious games outcomes: A pilot study for a new cognitive screening tool.

PubMed

Vallejo, Vanessa; Mitache, Andrei V; Tarnanas, Ioannis; Muri, Rene; Mosimann, Urs P; Nef, Tobias

2015-08-01

Computer games for a serious purpose - so called serious games can provide additional information for the screening and diagnosis of cognitive impairment. Moreover, they have the advantage of being an ecological tool by involving daily living tasks. However, there is a need for better comprehensive designs regarding the acceptance of this technology, as the target population is older adults that are not used to interact with novel technologies. Moreover given the complexity of the diagnosis and the need for precise assessment, an evaluation of the best approach to analyze the performance data is required. The present study examines the usability of a new screening tool and proposes several new outlines for data analysis.

Challenges Facing Design and Analysis Tools

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Broduer, Steve (Technical Monitor)

2001-01-01

The design and analysis of future aerospace systems will strongly rely on advanced engineering analysis tools used in combination with risk mitigation procedures. The implications of such a trend place increased demands on these tools to assess off-nominal conditions, residual strength, damage propagation, and extreme loading conditions in order to understand and quantify these effects as they affect mission success. Advances in computer hardware such as CPU processing speed, memory, secondary storage, and visualization provide significant resources for the engineer to exploit in engineering design. The challenges facing design and analysis tools fall into three primary areas. The first area involves mechanics needs such as constitutive modeling, contact and penetration simulation, crack growth prediction, damage initiation and progression prediction, transient dynamics and deployment simulations, and solution algorithms. The second area involves computational needs such as fast, robust solvers, adaptivity for model and solution strategies, control processes for concurrent, distributed computing for uncertainty assessments, and immersive technology. Traditional finite element codes still require fast direct solvers which when coupled to current CPU power enables new insight as a result of high-fidelity modeling. The third area involves decision making by the analyst. This area involves the integration and interrogation of vast amounts of information - some global in character while local details are critical and often drive the design. The proposed presentation will describe and illustrate these areas using composite structures, energy-absorbing structures, and inflatable space structures. While certain engineering approximations within the finite element model may be adequate for global response prediction, they generally are inadequate in a design setting or when local response prediction is critical. Pitfalls to be avoided and trends for emerging analysis tools will be described.

Tools for Atmospheric Radiative Transfer: Streamer and FluxNet. Revised

NASA Technical Reports Server (NTRS)

Key, Jeffrey R.; Schweiger, Axel J.

1998-01-01

Two tools for the solution of radiative transfer problems are presented. Streamer is a highly flexible medium spectral resolution radiative transfer model based on the plane-parallel theory of radiative transfer. Capable of computing either fluxes or radiances, it is suitable for studying radiative processes at the surface or within the atmosphere and for the development of remote-sensing algorithms. FluxNet is a fast neural network-based implementation of Streamer for computing surface fluxes. It allows for a sophisticated treatment of radiative processes in the analysis of large data sets and potential integration into geophysical models where computational efficiency is an issue. Documentation and tools for the development of alternative versions of Fluxnet are available. Collectively, Streamer and FluxNet solve a wide variety of problems related to radiative transfer: Streamer provides the detail and sophistication needed to perform basic research on most aspects of complex radiative processes while the efficiency and simplicity of FluxNet make it ideal for operational use.

APA Summit on Medical Student Education Task Force on Informatics and Technology: learning about computers and applying computer technology to education and practice.

PubMed

Hilty, Donald M; Hales, Deborah J; Briscoe, Greg; Benjamin, Sheldon; Boland, Robert J; Luo, John S; Chan, Carlyle H; Kennedy, Robert S; Karlinsky, Harry; Gordon, Daniel B; Yager, Joel; Yellowlees, Peter M

2006-01-01

This article provides a brief overview of important issues for educators regarding medical education and technology. The literature describes key concepts, prototypical technology tools, and model programs. A work group of psychiatric educators was convened three times by phone conference to discuss the literature. Findings were presented to and input was received from the 2005 Summit on Medical Student Education by APA and the American Directors of Medical Student Education in Psychiatry. Knowledge of, skills in, and attitudes toward medical informatics are important to life-long learning and modern medical practice. A needs assessment is a starting place, since student, faculty, institution, and societal factors bear consideration. Technology needs to "fit" into a curriculum in order to facilitate learning and teaching. Learning about computers and applying computer technology to education and clinical care are key steps in computer literacy for physicians.

The use of self-organising maps for anomalous behaviour detection in a digital investigation.

PubMed

Fei, B K L; Eloff, J H P; Olivier, M S; Venter, H S

2006-10-16

The dramatic increase in crime relating to the Internet and computers has caused a growing need for digital forensics. Digital forensic tools have been developed to assist investigators in conducting a proper investigation into digital crimes. In general, the bulk of the digital forensic tools available on the market permit investigators to analyse data that has been gathered from a computer system. However, current state-of-the-art digital forensic tools simply cannot handle large volumes of data in an efficient manner. With the advent of the Internet, many employees have been given access to new and more interesting possibilities via their desktop. Consequently, excessive Internet usage for non-job purposes and even blatant misuse of the Internet have become a problem in many organisations. Since storage media are steadily growing in size, the process of analysing multiple computer systems during a digital investigation can easily consume an enormous amount of time. Identifying a single suspicious computer from a set of candidates can therefore reduce human processing time and monetary costs involved in gathering evidence. The focus of this paper is to demonstrate how, in a digital investigation, digital forensic tools and the self-organising map (SOM)--an unsupervised neural network model--can aid investigators to determine anomalous behaviours (or activities) among employees (or computer systems) in a far more efficient manner. By analysing the different SOMs (one for each computer system), anomalous behaviours are identified and investigators are assisted to conduct the analysis more efficiently. The paper will demonstrate how the easy visualisation of the SOM enhances the ability of the investigators to interpret and explore the data generated by digital forensic tools so as to determine anomalous behaviours.

CASE tools and UML: state of the ART.

PubMed

Agarwal, S

2001-05-01

With increasing need for automated tools to assist complex systems development, software design methods are becoming popular. This article analyzes the state of art in computer-aided software engineering (CASE) tools and unified modeling language (UML), focusing on their evolution, merits, and industry usage. It identifies managerial issues for the tools' adoption and recommends an action plan to select and implement them. While CASE and UML offer inherent advantages like cheaper, shorter, and efficient development cycles, they suffer from poor user satisfaction. The critical success factors for their implementation include, among others, management and staff commitment, proper corporate infrastructure, and user training.

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

PubMed Central

2011-01-01

Background Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. Results We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Conclusions Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web-based tool for several different input formats, and it makes analysis of complex models accessible to a larger community, as it is platform independent as a web-service and does not require understanding of the underlying mathematics. PMID:21774817

Intelligent Information Retrieval: Diagnosing Information Need. Part I. The Theoretical Framework for Developing an Intelligent IR Tool.

ERIC Educational Resources Information Center

Cole, Charles

1998-01-01

Suggests that the principles underlying the procedure used by doctors to diagnose a patient's disease are useful in the design of intelligent information-retrieval systems because the task of the doctor is conceptually similar to the computer or human intermediary's task in information retrieval: to draw out the user's query/information need.…

Infrastructures for Distributed Computing: the case of BESIII

NASA Astrophysics Data System (ADS)

Pellegrino, J.

2018-05-01

The BESIII is an electron-positron collision experiment hosted at BEPCII in Beijing and aimed to investigate Tau-Charm physics. Now BESIII has been running for several years and gathered more than 1PB raw data. In order to analyze these data and perform massive Monte Carlo simulations, a large amount of computing and storage resources is needed. The distributed computing system is based up on DIRAC and it is in production since 2012. It integrates computing and storage resources from different institutes and a variety of resource types such as cluster, grid, cloud or volunteer computing. About 15 sites from BESIII Collaboration from all over the world joined this distributed computing infrastructure, giving a significant contribution to the IHEP computing facility. Nowadays cloud computing is playing a key role in the HEP computing field, due to its scalability and elasticity. Cloud infrastructures take advantages of several tools, such as VMDirac, to manage virtual machines through cloud managers according to the job requirements. With the virtually unlimited resources from commercial clouds, the computing capacity could scale accordingly in order to deal with any burst demands. General computing models have been discussed in the talk and are addressed herewith, with particular focus on the BESIII infrastructure. Moreover new computing tools and upcoming infrastructures will be addressed.

NDE and SHM Simulation for CFRP Composites

NASA Technical Reports Server (NTRS)

Leckey, Cara A. C.; Parker, F. Raymond

2014-01-01

Ultrasound-based nondestructive evaluation (NDE) is a common technique for damage detection in composite materials. There is a need for advanced NDE that goes beyond damage detection to damage quantification and characterization in order to enable data driven prognostics. The damage types that exist in carbon fiber-reinforced polymer (CFRP) composites include microcracking and delaminations, and can be initiated and grown via impact forces (due to ground vehicles, tool drops, bird strikes, etc), fatigue, and extreme environmental changes. X-ray microfocus computed tomography data, among other methods, have shown that these damage types often result in voids/discontinuities of a complex volumetric shape. The specific damage geometry and location within ply layers affect damage growth. Realistic threedimensional NDE and structural health monitoring (SHM) simulations can aid in the development and optimization of damage quantification and characterization techniques. This paper is an overview of ongoing work towards realistic NDE and SHM simulation tools for composites, and also discusses NASA's need for such simulation tools in aeronautics and spaceflight. The paper describes the development and implementation of a custom ultrasound simulation tool that is used to model ultrasonic wave interaction with realistic 3-dimensional damage in CFRP composites. The custom code uses elastodynamic finite integration technique and is parallelized to run efficiently on computing cluster or multicore machines.

A spline-based approach for computing spatial impulse responses.

PubMed

Ellis, Michael A; Guenther, Drake; Walker, William F

2007-05-01

Computer simulations are an essential tool for the design of phased-array ultrasonic imaging systems. FIELD II, which determines the two-way temporal response of a transducer at a point in space, is the current de facto standard for ultrasound simulation tools. However, the need often arises to obtain two-way spatial responses at a single point in time, a set of dimensions for which FIELD II is not well optimized. This paper describes an analytical approach for computing the two-way, far-field, spatial impulse response from rectangular transducer elements under arbitrary excitation. The described approach determines the response as the sum of polynomial functions, making computational implementation quite straightforward. The proposed algorithm, named DELFI, was implemented as a C routine under Matlab and results were compared to those obtained under similar conditions from the well-established FIELD II program. Under the specific conditions tested here, the proposed algorithm was approximately 142 times faster than FIELD II for computing spatial sensitivity functions with similar amounts of error. For temporal sensitivity functions with similar amounts of error, the proposed algorithm was about 1.7 times slower than FIELD II using rectangular elements and 19.2 times faster than FIELD II using triangular elements. DELFI is shown to be an attractive complement to FIELD II, especially when spatial responses are needed at a specific point in time.

A CFD/CSD Interaction Methodology for Aircraft Wings

NASA Technical Reports Server (NTRS)

Bhardwaj, Manoj K.

1997-01-01

With advanced subsonic transports and military aircraft operating in the transonic regime, it is becoming important to determine the effects of the coupling between aerodynamic loads and elastic forces. Since aeroelastic effects can contribute significantly to the design of these aircraft, there is a strong need in the aerospace industry to predict these aero-structure interactions computationally. To perform static aeroelastic analysis in the transonic regime, high fidelity computational fluid dynamics (CFD) analysis tools must be used in conjunction with high fidelity computational structural fluid dynamics (CSD) analysis tools due to the nonlinear behavior of the aerodynamics in the transonic regime. There is also a need to be able to use a wide variety of CFD and CSD tools to predict these aeroelastic effects in the transonic regime. Because source codes are not always available, it is necessary to couple the CFD and CSD codes without alteration of the source codes. In this study, an aeroelastic coupling procedure is developed which will perform static aeroelastic analysis using any CFD and CSD code with little code integration. The aeroelastic coupling procedure is demonstrated on an F/A-18 Stabilator using NASTD (an in-house McDonnell Douglas CFD code) and NASTRAN. In addition, the Aeroelastic Research Wing (ARW-2) is used for demonstration of the aeroelastic coupling procedure by using ENSAERO (NASA Ames Research Center CFD code) and a finite element wing-box code (developed as part of this research).

The expanded role of computers in Space Station Freedom real-time operations

NASA Technical Reports Server (NTRS)

Crawford, R. Paul; Cannon, Kathleen V.

1990-01-01

The challenges that NASA and its international partners face in their real-time operation of the Space Station Freedom necessitate an increased role on the part of computers. In building the operational concepts concerning the role of the computer, the Space Station program is using lessons learned experience from past programs, knowledge of the needs of future space programs, and technical advances in the computer industry. The computer is expected to contribute most significantly in real-time operations by forming a versatile operating architecture, a responsive operations tool set, and an environment that promotes effective and efficient utilization of Space Station Freedom resources.

Graphic Design Is Not a Medium.

ERIC Educational Resources Information Center

Gruber, John Edward, Jr.

2001-01-01

Discusses graphic design and reviews its development from analog processes to a digital tool with the use of computers. Topics include graphical user interfaces; the need for visual communication concepts; transmedia as opposed to repurposing; and graphic design instruction in higher education. (LRW)

Reproducible Bioinformatics Research for Biologists

USDA-ARS?s Scientific Manuscript database

This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

Technology for communicational development and learning in psychomotor disability

NASA Astrophysics Data System (ADS)

Trento, I.; Santucci, M.; Tula, S.; González, E.

2007-11-01

The applied investigation and experimental development project described in this paper has been carried out by Grupo Ingeniería Clínica of the Universidad Tecnológica Nacional together with two Special Education Schools dependent on the Ministry of Education of Córdoba Province. Its aim is the development of computer access assistive tools for students with mobility limitations, and with or without intellectual problems that need adaptations to access to a computer in order to learn, communicate, work, etc. On the other hand, it demonstrates the benefits that the use of a computer gives to these students. The evaluation of their performance was made trough Dr. Marianne Frostig's Developmental Test of Visual Perception and reading and writing graphic tests, comparing the results of the tests made on paper with those made on computer. Thus, an interdisciplinary team was formed by Engineering, Psychology and Special Education professionals, and 40 students were evaluated. The design of the mouse and keyboard had some adaptations. At present, the rating test stage is being achieved, and the preliminary results allow us to anticipate that pupils with psychomotor disabilities may manifest their perceptual ripeness and reach education in a more efficient way through the use of informatics tools according to their needs and possibilities.

Emergency Management Computer-Aided Trainer (EMCAT)

NASA Technical Reports Server (NTRS)

Rodriguez, R. C.; Johnson, R. P.

1986-01-01

The Emergency Management Computer-Aided Trainer (EMCAT) developed by Essex Corporation or NASA and the Federal Emergency Management Administration's (FEMA) National Fire Academy (NFA) is described. It is a computer based training system for fire fighting personnel. A prototype EMCAT system was developed by NASA first using video tape images and then video disk images when the technology became available. The EMCAT system is meant to fill the training needs of the fire fighting community with affordable state-of-the-art technologies. An automated real time simulation of the fire situation was needed to replace the outdated manual training methods currently being used. In order to be successful, this simulator had to provide realism, be user friendly, be affordable, and support multiple scenarios. The EMCAT system meets these requirements and therefore represents an innovative training tool, not only for the fire fighting community, but also for the needs of other disciplines.

National Fusion Collaboratory: Grid Computing for Simulations and Experiments

NASA Astrophysics Data System (ADS)

Greenwald, Martin

2004-05-01

The National Fusion Collaboratory Project is creating a computational grid designed to advance scientific understanding and innovation in magnetic fusion research by facilitating collaborations, enabling more effective integration of experiments, theory and modeling and allowing more efficient use of experimental facilities. The philosophy of FusionGrid is that data, codes, analysis routines, visualization tools, and communication tools should be thought of as network available services, easily used by the fusion scientist. In such an environment, access to services is stressed rather than portability. By building on a foundation of established computer science toolkits, deployment time can be minimized. These services all share the same basic infrastructure that allows for secure authentication and resource authorization which allows stakeholders to control their own resources such as computers, data and experiments. Code developers can control intellectual property, and fair use of shared resources can be demonstrated and controlled. A key goal is to shield scientific users from the implementation details such that transparency and ease-of-use are maximized. The first FusionGrid service deployed was the TRANSP code, a widely used tool for transport analysis. Tools for run preparation, submission, monitoring and management have been developed and shared among a wide user base. This approach saves user sites from the laborious effort of maintaining such a large and complex code while at the same time reducing the burden on the development team by avoiding the need to support a large number of heterogeneous installations. Shared visualization and A/V tools are being developed and deployed to enhance long-distance collaborations. These include desktop versions of the Access Grid, a highly capable multi-point remote conferencing tool and capabilities for sharing displays and analysis tools over local and wide-area networks.

In Internet-Based Visualization System Study about Breakthrough Applet Security Restrictions

NASA Astrophysics Data System (ADS)

Chen, Jie; Huang, Yan

In the process of realization Internet-based visualization system of the protein molecules, system needs to allow users to use the system to observe the molecular structure of the local computer, that is, customers can generate the three-dimensional graphics from PDB file on the client computer. This requires Applet access to local file, related to the Applet security restrictions question. In this paper include two realization methods: 1.Use such as signature tools, key management tools and Policy Editor tools provided by the JDK to digital signature and authentication for Java Applet, breakthrough certain security restrictions in the browser. 2. Through the use of Servlet agent implement indirect access data methods, breakthrough the traditional Java Virtual Machine sandbox model restriction of Applet ability. The two ways can break through the Applet's security restrictions, but each has its own strengths.

Covariance Analysis Tool (G-CAT) for Computing Ascent, Descent, and Landing Errors

NASA Technical Reports Server (NTRS)

Boussalis, Dhemetrios; Bayard, David S.

2013-01-01

G-CAT is a covariance analysis tool that enables fast and accurate computation of error ellipses for descent, landing, ascent, and rendezvous scenarios, and quantifies knowledge error contributions needed for error budgeting purposes. Because GCAT supports hardware/system trade studies in spacecraft and mission design, it is useful in both early and late mission/ proposal phases where Monte Carlo simulation capability is not mature, Monte Carlo simulation takes too long to run, and/or there is a need to perform multiple parametric system design trades that would require an unwieldy number of Monte Carlo runs. G-CAT is formulated as a variable-order square-root linearized Kalman filter (LKF), typically using over 120 filter states. An important property of G-CAT is that it is based on a 6-DOF (degrees of freedom) formulation that completely captures the combined effects of both attitude and translation errors on the propagated trajectories. This ensures its accuracy for guidance, navigation, and control (GN&C) analysis. G-CAT provides the desired fast turnaround analysis needed for error budgeting in support of mission concept formulations, design trade studies, and proposal development efforts. The main usefulness of a covariance analysis tool such as G-CAT is its ability to calculate the performance envelope directly from a single run. This is in sharp contrast to running thousands of simulations to obtain similar information using Monte Carlo methods. It does this by propagating the "statistics" of the overall design, rather than simulating individual trajectories. G-CAT supports applications to lunar, planetary, and small body missions. It characterizes onboard knowledge propagation errors associated with inertial measurement unit (IMU) errors (gyro and accelerometer), gravity errors/dispersions (spherical harmonics, masscons), and radar errors (multiple altimeter beams, multiple Doppler velocimeter beams). G-CAT is a standalone MATLAB- based tool intended to run on any engineer's desktop computer.

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.

A new DoD initiative: the Computational Research and Engineering Acquisition Tools and Environments (CREATE) program

NASA Astrophysics Data System (ADS)

Arevalo, S.; Atwood, C.; Bell, P.; Blacker, T. D.; Dey, S.; Fisher, D.; Fisher, D. A.; Genalis, P.; Gorski, J.; Harris, A.; Hill, K.; Hurwitz, M.; Kendall, R. P.; Meakin, R. L.; Morton, S.; Moyer, E. T.; Post, D. E.; Strawn, R.; Veldhuizen, D. v.; Votta, L. G.; Wynn, S.; Zelinski, G.

2008-07-01

In FY2008, the U.S. Department of Defense (DoD) initiated the Computational Research and Engineering Acquisition Tools and Environments (CREATE) program, a 360M program with a two-year planning phase and a ten-year execution phase. CREATE will develop and deploy three computational engineering tool sets for DoD acquisition programs to use to design aircraft, ships and radio-frequency antennas. The planning and execution of CREATE are based on the 'lessons learned' from case studies of large-scale computational science and engineering projects. The case studies stress the importance of a stable, close-knit development team; a focus on customer needs and requirements; verification and validation; flexible and agile planning, management, and development processes; risk management; realistic schedules and resource levels; balanced short- and long-term goals and deliverables; and stable, long-term support by the program sponsor. Since it began in FY2008, the CREATE program has built a team and project structure, developed requirements and begun validating them, identified candidate products, established initial connections with the acquisition programs, begun detailed project planning and development, and generated the initial collaboration infrastructure necessary for success by its multi-institutional, multidisciplinary teams.

Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom

PubMed Central

Yu, Zhicong; Noo, Frédéric; Dennerlein, Frank; Wunderlich, Adam; Lauritsch, Günter; Hornegger, Joachim

2012-01-01

Mathematical phantoms are essential for the development and early-stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp-Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly-higher complexity: software that allows computer simulations with the Shepp-Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files. PMID:22713335

Simulation tools for two-dimensional experiments in x-ray computed tomography using the FORBILD head phantom.

PubMed

Yu, Zhicong; Noo, Frédéric; Dennerlein, Frank; Wunderlich, Adam; Lauritsch, Günter; Hornegger, Joachim

2012-07-07

Mathematical phantoms are essential for the development and early stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp-Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly higher complexity: software that allows computer simulations with the Shepp-Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files.

Battery Pack Thermal Design

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

Pesaran, Ahmad

This presentation describes the thermal design of battery packs at the National Renewable Energy Laboratory. A battery thermal management system essential for xEVs for both normal operation during daily driving (achieving life and performance) and off-normal operation during abuse conditions (achieving safety). The battery thermal management system needs to be optimized with the right tools for the lowest cost. Experimental tools such as NREL's isothermal battery calorimeter, thermal imaging, and heat transfer setups are needed. Thermal models and computer-aided engineering tools are useful for robust designs. During abuse conditions, designs should prevent cell-to-cell propagation in a module/pack (i.e., keep themore » fire small and manageable). NREL's battery ISC device can be used for evaluating the robustness of a module/pack to cell-to-cell propagation.« less

GAPIT: genome association and prediction integrated tool.

PubMed

Lipka, Alexander E; Tian, Feng; Wang, Qishan; Peiffer, Jason; Li, Meng; Bradbury, Peter J; Gore, Michael A; Buckler, Edward S; Zhang, Zhiwu

2012-09-15

Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power, provide high prediction accuracy and run in a computationally efficient manner. We developed an R package called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10 000 individuals and 1 million single-nucleotide polymorphisms with minimal computational time, while providing user-friendly access and concise tables and graphs to interpret results. http://www.maizegenetics.net/GAPIT. zhiwu.zhang@cornell.edu Supplementary data are available at Bioinformatics online.

Automated support tool for variable rate irrigation prescriptions

USDA-ARS?s Scientific Manuscript database

Variable rate irrigation (VRI) enables center pivot management to better meet non-uniform water and fertility needs. This is accomplished through correctly matching system water application with spatial and temporal variability within the field. A computer program was modified to accommodate GIS dat...

SSOAP - A USEPA Toolbox for Sanitary Sewer Overflow Analysis and Control Planning - Presentation

EPA Science Inventory

The United States Environmental Protection Agency (USEPA) has identified a need to use proven methodologies to develop computer tools that help communities properly characterize rainfall-derived infiltration and inflow (RDII) into sanitary sewer systems and develop sanitary sewer...

Woodworking Technology.

ERIC Educational Resources Information Center

Kirk, Albert S.; And Others

1991-01-01

Three articles discuss the importance of wood processing to manufacturing and construction industries and the need for progressive change in the curriculum; the evolution of wood-based synthetic panel materials; and the technological advances in the computer control of machine tools and their incorporation into wood technology curricula. (JOW)

New Trends in Computer Assisted Language Learning and Teaching.

ERIC Educational Resources Information Center

Perez-Paredes, Pascual, Ed.; Cantos-Gomez, Pascual, Ed.

2002-01-01

Articles in this special issue include the following: "ICT and Modern Foreign Languages: Learning Opportunities and Training Needs" (Graham Davies); "Authoring, Pedagogy and the Web: Expectations Versus Reality" (Paul Bangs); "Web-based Instructional Environments: Tools and Techniques for Effective Second Language…

Progressive Damage and Failure Analysis of Composite Laminates

NASA Astrophysics Data System (ADS)

Joseph, Ashith P. K.

Composite materials are widely used in various industries for making structural parts due to higher strength to weight ratio, better fatigue life, corrosion resistance and material property tailorability. To fully exploit the capability of composites, it is required to know the load carrying capacity of the parts made of them. Unlike metals, composites are orthotropic in nature and fails in a complex manner under various loading conditions which makes it a hard problem to analyze. Lack of reliable and efficient failure analysis tools for composites have led industries to rely more on coupon and component level testing to estimate the design space. Due to the complex failure mechanisms, composite materials require a very large number of coupon level tests to fully characterize the behavior. This makes the entire testing process very time consuming and costly. The alternative is to use virtual testing tools which can predict the complex failure mechanisms accurately. This reduces the cost only to it's associated computational expenses making significant savings. Some of the most desired features in a virtual testing tool are - (1) Accurate representation of failure mechanism: Failure progression predicted by the virtual tool must be same as those observed in experiments. A tool has to be assessed based on the mechanisms it can capture. (2) Computational efficiency: The greatest advantages of a virtual tools are the savings in time and money and hence computational efficiency is one of the most needed features. (3) Applicability to a wide range of problems: Structural parts are subjected to a variety of loading conditions including static, dynamic and fatigue conditions. A good virtual testing tool should be able to make good predictions for all these different loading conditions. The aim of this PhD thesis is to develop a computational tool which can model the progressive failure of composite laminates under different quasi-static loading conditions. The analysis tool is validated by comparing the simulations against experiments for a selected number of quasi-static loading cases.

Flood damage assessment using computer-assisted analysis of color infrared photography

USGS Publications Warehouse

Anderson, William H.

1978-01-01

Use of digitized aerial photographs for flood damage assessment in agriculture is new and largely untested. However, under flooding circumstances similar to the 1975 Red River Valley flood, computer-assisted techniques can be extremely useful, especially if detailed crop damage estimates are needed within a relatively short period of time.Airphoto interpretation techniques, manual or computer-assisted, are not intended to replace conventional ground survey and sampling procedures. But their use should be considered a valuable addition to the tools currently available for assessing agricultural flood damage.

DYI digital holography

NASA Astrophysics Data System (ADS)

Zacharovas, Stanislovas; Nikolskij, Andrej; Kuchin, Jevgenij

2011-02-01

We have created a programming tool which uses image data provided by webcam connected to personal computer and gives user an ability to see the future digital hologram preview on his computer screen, before sending video data to holographic printing companies. In order to print digital hologram, one needs to have a sequence of images of the same scene taken from different angles and nowadays web cameras - stand-alone or incorporated into mobile computer, can be an acceptable source of such image sequences. In this article we are describing this DIY holographic imaging process in details.

Preliminary ISIS users manual

NASA Technical Reports Server (NTRS)

Grantham, C.

1979-01-01

The Interactive Software Invocation (ISIS), an interactive data management system, was developed to act as a buffer between the user and host computer system. The user is provided by ISIS with a powerful system for developing software or systems in the interactive environment. The user is protected from the idiosyncracies of the host computer system by providing such a complete range of capabilities that the user should have no need for direct access to the host computer. These capabilities are divided into four areas: desk top calculator, data editor, file manager, and tool invoker.

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

PubMed Central

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

Reads2Type: a web application for rapid microbial taxonomy identification.

PubMed

Saputra, Dhany; Rasmussen, Simon; Larsen, Mette V; Haddad, Nizar; Sperotto, Maria Maddalena; Aarestrup, Frank M; Lund, Ole; Sicheritz-Pontén, Thomas

2015-11-25

Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data. Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale. In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html.

ExGUtils: A Python Package for Statistical Analysis With the ex-Gaussian Probability Density.

PubMed

Moret-Tatay, Carmen; Gamermann, Daniel; Navarro-Pardo, Esperanza; Fernández de Córdoba Castellá, Pedro

2018-01-01

The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are often modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data. The complexity of this distribution makes the use of computational tools an essential element. Therefore, there is a strong need for efficient and versatile computational tools for the research in this area. In this manuscript we discuss some mathematical details of the ex-Gaussian distribution and apply the ExGUtils package, a set of functions and numerical tools, programmed for python, developed for numerical analysis of data involving the ex-Gaussian probability density. In order to validate the package, we present an extensive analysis of fits obtained with it, discuss advantages and differences between the least squares and maximum likelihood methods and quantitatively evaluate the goodness of the obtained fits (which is usually an overlooked point in most literature in the area). The analysis done allows one to identify outliers in the empirical datasets and criteriously determine if there is a need for data trimming and at which points it should be done.

ExGUtils: A Python Package for Statistical Analysis With the ex-Gaussian Probability Density

PubMed Central

Moret-Tatay, Carmen; Gamermann, Daniel; Navarro-Pardo, Esperanza; Fernández de Córdoba Castellá, Pedro

2018-01-01

The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are often modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data. The complexity of this distribution makes the use of computational tools an essential element. Therefore, there is a strong need for efficient and versatile computational tools for the research in this area. In this manuscript we discuss some mathematical details of the ex-Gaussian distribution and apply the ExGUtils package, a set of functions and numerical tools, programmed for python, developed for numerical analysis of data involving the ex-Gaussian probability density. In order to validate the package, we present an extensive analysis of fits obtained with it, discuss advantages and differences between the least squares and maximum likelihood methods and quantitatively evaluate the goodness of the obtained fits (which is usually an overlooked point in most literature in the area). The analysis done allows one to identify outliers in the empirical datasets and criteriously determine if there is a need for data trimming and at which points it should be done. PMID:29765345

A remote sensing computer-assisted learning tool developed using the unified modeling language

NASA Astrophysics Data System (ADS)

Friedrich, J.; Karslioglu, M. O.

The goal of this work has been to create an easy-to-use and simple-to-make learning tool for remote sensing at an introductory level. Many students struggle to comprehend what seems to be a very basic knowledge of digital images, image processing and image arithmetic, for example. Because professional programs are generally too complex and overwhelming for beginners and often not tailored to the specific needs of a course regarding functionality, a computer-assisted learning (CAL) program was developed based on the unified modeling language (UML), the present standard for object-oriented (OO) system development. A major advantage of this approach is an easier transition from modeling to coding of such an application, if modern UML tools are being used. After introducing the constructed UML model, its implementation is briefly described followed by a series of learning exercises. They illustrate how the resulting CAL tool supports students taking an introductory course in remote sensing at the author's institution.

The IBM PC at NASA Ames

NASA Technical Reports Server (NTRS)

Peredo, James P.

1988-01-01

Like many large companies, Ames relies very much on its computing power to get work done. And, like many other large companies, finding the IBM PC a reliable tool, Ames uses it for many of the same types of functions as other companies. Presentation and clarification needs demand much of graphics packages. Programming and text editing needs require simpler, more-powerful packages. The storage space needed by NASA's scientists and users for the monumental amounts of data that Ames needs to keep demand the best database packages that are large and easy to use. Availability to the Micom Switching Network combines the powers of the IBM PC with the capabilities of other computers and mainframes and allows users to communicate electronically. These four primary capabilities of the PC are vital to the needs of NASA's users and help to continue and support the vast amounts of work done by the NASA employees.

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

DOE PAGES

Yim, Won Cheol; Cushman, John C.

2017-07-22

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

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

Yim, Won Cheol; Cushman, John C.

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

Advanced engineering environment collaboration project.

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

Lamph, Jane Ann; Pomplun, Alan R.; Kiba, Grant W.

2008-12-01

The Advanced Engineering Environment (AEE) is a model for an engineering design and communications system that will enhance project collaboration throughout the nuclear weapons complex (NWC). Sandia National Laboratories and Parametric Technology Corporation (PTC) worked together on a prototype project to evaluate the suitability of a portion of PTC's Windchill 9.0 suite of data management, design and collaboration tools as the basis for an AEE. The AEE project team implemented Windchill 9.0 development servers in both classified and unclassified domains and used them to test and evaluate the Windchill tool suite relative to the needs of the NWC using weaponsmore » project use cases. A primary deliverable was the development of a new real time collaborative desktop design and engineering process using PDMLink (data management tool), Pro/Engineer (mechanical computer aided design tool) and ProductView Lite (visualization tool). Additional project activities included evaluations of PTC's electrical computer aided design, visualization, and engineering calculations applications. This report documents the AEE project work to share information and lessons learned with other NWC sites. It also provides PTC with recommendations for improving their products for NWC applications.« less

A semi-automatic annotation tool for cooking video

NASA Astrophysics Data System (ADS)

Bianco, Simone; Ciocca, Gianluigi; Napoletano, Paolo; Schettini, Raimondo; Margherita, Roberto; Marini, Gianluca; Gianforme, Giorgio; Pantaleo, Giuseppe

2013-03-01

In order to create a cooking assistant application to guide the users in the preparation of the dishes relevant to their profile diets and food preferences, it is necessary to accurately annotate the video recipes, identifying and tracking the foods of the cook. These videos present particular annotation challenges such as frequent occlusions, food appearance changes, etc. Manually annotate the videos is a time-consuming, tedious and error-prone task. Fully automatic tools that integrate computer vision algorithms to extract and identify the elements of interest are not error free, and false positive and false negative detections need to be corrected in a post-processing stage. We present an interactive, semi-automatic tool for the annotation of cooking videos that integrates computer vision techniques under the supervision of the user. The annotation accuracy is increased with respect to completely automatic tools and the human effort is reduced with respect to completely manual ones. The performance and usability of the proposed tool are evaluated on the basis of the time and effort required to annotate the same video sequences.

A Data-Driven Framework for Incorporating New Tools for ...

EPA Pesticide Factsheets

This talk was given during the “Exposure-Based Toxicity Testing” session at the annual meeting of the International Society for Exposure Science. It provided an update on the state of the science and tools that may be employed in risk-based prioritization efforts. It outlined knowledge gained from the data provided using these high-throughput tools to assess chemical bioactivity and to predict chemical exposures and also identified future needs. It provided an opportunity to showcase ongoing research efforts within the National Exposure Research Laboratory and the National Center for Computational Toxicology within the Office of Research and Development to an international audience. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates data, decision-support tools, and models to be applied to media-specific or receptor-specific problem areas. CED uses modeling-based approaches to characterize exposures, evaluate fate and transport, and support environmental diagnostics/forensics with input from multiple data sources. It also develops media- and receptor-specific models, process models, and decision support tools for use both within and outside of EPA.

The hierarchical expert tuning of PID controllers using tools of soft computing.

PubMed

Karray, F; Gueaieb, W; Al-Sharhan, S

2002-01-01

We present soft computing-based results pertaining to the hierarchical tuning process of PID controllers located within the control loop of a class of nonlinear systems. The results are compared with PID controllers implemented either in a stand alone scheme or as a part of conventional gain scheduling structure. This work is motivated by the increasing need in the industry to design highly reliable and efficient controllers for dealing with regulation and tracking capabilities of complex processes characterized by nonlinearities and possibly time varying parameters. The soft computing-based controllers proposed are hybrid in nature in that they integrate within a well-defined hierarchical structure the benefits of hard algorithmic controllers with those having supervisory capabilities. The controllers proposed also have the distinct features of learning and auto-tuning without the need for tedious and computationally extensive online systems identification schemes.

Navy Enhanced Sierra Mechanics (NESM): Toolbox for predicting Navy shock and damage

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

Moyer, Thomas; Stergiou, Jonathan; Reese, Garth

Here, the US Navy is developing a new suite of computational mechanics tools (Navy Enhanced Sierra Mechanics) for the prediction of ship response, damage, and shock environments transmitted to vital systems during threat weapon encounters. NESM includes fully coupled Euler-Lagrange solvers tailored to ship shock/damage predictions. NESM is optimized to support high-performance computing architectures, providing the physics-based ship response/threat weapon damage predictions needed to support the design and assessment of highly survivable ships. NESM is being employed to support current Navy ship design and acquisition programs while being further developed for future Navy fleet needs.

Shipping Science Worldwide with Open Source Containers

NASA Astrophysics Data System (ADS)

Molineaux, J. P.; McLaughlin, B. D.; Pilone, D.; Plofchan, P. G.; Murphy, K. J.

2014-12-01

Scientific applications often present difficult web-hosting needs. Their compute- and data-intensive nature, as well as an increasing need for high-availability and distribution, combine to create a challenging set of hosting requirements. In the past year, advancements in container-based virtualization and related tooling have offered new lightweight and flexible ways to accommodate diverse applications with all the isolation and portability benefits of traditional virtualization. This session will introduce and demonstrate an open-source, single-interface, Platform-as-a-Serivce (PaaS) that empowers application developers to seamlessly leverage geographically distributed, public and private compute resources to achieve highly-available, performant hosting for scientific applications.

Navy Enhanced Sierra Mechanics (NESM): Toolbox for predicting Navy shock and damage

DOE PAGES

Moyer, Thomas; Stergiou, Jonathan; Reese, Garth; ...

2016-05-25

Here, the US Navy is developing a new suite of computational mechanics tools (Navy Enhanced Sierra Mechanics) for the prediction of ship response, damage, and shock environments transmitted to vital systems during threat weapon encounters. NESM includes fully coupled Euler-Lagrange solvers tailored to ship shock/damage predictions. NESM is optimized to support high-performance computing architectures, providing the physics-based ship response/threat weapon damage predictions needed to support the design and assessment of highly survivable ships. NESM is being employed to support current Navy ship design and acquisition programs while being further developed for future Navy fleet needs.

A computational approach to climate science education with CLIMLAB

NASA Astrophysics Data System (ADS)

Rose, B. E. J.

2017-12-01

CLIMLAB is a Python-based software toolkit for interactive, process-oriented climate modeling for use in education and research. It is motivated by the need for simpler tools and more reproducible workflows with which to "fill in the gaps" between blackboard-level theory and the results of comprehensive climate models. With CLIMLAB you can interactively mix and match physical model components, or combine simpler process models together into a more comprehensive model. I use CLIMLAB in the classroom to put models in the hands of students (undergraduate and graduate), and emphasize a hierarchical, process-oriented approach to understanding the key emergent properties of the climate system. CLIMLAB is equally a tool for climate research, where the same needs exist for more robust, process-based understanding and reproducible computational results. I will give an overview of CLIMLAB and an update on recent developments, including: a full-featured, well-documented, interactive implementation of a widely-used radiation model (RRTM) packaging with conda-forge for compiler-free (and hassle-free!) installation on Mac, Windows and Linux interfacing with xarray for i/o and graphics with gridded model data a rich and growing collection of examples and self-computing lecture notes in Jupyter notebook format

Tools4miRs – one place to gather all the tools for miRNA analysis

PubMed Central

Lukasik, Anna; Wójcikowski, Maciej; Zielenkiewicz, Piotr

2016-01-01

Summary: MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data. Availability and Implementation: Tools4miRs is implemented in Python using Django and is freely available at tools4mirs.org. Contact: piotr@ibb.waw.pl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153626

Tools4miRs - one place to gather all the tools for miRNA analysis.

PubMed

Lukasik, Anna; Wójcikowski, Maciej; Zielenkiewicz, Piotr

2016-09-01

MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data. Tools4miRs is implemented in Python using Django and is freely available at tools4mirs.org. piotr@ibb.waw.pl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

MacDoctor: The Macintosh diagnoser

NASA Technical Reports Server (NTRS)

Lavery, David B.; Brooks, William D.

1990-01-01

When the Macintosh computer was first released, the primary user was a computer hobbyist who typically had a significant technical background and was highly motivated to understand the internal structure and operational intricacies of the computer. In recent years the Macintosh computer has become a widely-accepted general purpose computer which is being used by an ever-increasing non-technical audience. This has lead to a large base of users which has neither the interest nor the background to understand what is happening 'behind the scenes' when the Macintosh is put to use - or what should be happening when something goes wrong. Additionally, the Macintosh itself has evolved from a simple closed design to a complete family of processor platforms and peripherals with a tremendous number of possible configurations. With the increasing popularity of the Macintosh series, software and hardware developers are producing a product for every user's need. As the complexity of configuration possibilities grows, the need for experienced or even expert knowledge is required to diagnose problems. This presents a problem to uneducated or casual users. This problem indicates a new Macintosh consumer need; that is, a diagnostic tool able to determine the problem for the user. As the volume of Macintosh products has increased, this need has also increased.

Hospital influenza pandemic stockpiling needs: A computer simulation.

PubMed

Abramovich, Mark N; Hershey, John C; Callies, Byron; Adalja, Amesh A; Tosh, Pritish K; Toner, Eric S

2017-03-01

A severe influenza pandemic could overwhelm hospitals but planning guidance that accounts for the dynamic interrelationships between planning elements is lacking. We developed a methodology to calculate pandemic supply needs based on operational considerations in hospitals and then tested the methodology at Mayo Clinic in Rochester, MN. We upgraded a previously designed computer modeling tool and input carefully researched resource data from the hospital to run 10,000 Monte Carlo simulations using various combinations of variables to determine resource needs across a spectrum of scenarios. Of 10,000 iterations, 1,315 fell within the parameters defined by our simulation design and logical constraints. From these valid iterations, we projected supply requirements by percentile for key supplies, pharmaceuticals, and personal protective equipment requirements needed in a severe pandemic. We projected supplies needs for a range of scenarios that use up to 100% of Mayo Clinic-Rochester's surge capacity of beds and ventilators. The results indicate that there are diminishing patient care benefits for stockpiling on the high side of the range, but that having some stockpile of critical resources, even if it is relatively modest, is most important. We were able to display the probabilities of needing various supply levels across a spectrum of scenarios. The tool could be used to model many other hospital preparedness issues, but validation in other settings is needed. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Clinical nursing informatics. Developing tools for knowledge workers.

PubMed

Ozbolt, J G; Graves, J R

1993-06-01

Current research in clinical nursing informatics is proceeding along three important dimensions: (1) identifying and defining nursing's language and structuring its data; (2) understanding clinical judgment and how computer-based systems can facilitate and not replace it; and (3) discovering how well-designed systems can transform nursing practice. A number of efforts are underway to find and use language that accurately represents nursing and that can be incorporated into computer-based information systems. These efforts add to understanding nursing problems, interventions, and outcomes, and provide the elements for databases from which nursing's costs and effectiveness can be studied. Research on clinical judgment focuses on how nurses (perhaps with different levels of expertise) assess patient needs, set goals, and plan and deliver care, as well as how computer-based systems can be developed to aid these cognitive processes. Finally, investigators are studying not only how computers can help nurses with the mechanics and logistics of processing information but also and more importantly how access to informatics tools changes nursing care.

Automatic Estimation of the Radiological Inventory for the Dismantling of Nuclear Facilities

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

Garcia-Bermejo, R.; Felipe, A.; Gutierrez, S.

The estimation of the radiological inventory of Nuclear Facilities to be dismantled is a process that included information related with the physical inventory of all the plant and radiological survey. Estimation of the radiological inventory for all the components and civil structure of the plant could be obtained with mathematical models with statistical approach. A computer application has been developed in order to obtain the radiological inventory in an automatic way. Results: A computer application that is able to estimate the radiological inventory from the radiological measurements or the characterization program has been developed. In this computer applications has beenmore » included the statistical functions needed for the estimation of the central tendency and variability, e.g. mean, median, variance, confidence intervals, variance coefficients, etc. This computer application is a necessary tool in order to be able to estimate the radiological inventory of a nuclear facility and it is a powerful tool for decision taken in future sampling surveys.« less

The Impact of New Technology on Accounting Education.

ERIC Educational Resources Information Center

Shaoul, Jean

The introduction of computers in the Department of Accounting and Finance at Manchester University is described. General background outlining the increasing need for microcomputers in the accounting curriculum (including financial modelling tools and decision support systems such as linear programming, statistical packages, and simulation) is…

Mathematical and Computational Aspects Related to Soil Modeling and Simulation

DTIC Science & Technology

2017-09-26

and simulation challenges at the interface of applied math (homogenization, handling of discontinuous behavior, discrete vs. continuum representations...applied math tools need to be established and used to figure out how to impose compatible boundary conditions, how to better approximate the gradient

[Development of laboratory sequence analysis software based on WWW and UNIX].

PubMed

Huang, Y; Gu, J R

2001-01-01

Sequence analysis tools based on WWW and UNIX were developed in our laboratory to meet the needs of molecular genetics research in our laboratory. General principles of computer analysis of DNA and protein sequences were also briefly discussed in this paper.

The "Terminology Market."

ERIC Educational Resources Information Center

Galinski, Christian

This paper examines needs, resources, and trends in the computer-based development of field-specific terminologies in varied languages. The range of special terminologies, their users, and their producers is noted, and the kinds of resources produced (data and tools) are outlined. Data types include: terminological information proper (information…

Future Operating Concept - Joint Computer Network Operations

DTIC Science & Technology

2010-02-17

into the system‖ at a later date by circumventing the need for access privileges 3. Cyberwarfare Tools 67 • Social Engineering • Hacking ...Forces Command, Joint Operating Environment 2008, November 2008https://us.jfcom.mil/sites/ J5 /j59/default.aspx VIII Appendix V

High performance TWT development for the microwave power module

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

Whaley, D.R.; Armstrong, C.M.; Groshart, G.

1996-12-31

Northrop Grumman`s ongoing development of microwave power modules (MPM) provides microwave power at various power levels, frequencies, and bandwidths for a variety of applications. Present day requirements for the vacuum power booster traveling wave tubes of the microwave power module are becoming increasingly more demanding, necessitating the need for further enhancement of tube performance. The MPM development program at Northrop Grumman is designed specifically to meet this need by construction and test of a series of new tubes aimed at verifying computation and reaching high efficiency design goals. Tubes under test incorporate several different helix designs, as well as varyingmore » electron gun and magnetic confinement configurations. Current efforts also include further development of state-of-the-art TWT modeling and computational methods at Northrop Grumman incorporating new, more accurate models into existing design tools and developing new tools to be used in all aspects of traveling wave tube design. Current status of the Northrop Grumman MPM TWT development program will be presented.« less

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

PubMed

Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

2012-07-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

Savant Genome Browser 2: visualization and analysis for population-scale genomics

PubMed Central

Smith, Eric J. M.; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M.; Robinson, Mark D.; Wodak, Shoshana J.; Brudno, Michael

2012-01-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com. PMID:22638571

Thrust chamber performance using Navier-Stokes solution. [space shuttle main engine viscous nozzle calculation

NASA Technical Reports Server (NTRS)

Chan, J. S.; Freeman, J. A.

1984-01-01

The viscous, axisymmetric flow in the thrust chamber of the space shuttle main engine (SSME) was computed on the CRAY 205 computer using the general interpolants method (GIM) code. Results show that the Navier-Stokes codes can be used for these flows to study trends and viscous effects as well as determine flow patterns; but further research and development is needed before they can be used as production tools for nozzle performance calculations. The GIM formulation, numerical scheme, and computer code are described. The actual SSME nozzle computation showing grid points, flow contours, and flow parameter plots is discussed. The computer system and run times/costs are detailed.

A regional land use survey based on remote sensing and other data: A report on a LANDSAT and computer mapping project, volume 2

NASA Technical Reports Server (NTRS)

Nez, G. (Principal Investigator); Mutter, D.

1977-01-01

The author has identified the following significant results. The project mapped land use/cover classifications from LANDSAT computer compatible tape data and combined those results with other multisource data via computer mapping/compositing techniques to analyze various land use planning/natural resource management problems. Data were analyzed on 1:24,000 scale maps at 1.1 acre resolution. LANDSAT analysis software and linkages with other computer mapping software were developed. Significant results were also achieved in training, communication, and identification of needs for developing the LANDSAT/computer mapping technologies into operational tools for use by decision makers.

Modeling Methodologies for Design and Control of Solid Oxide Fuel Cell APUs

NASA Astrophysics Data System (ADS)

Pianese, C.; Sorrentino, M.

2009-08-01

Among the existing fuel cell technologies, Solid Oxide Fuel Cells (SOFC) are particularly suitable for both stationary and mobile applications, due to their high energy conversion efficiencies, modularity, high fuel flexibility, low emissions and noise. Moreover, the high working temperatures enable their use for efficient cogeneration applications. SOFCs are entering in a pre-industrial era and a strong interest for designing tools has growth in the last years. Optimal system configuration, components sizing, control and diagnostic system design require computational tools that meet the conflicting needs of accuracy, affordable computational time, limited experimental efforts and flexibility. The paper gives an overview on control-oriented modeling of SOFC at both single cell and stack level. Such an approach provides useful simulation tools for designing and controlling SOFC-APUs destined to a wide application area, ranging from automotive to marine and airplane APUs.

Physically Based Virtual Surgery Planning and Simulation Tools for Personal Health Care Systems

NASA Astrophysics Data System (ADS)

Dogan, Firat; Atilgan, Yasemin

The virtual surgery planning and simulation tools have gained a great deal of importance in the last decade in a consequence of increasing capacities at the information technology level. The modern hardware architectures, large scale database systems, grid based computer networks, agile development processes, better 3D visualization and all the other strong aspects of the information technology brings necessary instruments into almost every desk. The last decade’s special software and sophisticated super computer environments are now serving to individual needs inside “tiny smart boxes” for reasonable prices. However, resistance to learning new computerized environments, insufficient training and all the other old habits prevents effective utilization of IT resources by the specialists of the health sector. In this paper, all the aspects of the former and current developments in surgery planning and simulation related tools are presented, future directions and expectations are investigated for better electronic health care systems.

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

The Virtual Physiological Human ToolKit.

PubMed

Cooper, Jonathan; Cervenansky, Frederic; De Fabritiis, Gianni; Fenner, John; Friboulet, Denis; Giorgino, Toni; Manos, Steven; Martelli, Yves; Villà-Freixa, Jordi; Zasada, Stefan; Lloyd, Sharon; McCormack, Keith; Coveney, Peter V

2010-08-28

The Virtual Physiological Human (VPH) is a major European e-Science initiative intended to support the development of patient-specific computer models and their application in personalized and predictive healthcare. The VPH Network of Excellence (VPH-NoE) project is tasked with facilitating interaction between the various VPH projects and addressing issues of common concern. A key deliverable is the 'VPH ToolKit'--a collection of tools, methodologies and services to support and enable VPH research, integrating and extending existing work across Europe towards greater interoperability and sustainability. Owing to the diverse nature of the field, a single monolithic 'toolkit' is incapable of addressing the needs of the VPH. Rather, the VPH ToolKit should be considered more as a 'toolbox' of relevant technologies, interacting around a common set of standards. The latter apply to the information used by tools, including any data and the VPH models themselves, and also to the naming and categorizing of entities and concepts involved. Furthermore, the technologies and methodologies available need to be widely disseminated, and relevant tools and services easily found by researchers. The VPH-NoE has thus created an online resource for the VPH community to meet this need. It consists of a database of tools, methods and services for VPH research, with a Web front-end. This has facilities for searching the database, for adding or updating entries, and for providing user feedback on entries. Anyone is welcome to contribute.

Computer vision-based analysis of foods: a non-destructive colour measurement tool to monitor quality and safety.

PubMed

Mogol, Burçe Ataç; Gökmen, Vural

2014-05-01

Computer vision-based image analysis has been widely used in food industry to monitor food quality. It allows low-cost and non-contact measurements of colour to be performed. In this paper, two computer vision-based image analysis approaches are discussed to extract mean colour or featured colour information from the digital images of foods. These types of information may be of particular importance as colour indicates certain chemical changes or physical properties in foods. As exemplified here, the mean CIE a* value or browning ratio determined by means of computer vision-based image analysis algorithms can be correlated with acrylamide content of potato chips or cookies. Or, porosity index as an important physical property of breadcrumb can be calculated easily. In this respect, computer vision-based image analysis provides a useful tool for automatic inspection of food products in a manufacturing line, and it can be actively involved in the decision-making process where rapid quality/safety evaluation is needed. © 2013 Society of Chemical Industry.

CMS Distributed Computing Integration in the LHC sustained operations era

NASA Astrophysics Data System (ADS)

Grandi, C.; Bockelman, B.; Bonacorsi, D.; Fisk, I.; González Caballero, I.; Farina, F.; Hernández, J. M.; Padhi, S.; Sarkar, S.; Sciabà, A.; Sfiligoi, I.; Spiga, F.; Úbeda García, M.; Van Der Ster, D. C.; Zvada, M.

2011-12-01

After many years of preparation the CMS computing system has reached a situation where stability in operations limits the possibility to introduce innovative features. Nevertheless it is the same need of stability and smooth operations that requires the introduction of features that were considered not strategic in the previous phases. Examples are: adequate authorization to control and prioritize the access to storage and computing resources; improved monitoring to investigate problems and identify bottlenecks on the infrastructure; increased automation to reduce the manpower needed for operations; effective process to deploy in production new releases of the software tools. We present the work of the CMS Distributed Computing Integration Activity that is responsible for providing a liaison between the CMS distributed computing infrastructure and the software providers, both internal and external to CMS. In particular we describe the introduction of new middleware features during the last 18 months as well as the requirements to Grid and Cloud software developers for the future.

Overview of MSFC's Applied Fluid Dynamics Analysis Group Activities

NASA Technical Reports Server (NTRS)

Garcia, Roberto; Wang, Tee-See; Griffin, Lisa; Turner, James E. (Technical Monitor)

2001-01-01

This document is a presentation graphic which reviews the activities of the Applied Fluid Dynamics Analysis Group at Marshall Space Flight Center (i.e., Code TD64). The work of this group focused on supporting the space transportation programs. The work of the group is in Computational Fluid Dynamic tool development. This development is driven by hardware design needs. The major applications for the design and analysis tools are: turbines, pumps, propulsion-to-airframe integration, and combustion devices.

Integrating Commercial Off-The-Shelf (COTS) graphics and extended memory packages with CLIPS

NASA Technical Reports Server (NTRS)

Callegari, Andres C.

1990-01-01

This paper addresses the question of how to mix CLIPS with graphics and how to overcome PC's memory limitations by using the extended memory available in the computer. By adding graphics and extended memory capabilities, CLIPS can be converted into a complete and powerful system development tool, on the other most economical and popular computer platform. New models of PCs have amazing processing capabilities and graphic resolutions that cannot be ignored and should be used to the fullest of their resources. CLIPS is a powerful expert system development tool, but it cannot be complete without the support of a graphics package needed to create user interfaces and general purpose graphics, or without enough memory to handle large knowledge bases. Now, a well known limitation on the PC's is the usage of real memory which limits CLIPS to use only 640 Kb of real memory, but now that problem can be solved by developing a version of CLIPS that uses extended memory. The user has access of up to 16 MB of memory on 80286 based computers and, practically, all the available memory (4 GB) on computers that use the 80386 processor. So if we give CLIPS a self-configuring graphics package that will automatically detect the graphics hardware and pointing device present in the computer, and we add the availability of the extended memory that exists in the computer (with no special hardware needed), the user will be able to create more powerful systems at a fraction of the cost and on the most popular, portable, and economic platform available such as the PC platform.

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

DOE PAGES

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

2015-01-01

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

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

PubMed Central

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

2014-01-01

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

Building a Data Science capability for USGS water research and communication

NASA Astrophysics Data System (ADS)

Appling, A.; Read, E. K.

2015-12-01

Interpreting and communicating water issues in an era of exponentially increasing information requires a blend of domain expertise, computational proficiency, and communication skills. The USGS Office of Water Information has established a Data Science team to meet these needs, providing challenging careers for diverse domain scientists and innovators in the fields of information technology and data visualization. Here, we detail the experience of building a Data Science capability as a bridging element between traditional water resources analyses and modern computing tools and data management techniques. This approach includes four major components: 1) building reusable research tools, 2) documenting data-intensive research approaches in peer reviewed journals, 3) communicating complex water resources issues with interactive web visualizations, and 4) offering training programs for our peers in scientific computing. These components collectively improve the efficiency, transparency, and reproducibility of USGS data analyses and scientific workflows.

New Trends in E-Science: Machine Learning and Knowledge Discovery in Databases

NASA Astrophysics Data System (ADS)

Brescia, Massimo

2012-11-01

Data mining, or Knowledge Discovery in Databases (KDD), while being the main methodology to extract the scientific information contained in Massive Data Sets (MDS), needs to tackle crucial problems since it has to orchestrate complex challenges posed by transparent access to different computing environments, scalability of algorithms, reusability of resources. To achieve a leap forward for the progress of e-science in the data avalanche era, the community needs to implement an infrastructure capable of performing data access, processing and mining in a distributed but integrated context. The increasing complexity of modern technologies carried out a huge production of data, whose related warehouse management and the need to optimize analysis and mining procedures lead to a change in concept on modern science. Classical data exploration, based on local user own data storage and limited computing infrastructures, is no more efficient in the case of MDS, worldwide spread over inhomogeneous data centres and requiring teraflop processing power. In this context modern experimental and observational science requires a good understanding of computer science, network infrastructures, Data Mining, etc. i.e. of all those techniques which fall into the domain of the so called e-science (recently assessed also by the Fourth Paradigm of Science). Such understanding is almost completely absent in the older generations of scientists and this reflects in the inadequacy of most academic and research programs. A paradigm shift is needed: statistical pattern recognition, object oriented programming, distributed computing, parallel programming need to become an essential part of scientific background. A possible practical solution is to provide the research community with easy-to understand, easy-to-use tools, based on the Web 2.0 technologies and Machine Learning methodology. Tools where almost all the complexity is hidden to the final user, but which are still flexible and able to produce efficient and reliable scientific results. All these considerations will be described in the detail in the chapter. Moreover, examples of modern applications offering to a wide variety of e-science communities a large spectrum of computational facilities to exploit the wealth of available massive data sets and powerful machine learning and statistical algorithms will be also introduced.

Applications of Automation Methods for Nonlinear Fracture Test Analysis

NASA Technical Reports Server (NTRS)

Allen, Phillip A.; Wells, Douglas N.

2013-01-01

Using automated and standardized computer tools to calculate the pertinent test result values has several advantages such as: 1. allowing high-fidelity solutions to complex nonlinear phenomena that would be impractical to express in written equation form, 2. eliminating errors associated with the interpretation and programing of analysis procedures from the text of test standards, 3. lessening the need for expertise in the areas of solid mechanics, fracture mechanics, numerical methods, and/or finite element modeling, to achieve sound results, 4. and providing one computer tool and/or one set of solutions for all users for a more "standardized" answer. In summary, this approach allows a non-expert with rudimentary training to get the best practical solution based on the latest understanding with minimum difficulty.Other existing ASTM standards that cover complicated phenomena use standard computer programs: 1. ASTM C1340/C1340M-10- Standard Practice for Estimation of Heat Gain or Loss Through Ceilings Under Attics Containing Radiant Barriers by Use of a Computer Program 2. ASTM F 2815 - Standard Practice for Chemical Permeation through Protective Clothing Materials: Testing Data Analysis by Use of a Computer Program 3. ASTM E2807 - Standard Specification for 3D Imaging Data Exchange, Version 1.0 The verification, validation, and round-robin processes required of a computer tool closely parallel the methods that are used to ensure the solution validity for equations included in test standard. The use of automated analysis tools allows the creation and practical implementation of advanced fracture mechanics test standards that capture the physics of a nonlinear fracture mechanics problem without adding undue burden or expense to the user. The presented approach forms a bridge between the equation-based fracture testing standards of today and the next generation of standards solving complex problems through analysis automation.

A method of extracting ontology module using concept relations for sharing knowledge in mobile cloud computing environment.

PubMed

Lee, Keonsoo; Rho, Seungmin; Lee, Seok-Won

2014-01-01

In mobile cloud computing environment, the cooperation of distributed computing objects is one of the most important requirements for providing successful cloud services. To satisfy this requirement, all the members, who are employed in the cooperation group, need to share the knowledge for mutual understanding. Even if ontology can be the right tool for this goal, there are several issues to make a right ontology. As the cost and complexity of managing knowledge increase according to the scale of the knowledge, reducing the size of ontology is one of the critical issues. In this paper, we propose a method of extracting ontology module to increase the utility of knowledge. For the given signature, this method extracts the ontology module, which is semantically self-contained to fulfill the needs of the service, by considering the syntactic structure and semantic relation of concepts. By employing this module, instead of the original ontology, the cooperation of computing objects can be performed with less computing load and complexity. In particular, when multiple external ontologies need to be combined for more complex services, this method can be used to optimize the size of shared knowledge.

Development, Testing, and Validation of a Model-Based Tool to Predict Operator Responses in Unexpected Workload Transitions

NASA Technical Reports Server (NTRS)

Sebok, Angelia; Wickens, Christopher; Sargent, Robert

2015-01-01

One human factors challenge is predicting operator performance in novel situations. Approaches such as drawing on relevant previous experience, and developing computational models to predict operator performance in complex situations, offer potential methods to address this challenge. A few concerns with modeling operator performance are that models need to realistic, and they need to be tested empirically and validated. In addition, many existing human performance modeling tools are complex and require that an analyst gain significant experience to be able to develop models for meaningful data collection. This paper describes an effort to address these challenges by developing an easy to use model-based tool, using models that were developed from a review of existing human performance literature and targeted experimental studies, and performing an empirical validation of key model predictions.

Taking Care of the Small Computer: A Guide for Librarians.

ERIC Educational Resources Information Center

Williams, Gene

1986-01-01

Describes how to identify microcomputer problems and determine whether the services of a technician are required by troubleshooting, or using a process of elimination, without needing a technical background or special tools. Prevention methods and the use of diagnostic programs are also explained. (EM)

Ensuring long-term utility of the AOP framework and knowledge for multiple stakeholders

EPA Science Inventory

1.Introduction There is a need to increase the development and implementation of predictive approaches to support chemical safety assessment. These predictive approaches feature generation of data from tools such as computational models, pathway-based in vitro assays, and short-t...

What Makes a Computer Lab: Use These Ideas to Design Your Own.

ERIC Educational Resources Information Center

Day, C. William; Herlihy, John J.

1989-01-01

Although educators have succeeded in informing the public about the transformative power of electronic and telecommunications tools, they have frequently overlooked physical features of spaces needed to house them. This article discusses workspace, arrangements, flooring, environment, electrical wiring, lighting, acoustics, and security features…

Optimal design of low-density SNP arrays for genomic prediction: algorithm and applications

USDA-ARS?s Scientific Manuscript database

Low-density (LD) single nucleotide polymorphism (SNP) arrays provide a cost-effective solution for genomic prediction and selection, but algorithms and computational tools are needed for their optimal design. A multiple-objective, local optimization (MOLO) algorithm was developed for design of optim...

Electronic Networks: Crossing Boundaries/Creating Communities.

ERIC Educational Resources Information Center

Howard, Tharon, Ed.; Benson, Chris, Ed.; Gooch, Rocky; Goswami, Dixie

Written by practicing teachers about actual instructional computing projects, this book provides information teachers need to integrate instructional technologies into their classrooms. The book is divided into three parts. Part 1, "New Tools for the Classroom: An Introduction to Networked Learning," includes chapters: (1) "Getting Started in a…

Water System Adaptation To Hydrological Changes: Module 12, Models and Tools for Stormwater and Wastewater System Adaptation

EPA Science Inventory

This course will introduce students to the fundamental principles of water system adaptation to hydrological changes, with emphasis on data analysis and interpretation, technical planning, and computational modeling. Starting with real-world scenarios and adaptation needs, the co...

Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

ERIC Educational Resources Information Center

Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

2008-01-01

Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

"Extreme Programming" in a Bioinformatics Class

ERIC Educational Resources Information Center

Kelley, Scott; Alger, Christianna; Deutschman, Douglas

2009-01-01

The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

Performance evaluation of the Engineering Analysis and Data Systems (EADS) 2

NASA Technical Reports Server (NTRS)

Debrunner, Linda S.

1994-01-01

The Engineering Analysis and Data System (EADS)II (1) was installed in March 1993 to provide high performance computing for science and engineering at Marshall Space Flight Center (MSFC). EADS II increased the computing capabilities over the existing EADS facility in the areas of throughput and mass storage. EADS II includes a Vector Processor Compute System (VPCS), a Virtual Memory Compute System (CFS), a Common Output System (COS), as well as Image Processing Station, Mini Super Computers, and Intelligent Workstations. These facilities are interconnected by a sophisticated network system. This work considers only the performance of the VPCS and the CFS. The VPCS is a Cray YMP. The CFS is implemented on an RS 6000 using the UniTree Mass Storage System. To better meet the science and engineering computing requirements, EADS II must be monitored, its performance analyzed, and appropriate modifications for performance improvement made. Implementing this approach requires tool(s) to assist in performance monitoring and analysis. In Spring 1994, PerfStat 2.0 was purchased to meet these needs for the VPCS and the CFS. PerfStat(2) is a set of tools that can be used to analyze both historical and real-time performance data. Its flexible design allows significant user customization. The user identifies what data is collected, how it is classified, and how it is displayed for evaluation. Both graphical and tabular displays are supported. The capability of the PerfStat tool was evaluated, appropriate modifications to EADS II to optimize throughput and enhance productivity were suggested and implemented, and the effects of these modifications on the systems performance were observed. In this paper, the PerfStat tool is described, then its use with EADS II is outlined briefly. Next, the evaluation of the VPCS, as well as the modifications made to the system are described. Finally, conclusions are drawn and recommendations for future worked are outlined.

Human Centered Computing for Mars Exploration

NASA Technical Reports Server (NTRS)

Trimble, Jay

2005-01-01

The science objectives are to determine the aqueous, climatic, and geologic history of a site on Mars where conditions may have been favorable to the preservation of evidence of prebiotic or biotic processes. Human Centered Computing is a development process that starts with users and their needs, rather than with technology. The goal is a system design that serves the user, where the technology fits the task and the complexity is that of the task not of the tool.

Stream Splitting in Support of Intrusion Detection

DTIC Science & Technology

2003-06-01

increased. Every computer on the Internet has no need to see the traffic of every other computer on the Internet. Indeed if this was so, nothing would get ...distinguishes the stream splitter from other network analysis tools. B. HIGH LEVEL DESIGN To get the desired level of performance, a multi-threaded...of greater concern than added accuracy of a Bayesian model. This is a case where close is good enough . b. PassiveSensors Though similar to active

Use of cone-beam computed tomography in the diagnosis of sensory nerve paresthesia secondary to orthodontic tooth movement: a clinical report.

PubMed

Chana, Randeep S; Wiltshire, William A; Cholakis, Anastasia; Levine, Gary

2013-08-01

In this article, we report an incident of transient neuropathy secondary to tooth movement involving the inferior alveolar nerve. This clinical report reflects the need to thoroughly examine potentially high-risk patients for neuropathy using advanced diagnostic tools such as cone-beam computed tomography when diagnosing and planning treatment. Copyright © 2013 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: Challenges, opportunities, and research needs

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

Burgess-Herbert, Sarah L., E-mail: sarah.burgess@alum.mit.edu; Euling, Susan Y.

A critical challenge for environmental chemical risk assessment is the characterization and reduction of uncertainties introduced when extrapolating inferences from one species to another. The purpose of this article is to explore the challenges, opportunities, and research needs surrounding the issue of how genomics data and computational and systems level approaches can be applied to inform differences in response to environmental chemical exposure across species. We propose that the data, tools, and evolutionary framework of comparative genomics be adapted to inform interspecies differences in chemical mechanisms of action. We compare and contrast existing approaches, from disciplines as varied as evolutionarymore » biology, systems biology, mathematics, and computer science, that can be used, modified, and combined in new ways to discover and characterize interspecies differences in chemical mechanism of action which, in turn, can be explored for application to risk assessment. We consider how genetic, protein, pathway, and network information can be interrogated from an evolutionary biology perspective to effectively characterize variations in biological processes of toxicological relevance among organisms. We conclude that comparative genomics approaches show promise for characterizing interspecies differences in mechanisms of action, and further, for improving our understanding of the uncertainties inherent in extrapolating inferences across species in both ecological and human health risk assessment. To achieve long-term relevance and consistent use in environmental chemical risk assessment, improved bioinformatics tools, computational methods robust to data gaps, and quantitative approaches for conducting extrapolations across species are critically needed. Specific areas ripe for research to address these needs are recommended.« less

In Pursuit of Improving Airburst and Ground Damage Predictions: Recent Advances in Multi-Body Aerodynamic Testing and Computational Tools Validation

NASA Technical Reports Server (NTRS)

Venkatapathy, Ethiraj; Gulhan, Ali; Aftosmis, Michael; Brock, Joseph; Mathias, Donovan; Need, Dominic; Rodriguez, David; Seltner, Patrick; Stern, Eric; Wiles, Sebastian

2017-01-01

An airburst from a large asteroid during entry can cause significant ground damage. The damage depends on the energy and the altitude of airburst. Breakup of asteroids into fragments and their lateral spread have been observed. Modeling the underlying physics of fragmented bodies interacting at hypersonic speeds and the spread of fragments is needed for a true predictive capability. Current models use heuristic arguments and assumptions such as pancaking or point source explosive energy release at pre-determined altitude or an assumed fragmentation spread rate to predict airburst damage. A multi-year collaboration between German Aerospace Center (DLR) and NASA has been established to develop validated computational tools to address the above challenge.

EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing.

PubMed

Berndsen, Zachary; Bowman, Charles; Jang, Haerin; Ward, Andrew B

2017-12-01

The Electron Microscopy Hole Punch (EMHP) is a streamlined suite of tools for quick assessment, sorting and hole masking of electron micrographs. With recent advances in single-particle electron cryo-microscopy (cryo-EM) data processing allowing for the rapid determination of protein structures using a smaller computational footprint, we saw the need for a fast and simple tool for data pre-processing that could run independent of existing high-performance computing (HPC) infrastructures. EMHP provides a data preprocessing platform in a small package that requires minimal python dependencies to function. https://www.bitbucket.org/chazbot/emhp Apache 2.0 License. bowman@scripps.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Computational thinking in life science education.

PubMed

Rubinstein, Amir; Chor, Benny

2014-11-01

We join the increasing call to take computational education of life science students a step further, beyond teaching mere programming and employing existing software tools. We describe a new course, focusing on enriching the curriculum of life science students with abstract, algorithmic, and logical thinking, and exposing them to the computational "culture." The design, structure, and content of our course are influenced by recent efforts in this area, collaborations with life scientists, and our own instructional experience. Specifically, we suggest that an effective course of this nature should: (1) devote time to explicitly reflect upon computational thinking processes, resisting the temptation to drift to purely practical instruction, (2) focus on discrete notions, rather than on continuous ones, and (3) have basic programming as a prerequisite, so students need not be preoccupied with elementary programming issues. We strongly recommend that the mere use of existing bioinformatics tools and packages should not replace hands-on programming. Yet, we suggest that programming will mostly serve as a means to practice computational thinking processes. This paper deals with the challenges and considerations of such computational education for life science students. It also describes a concrete implementation of the course and encourages its use by others.

Exploring the architectural trade space of NASAs Space Communication and Navigation Program

NASA Astrophysics Data System (ADS)

Sanchez, M.; Selva, D.; Cameron, B.; Crawley, E.; Seas, A.; Seery, B.

NASAs Space Communication and Navigation (SCaN) Program is responsible for providing communication and navigation services to space missions and other users in and beyond low Earth orbit. The current SCaN architecture consists of three independent networks: the Space Network (SN), which contains the TDRS relay satellites in GEO; the Near Earth Network (NEN), which consists of several NASA owned and commercially operated ground stations; and the Deep Space Network (DSN), with three ground stations in Goldstone, Madrid, and Canberra. The first task of this study is the stakeholder analysis. The goal of the stakeholder analysis is to identify the main stakeholders of the SCaN system and their needs. Twenty-one main groups of stakeholders have been identified and put on a stakeholder map. Their needs are currently being elicited by means of interviews and an extensive literature review. The data will then be analyzed by applying Cameron and Crawley's stakeholder analysis theory, with a view to highlighting dominant needs and conflicting needs. The second task of this study is the architectural tradespace exploration of the next generation TDRSS. The space of possible architectures for SCaN is represented by a set of architectural decisions, each of which has a discrete set of options. A computational tool is used to automatically synthesize a very large number of possible architectures by enumerating different combinations of decisions and options. The same tool contains models to evaluate the architectures in terms of performance and cost. The performance model uses the stakeholder needs and requirements identified in the previous steps as inputs, and it is based in the VASSAR methodology presented in a companion paper. This paper summarizes the current status of the MIT SCaN architecture study. It starts by motivating the need to perform tradespace exploration studies in the context of relay data systems through a description of the history NASA's space communicati- n networks. It then presents the generalities of possible architectures for future space communication and navigation networks. Finally, it describes the tools and methods being developed, clearly indicating the architectural decisions that have been taken into account as well as the systematic approach followed to model them. The purpose of this study is to explore the SCaN architectural tradespace by means of a computational tool. This paper describes the tool, while the tradespace exploration is underway.

Using CASE tools to write engineering specifications

NASA Astrophysics Data System (ADS)

Henry, James E.; Howard, Robert W.; Iveland, Scott T.

1993-08-01

There are always a wide variety of obstacles to writing and maintaining engineering documentation. To combat these problems, documentation generation can be linked to the process of engineering development. The same graphics and communication tools used for structured system analysis and design (SSA/SSD) also form the basis for the documentation. The goal is to build a living document, such that as an engineering design changes, the documentation will `automatically' revise. `Automatic' is qualified by the need to maintain textual descriptions associated with the SSA/SSD graphics, and the need to generate new documents. This paper describes a methodology and a computer aided system engineering toolset that enables a relatively seamless transition into document generation for the development engineering team.

Purple Computational Environment With Mappings to ACE Requirements for the General Availability User Environment Capabilities

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

Barney, B; Shuler, J

2006-08-21

Purple is an Advanced Simulation and Computing (ASC) funded massively parallel supercomputer located at Lawrence Livermore National Laboratory (LLNL). The Purple Computational Environment documents the capabilities and the environment provided for the FY06 LLNL Level 1 General Availability Milestone. This document describes specific capabilities, tools, and procedures to support both local and remote users. The model is focused on the needs of the ASC user working in the secure computing environments at Los Alamos National Laboratory, Lawrence Livermore National Laboratory, and Sandia National Laboratories, but also documents needs of the LLNL and Alliance users working in the unclassified environment. Additionally,more » the Purple Computational Environment maps the provided capabilities to the Trilab ASC Computing Environment (ACE) Version 8.0 requirements. The ACE requirements reflect the high performance computing requirements for the General Availability user environment capabilities of the ASC community. Appendix A lists these requirements and includes a description of ACE requirements met and those requirements that are not met for each section of this document. The Purple Computing Environment, along with the ACE mappings, has been issued and reviewed throughout the Tri-lab community.« less

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

Favorite, Jeffrey A.

SENSMG is a tool for computing first-order sensitivities of neutron reaction rates, reaction-rate ratios, leakage, k eff, and α using the PARTISN multigroup discrete-ordinates code. SENSMG computes sensitivities to all of the transport cross sections and data (total, fission, nu, chi, and all scattering moments), two edit cross sections (absorption and capture), and the density for every isotope and energy group. It also computes sensitivities to the mass density for every material and derivatives with respect to all interface locations. The tool can be used for one-dimensional spherical (r) and two-dimensional cylindrical (r-z) geometries. The tool can be used formore » fixed-source and eigenvalue problems. The tool implements Generalized Perturbation Theory (GPT) as discussed by Williams and Stacey. Section II of this report describes the theory behind adjoint-based sensitivities, gives the equations that SENSMG solves, and defines the sensitivities that are output. Section III describes the user interface, including the input file and command line options. Section IV describes the output. Section V gives some notes about the coding that may be of interest. Section VI discusses verification, which is ongoing. Section VII lists needs and ideas for future work. Appendix A lists all of the input files whose results are presented in Sec. VI.« less

Instrumentation, performance visualization, and debugging tools for multiprocessors

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Fineman, Charles E.; Hontalas, Philip J.

1991-01-01

The need for computing power has forced a migration from serial computation on a single processor to parallel processing on multiprocessor architectures. However, without effective means to monitor (and visualize) program execution, debugging, and tuning parallel programs becomes intractably difficult as program complexity increases with the number of processors. Research on performance evaluation tools for multiprocessors is being carried out at ARC. Besides investigating new techniques for instrumenting, monitoring, and presenting the state of parallel program execution in a coherent and user-friendly manner, prototypes of software tools are being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Our current tool set, the Ames Instrumentation Systems (AIMS), incorporates features from various software systems developed in academia and industry. The execution of FORTRAN programs on the Intel iPSC/860 can be automatically instrumented and monitored. Performance data collected in this manner can be displayed graphically on workstations supporting X-Windows. We have successfully compared various parallel algorithms for computational fluid dynamics (CFD) applications in collaboration with scientists from the Numerical Aerodynamic Simulation Systems Division. By performing these comparisons, we show that performance monitors and debuggers such as AIMS are practical and can illuminate the complex dynamics that occur within parallel programs.

Development of Experimental and Computational Aeroacoustic Tools for Advanced Liner Evaluation

NASA Technical Reports Server (NTRS)

Jones, Michael G.; Watson, Willie R.; Nark, Douglas N.; Parrott, Tony L.; Gerhold, Carl H.; Brown, Martha C.

2006-01-01

Acoustic liners in aircraft engine nacelles suppress radiated noise. Therefore, as air travel increases, increasingly sophisticated tools are needed to maximize noise suppression. During the last 30 years, NASA has invested significant effort in development of experimental and computational acoustic liner evaluation tools. The Curved Duct Test Rig is a 152-mm by 381- mm curved duct that supports liner evaluation at Mach numbers up to 0.3 and source SPLs up to 140 dB, in the presence of user-selected modes. The Grazing Flow Impedance Tube is a 51- mm by 63-mm duct currently being fabricated to operate at Mach numbers up to 0.6 with source SPLs up to at least 140 dB, and will replace the existing 51-mm by 51-mm duct. Together, these test rigs allow evaluation of advanced acoustic liners over a range of conditions representative of those observed in aircraft engine nacelles. Data acquired with these test ducts are processed using three aeroacoustic propagation codes. Two are based on finite element solutions to convected Helmholtz and linearized Euler equations. The third is based on a parabolic approximation to the convected Helmholtz equation. The current status of these computational tools and their associated usage with the Langley test rigs is provided.

Scalable Node Monitoring

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

Drotar, Alexander P.; Quinn, Erin E.; Sutherland, Landon D.

2012-07-30

Project description is: (1) Build a high performance computer; and (2) Create a tool to monitor node applications in Component Based Tool Framework (CBTF) using code from Lightweight Data Metric Service (LDMS). The importance of this project is that: (1) there is a need a scalable, parallel tool to monitor nodes on clusters; and (2) New LDMS plugins need to be able to be easily added to tool. CBTF stands for Component Based Tool Framework. It's scalable and adjusts to different topologies automatically. It uses MRNet (Multicast/Reduction Network) mechanism for information transport. CBTF is flexible and general enough to bemore » used for any tool that needs to do a task on many nodes. Its components are reusable and 'EASILY' added to a new tool. There are three levels of CBTF: (1) frontend node - interacts with users; (2) filter nodes - filters or concatenates information from backend nodes; and (3) backend nodes - where the actual work of the tool is done. LDMS stands for lightweight data metric servies. It's a tool used for monitoring nodes. Ltool is the name of the tool we derived from LDMS. It's dynamically linked and includes the following components: Vmstat, Meminfo, Procinterrupts and more. It works by: Ltool command is run on the frontend node; Ltool collects information from the backend nodes; backend nodes send information to the filter nodes; and filter nodes concatenate information and send to a database on the front end node. Ltool is a useful tool when it comes to monitoring nodes on a cluster because the overhead involved with running the tool is not particularly high and it will automatically scale to any size cluster.« less

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2015-01-01

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

Advanced tools for smartphone-based experiments: phyphox

NASA Astrophysics Data System (ADS)

Staacks, S.; Hütz, S.; Heinke, H.; Stampfer, C.

2018-07-01

The sensors in modern smartphones are a promising and cost-effective tool for experimentation in physics education, but many experiments face practical problems. Often the phone is inaccessible during the experiment and the data usually needs to be analyzed subsequently on a computer. We address both problems by introducing a new app, called ‘phyphox’, which is specifically designed for utilizing experiments in physics teaching. The app is free and designed to offer the same set of features on Android and iOS.

Apollo: a sequence annotation editor

PubMed Central

Lewis, SE; Searle, SMJ; Harris, N; Gibson, M; Iyer, V; Richter, J; Wiel, C; Bayraktaroglu, L; Birney, E; Crosby, MA; Kaminker, JS; Matthews, BB; Prochnik, SE; Smith, CD; Tupy, JL; Rubin, GM; Misra, S; Mungall, CJ; Clamp, ME

2002-01-01

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects. PMID:12537571

Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

PubMed Central

Náray-Szabó, Gábor; Oláh, Julianna; Krámos, Balázs

2013-01-01

Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods. PMID:24970187

Soil Erosion Study through Simulation: An Educational Tool.

ERIC Educational Resources Information Center

Huber, Thomas P.; Falkenmayer, Karen

1987-01-01

Discusses the need for education about soil erosion and advocates the use of the Universal Soil Loss Equation (USLE) to show the impacts of human and natural action on the land. Describes the use of a computer simulated version of the USLE in several environmental and farming situations. (TW)

Water System Adaptation To Hydrological Changes: Module 14, Life Cycle Analysis (LCA) and Prioritization Tools in Water System Adaptation

EPA Science Inventory

This course will introduce students to the fundamental principles of water system adaptation to hydrological changes, with emphasis on data analysis and interpretation, technical planning, and computational modeling. Starting with real-world scenarios and adaptation needs, the co...

Investigating Student Use of Electronic Support Tools and Mathematical Reasoning

ERIC Educational Resources Information Center

Higgins, Kristina N.; Crawford, Lindy; Huscroft-D'Angelo, Jacqueline; Horney, Mark

2016-01-01

Mathematical reasoning involves comprehending mathematical information and concepts in a logical way and forming conclusions and generalizations based on this comprehension. Computer-based learning has been incorporated into classrooms across the country, and specific aspects of technology need to be studied to determine how programs are…

Computer Aided Lip Reading Training Tool

ERIC Educational Resources Information Center

Sarmasik, Gamze; Dalkilic, Gokhan; Kut, Alp; Cebi, Yalcin; Serbetcioglu, Bulent

2007-01-01

Worldwide auditory-verbal education is becoming widespread for deaf children. But many prelingually, late-diagnosed deaf children and adults may utilize neither hearing aids nor cochlear implants and needed the support of lip-reading. Therefore, lip-reading skill remains to be important for oral education programmes of hearing impaired. The…

Computer hardware description languages - A tutorial

NASA Technical Reports Server (NTRS)

Shiva, S. G.

1979-01-01

The paper introduces hardware description languages (HDL) as useful tools for hardware design and documentation. The capabilities and limitations of HDLs are discussed along with the guidelines needed in selecting an appropriate HDL. The directions for future work are provided and attention is given to the implementation of HDLs in microcomputers.

A tiered approach to incorporate exposure and pharmacokinetics considerations in in vitro based safety assessment

EPA Science Inventory

Application of in vitro based safety assessment requires reconciling chemical concentrations sufficient to produce bioactivity in vitro with those that trigger a molecular initiating event at the relevant in vivo target site. To address such need, computational tools such as phy...

Assessing Teaching Skills with a Mobile Simulation

ERIC Educational Resources Information Center

Gibson, David

2013-01-01

Because mobile technologies are overtaking personal computers as the primary tools of Internet access, and cloud-based resources are fundamentally transforming the world's knowledge, new forms of teaching and assessment are required to foster 21st century literacies, including those needed by K-12 teachers. A key feature of mobile technology…

A COMPUTER-CONTROLLED SYSTEM FOR GENERATING UNIFORM SURFACE DEPOSITS TO STUDY THE TRANSPORT OF PARTICULATE MATTER

EPA Science Inventory

Improved methods for measuring and assessing microenvironmental exposure in individuals are needed. How human activities affect particulate matter in the personal cloud is poorly understood. A quality assurance tool to aid the study of particle transport mechanisms (e.g., re-en...

Improving Demonstration Using Better Interaction Techniques

DTIC Science & Technology

1997-01-14

Programming by demonstration (PBD) can be used to create tools and methods that eliminate the need to learn difficult computer languages. Gamut is a...do this, Gamut uses advanced interaction techniques that make it easier for a software author to express all needed aspects of one’s program. These...techniques include a simplified way to demonstrate new examples, called nudges, and a way to highlight objects to show they are important. Also, Gamut

On the design of computer-based models for integrated environmental science.

PubMed

McIntosh, Brian S; Jeffrey, Paul; Lemon, Mark; Winder, Nick

2005-06-01

The current research agenda in environmental science is dominated by calls to integrate science and policy to better understand and manage links between social (human) and natural (nonhuman) processes. Freshwater resource management is one area where such calls can be heard. Designing computer-based models for integrated environmental science poses special challenges to the research community. At present it is not clear whether such tools, or their outputs, receive much practical policy or planning application. It is argued that this is a result of (1) a lack of appreciation within the research modeling community of the characteristics of different decision-making processes including policy, planning, and (2) participation, (3) a lack of appreciation of the characteristics of different decision-making contexts, (4) the technical difficulties in implementing the necessary support tool functionality, and (5) the socio-technical demands of designing tools to be of practical use. This article presents a critical synthesis of ideas from each of these areas and interprets them in terms of design requirements for computer-based models being developed to provide scientific information support for policy and planning. Illustrative examples are given from the field of freshwater resources management. Although computer-based diagramming and modeling tools can facilitate processes of dialogue, they lack adequate simulation capabilities. Component-based models and modeling frameworks provide such functionality and may be suited to supporting problematic or messy decision contexts. However, significant technical (implementation) and socio-technical (use) challenges need to be addressed before such ambition can be realized.

Computational Prediction of miRNA Genes from Small RNA Sequencing Data

PubMed Central

Kang, Wenjing; Friedländer, Marc R.

2015-01-01

Next-generation sequencing now for the first time allows researchers to gage the depth and variation of entire transcriptomes. However, now as rare transcripts can be detected that are present in cells at single copies, more advanced computational tools are needed to accurately annotate and profile them. microRNAs (miRNAs) are 22 nucleotide small RNAs (sRNAs) that post-transcriptionally reduce the output of protein coding genes. They have established roles in numerous biological processes, including cancers and other diseases. During miRNA biogenesis, the sRNAs are sequentially cleaved from precursor molecules that have a characteristic hairpin RNA structure. The vast majority of new miRNA genes that are discovered are mined from small RNA sequencing (sRNA-seq), which can detect more than a billion RNAs in a single run. However, given that many of the detected RNAs are degradation products from all types of transcripts, the accurate identification of miRNAs remain a non-trivial computational problem. Here, we review the tools available to predict animal miRNAs from sRNA sequencing data. We present tools for generalist and specialist use cases, including prediction from massively pooled data or in species without reference genome. We also present wet-lab methods used to validate predicted miRNAs, and approaches to computationally benchmark prediction accuracy. For each tool, we reference validation experiments and benchmarking efforts. Last, we discuss the future of the field. PMID:25674563

Implementing iRound: A Computer-Based Auditing Tool.

PubMed

Brady, Darcie

Many hospitals use rounding or auditing as a tool to help identify gaps and needs in quality and process performance. Some hospitals are also using rounding to help improve patient experience. It is known that purposeful rounding helps improve Hospital Consumer Assessment of Healthcare Providers and Systems scores by helping manage patient expectations, provide service recovery, and recognize quality caregivers. Rounding works when a standard method is used across the facility, where data are comparable and trustworthy. This facility had a pen-and-paper process in place that made data reporting difficult, created a silo culture between departments, and most audits and rounds were completed differently on each unit. It was recognized that this facility needed to standardize the rounding and auditing process. The tool created by the Advisory Board called iRound was chosen as the tool this facility would use for patient experience rounds as well as process and quality rounding. The success of the iRound tool in this facility depended on several factors that started many months before implementation to current everyday usage.

A prototype expert/information system for examining environmental risks of KSC activities

NASA Technical Reports Server (NTRS)

Engel, Bernard A.

1993-01-01

Protection of the environment and natural resources at the Kennedy Space Center (KSC) is of great concern. An expert/information system to replace the paper-based KSC Environmental Checklist was developed. The computer-based system requests information only as a required and supplies assistance as needed. The most comprehensive portion of the system provides information about endangered species habitat at KSC. This module uses geographic information system (GIS) data and tools, expert rules, color graphics, computer-based video, and hypertext to provide information.

A Management System for Computer Performance Evaluation.

DTIC Science & Technology

1981-12-01

AD-AIlS 538 AIR FORCE INST OF TECH WRIGHT-PATTERSON AFB OH SCHOO-ETC F/6 S/1 MANAGEMENT SYSTEM FOR COMPUTER PERFORMANCE EVALUATION. (U DEC 81 H K...release; distribution unlimited. AFIT/GCS/1,Y/81 D)-i PREFACE As an installation manager of a Burroughs 3500 1 erncountered many problems concerning its...techniques to select, and finally, how do I organize the effort. As a manager I felt that I needed a reference or tool that would broaden my OPE

Optical 3D surface digitizing in forensic medicine: 3D documentation of skin and bone injuries.

PubMed

Thali, Michael J; Braun, Marcel; Dirnhofer, Richard

2003-11-26

Photography process reduces a three-dimensional (3D) wound to a two-dimensional level. If there is a need for a high-resolution 3D dataset of an object, it needs to be three-dimensionally scanned. No-contact optical 3D digitizing surface scanners can be used as a powerful tool for wound and injury-causing instrument analysis in trauma cases. The 3D skin wound and a bone injury documentation using the optical scanner Advanced TOpometric Sensor (ATOS II, GOM International, Switzerland) will be demonstrated using two illustrative cases. Using this 3D optical digitizing method the wounds (the virtual 3D computer model of the skin and the bone injuries) and the virtual 3D model of the injury-causing tool are graphically documented in 3D in real-life size and shape and can be rotated in the CAD program on the computer screen. In addition, the virtual 3D models of the bone injuries and tool can now be compared in a 3D CAD program against one another in virtual space, to see if there are matching areas. Further steps in forensic medicine will be a full 3D surface documentation of the human body and all the forensic relevant injuries using optical 3D scanners.

Performance limits and trade-offs in entropy-driven biochemical computers.

PubMed

Chu, Dominique

2018-04-14

It is now widely accepted that biochemical reaction networks can perform computations. Examples are kinetic proof reading, gene regulation, or signalling networks. For many of these systems it was found that their computational performance is limited by a trade-off between the metabolic cost, the speed and the accuracy of the computation. In order to gain insight into the origins of these trade-offs, we consider entropy-driven computers as a model of biochemical computation. Using tools from stochastic thermodynamics, we show that entropy-driven computation is subject to a trade-off between accuracy and metabolic cost, but does not involve time-trade-offs. Time trade-offs appear when it is taken into account that the result of the computation needs to be measured in order to be known. We argue that this measurement process, although usually ignored, is a major contributor to the cost of biochemical computation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Are people with epilepsy using eHealth-tools?

PubMed

Leenen, Loes A M; Wijnen, Ben F M; de Kinderen, Reina J A; van Heugten, Caroline M; Evers, Silvia M A A; Majoie, Marian H J M

2016-11-01

Self-management for people with epilepsy (PWE) should lead to shared decision-making and thus to adherence to the treatment plan. eHealth is an important way of supporting PWE in their self-management. In this survey, we used a mixed method to explore the following: 1) which factors were monitored by PWE and how (using pen and paper or eHealth-tools), 2) how many PWE own a computer or smartphone, and 3) how do they perceive the use of eHealth. A consecutive series of 1000 PWE attending the outpatient clinic of a tertiary epilepsy center were asked to fill in a questionnaire. In comparison with the general population, fewer PWE owned a computer or smartphone. They were, however, more likely to self-monitor their health than other patients suffering from a chronic condition. Although PWE did not use eHealth-tools often, they perceived it as a user-friendly tool, promoting health behavior as well as adherence. On the other hand, problems with privacy and the perception that not everyone is able to use eHealth were considered as disadvantages by PWE. Promoting self-care was perceived as both an advantage and a disadvantage. It was seen as an advantage when PWE mentioned the option of eHealth-tools in order to gain insight into one's epilepsy. At the same time, it was seen as a disadvantage because it confronts PWE with their disease, which causes emotional stress. The high level of self-monitoring combined with a low usage of eHealth-tools seems to indicate that there is a need for a more tailored approach to stimulate the use of eHealth-tools by PWE. Further research should focus on this aspect, e.g., what PWE need in order to make more use of eHealth-tools in their self-care. Copyright © 2016 Elsevier Inc. All rights reserved.

iTools: a framework for classification, categorization and integration of computational biology resources.

PubMed

Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

2008-05-28

The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

PubMed Central

Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

2008-01-01

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu. PMID:18509477

Configuration Management and Infrastructure Monitoring Using CFEngine and Icinga for Real-time Heterogeneous Data Taking Environment

NASA Astrophysics Data System (ADS)

Poat, M. D.; Lauret, J.; Betts, W.

2015-12-01

The STAR online computing environment is an intensive ever-growing system used for real-time data collection and analysis. Composed of heterogeneous and sometimes groups of custom-tuned machines, the computing infrastructure was previously managed by manual configurations and inconsistently monitored by a combination of tools. This situation led to configuration inconsistency and an overload of repetitive tasks along with lackluster communication between personnel and machines. Globally securing this heterogeneous cyberinfrastructure was tedious at best and an agile, policy-driven system ensuring consistency, was pursued. Three configuration management tools, Chef, Puppet, and CFEngine have been compared in reliability, versatility and performance along with a comparison of infrastructure monitoring tools Nagios and Icinga. STAR has selected the CFEngine configuration management tool and the Icinga infrastructure monitoring system leading to a versatile and sustainable solution. By leveraging these two tools STAR can now swiftly upgrade and modify the environment to its needs with ease as well as promptly react to cyber-security requests. By creating a sustainable long term monitoring solution, the detection of failures was reduced from days to minutes, allowing rapid actions before the issues become dire problems, potentially causing loss of precious experimental data or uptime.

Rapid Prototyping of Hydrologic Model Interfaces with IPython

NASA Astrophysics Data System (ADS)

Farthing, M. W.; Winters, K. D.; Ahmadia, A. J.; Hesser, T.; Howington, S. E.; Johnson, B. D.; Tate, J.; Kees, C. E.

2014-12-01

A significant gulf still exists between the state of practice and state of the art in hydrologic modeling. Part of this gulf is due to the lack of adequate pre- and post-processing tools for newly developed computational models. The development of user interfaces has traditionally lagged several years behind the development of a particular computational model or suite of models. As a result, models with mature interfaces often lack key advancements in model formulation, solution methods, and/or software design and technology. Part of the problem has been a focus on developing monolithic tools to provide comprehensive interfaces for the entire suite of model capabilities. Such efforts require expertise in software libraries and frameworks for creating user interfaces (e.g., Tcl/Tk, Qt, and MFC). These tools are complex and require significant investment in project resources (time and/or money) to use. Moreover, providing the required features for the entire range of possible applications and analyses creates a cumbersome interface. For a particular site or application, the modeling requirements may be simplified or at least narrowed, which can greatly reduce the number and complexity of options that need to be accessible to the user. However, monolithic tools usually are not adept at dynamically exposing specific workflows. Our approach is to deliver highly tailored interfaces to users. These interfaces may be site and/or process specific. As a result, we end up with many, customized interfaces rather than a single, general-use tool. For this approach to be successful, it must be efficient to create these tailored interfaces. We need technology for creating quality user interfaces that is accessible and has a low barrier for integration into model development efforts. Here, we present efforts to leverage IPython notebooks as tools for rapid prototyping of site and application-specific user interfaces. We provide specific examples from applications in near-shore environments as well as levee analysis. We discuss our design decisions and methodology for developing customized interfaces, strategies for delivery of the interfaces to users in various computing environments, as well as implications for the design/implementation of simulation models.

[Dietopro.com: a new tool for dietotherapeutical management based on cloud computing technology].

PubMed

García, Candido Gabriel; Sebastià, Natividad; Blasco, Esther; Soriano, José Miguel

2014-09-01

dietotherapeutical softwares are now a basic tool in the dietary management of patients, either from a physiological point of view and / or pathological. New technologies and research in this regard, have favored the emergence of new applications for the dietary and nutritional management that facilitate the management of the dietotherapeutical company. To comparatively study the main dietotherapeutical applications on the market to give criteria to the professional users of diet and nutrition in the selection of one of the main tools for these. Dietopro.com is, from our point of view, one of the most comprehensive management of patients dietotherapeutical applications. Based on the need of the user, it has different dietary sofwares choice.We conclude that there is no better or worse than another application, but applications roughly adapted to the needs of professionals. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Health literacy and usability of clinical trial search engines.

PubMed

Utami, Dina; Bickmore, Timothy W; Barry, Barbara; Paasche-Orlow, Michael K

2014-01-01

Several web-based search engines have been developed to assist individuals to find clinical trials for which they may be interested in volunteering. However, these search engines may be difficult for individuals with low health and computer literacy to navigate. The authors present findings from a usability evaluation of clinical trial search tools with 41 participants across the health and computer literacy spectrum. The study consisted of 3 parts: (a) a usability study of an existing web-based clinical trial search tool; (b) a usability study of a keyword-based clinical trial search tool; and (c) an exploratory study investigating users' information needs when deciding among 2 or more candidate clinical trials. From the first 2 studies, the authors found that users with low health literacy have difficulty forming queries using keywords and have significantly more difficulty using a standard web-based clinical trial search tool compared with users with adequate health literacy. From the third study, the authors identified the search factors most important to individuals searching for clinical trials and how these varied by health literacy level.

Integrated modeling of advanced optical systems

NASA Astrophysics Data System (ADS)

Briggs, Hugh C.; Needels, Laura; Levine, B. Martin

1993-02-01

This poster session paper describes an integrated modeling and analysis capability being developed at JPL under funding provided by the JPL Director's Discretionary Fund and the JPL Control/Structure Interaction Program (CSI). The posters briefly summarize the program capabilities and illustrate them with an example problem. The computer programs developed under this effort will provide an unprecedented capability for integrated modeling and design of high performance optical spacecraft. The engineering disciplines supported include structural dynamics, controls, optics and thermodynamics. Such tools are needed in order to evaluate the end-to-end system performance of spacecraft such as OSI, POINTS, and SMMM. This paper illustrates the proof-of-concept tools that have been developed to establish the technology requirements and demonstrate the new features of integrated modeling and design. The current program also includes implementation of a prototype tool based upon the CAESY environment being developed under the NASA Guidance and Control Research and Technology Computational Controls Program. This prototype will be available late in FY-92. The development plan proposes a major software production effort to fabricate, deliver, support and maintain a national-class tool from FY-93 through FY-95.

Review of Real-Time Simulator and the Steps Involved for Implementation of a Model from MATLAB/SIMULINK to Real-Time

NASA Astrophysics Data System (ADS)

Mikkili, Suresh; Panda, Anup Kumar; Prattipati, Jayanthi

2015-06-01

Nowadays the researchers want to develop their model in real-time environment. Simulation tools have been widely used for the design and improvement of electrical systems since the mid twentieth century. The evolution of simulation tools has progressed in step with the evolution of computing technologies. In recent years, computing technologies have improved dramatically in performance and become widely available at a steadily decreasing cost. Consequently, simulation tools have also seen dramatic performance gains and steady cost decreases. Researchers and engineers now have the access to affordable, high performance simulation tools that were previously too cost prohibitive, except for the largest manufacturers. This work has introduced a specific class of digital simulator known as a real-time simulator by answering the questions "what is real-time simulation", "why is it needed" and "how it works". The latest trend in real-time simulation consists of exporting simulation models to FPGA. In this article, the Steps involved for implementation of a model from MATLAB to REAL-TIME are provided in detail.

Integrating Cache Performance Modeling and Tuning Support in Parallelization Tools

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

With the resurgence of distributed shared memory (DSM) systems based on cache-coherent Non Uniform Memory Access (ccNUMA) architectures and increasing disparity between memory and processors speeds, data locality overheads are becoming the greatest bottlenecks in the way of realizing potential high performance of these systems. While parallelization tools and compilers facilitate the users in porting their sequential applications to a DSM system, a lot of time and effort is needed to tune the memory performance of these applications to achieve reasonable speedup. In this paper, we show that integrating cache performance modeling and tuning support within a parallelization environment can alleviate this problem. The Cache Performance Modeling and Prediction Tool (CPMP), employs trace-driven simulation techniques without the overhead of generating and managing detailed address traces. CPMP predicts the cache performance impact of source code level "what-if" modifications in a program to assist a user in the tuning process. CPMP is built on top of a customized version of the Computer Aided Parallelization Tools (CAPTools) environment. Finally, we demonstrate how CPMP can be applied to tune a real Computational Fluid Dynamics (CFD) application.

Computational chemistry

NASA Technical Reports Server (NTRS)

Arnold, J. O.

1987-01-01

With the advent of supercomputers, modern computational chemistry algorithms and codes, a powerful tool was created to help fill NASA's continuing need for information on the properties of matter in hostile or unusual environments. Computational resources provided under the National Aerodynamics Simulator (NAS) program were a cornerstone for recent advancements in this field. Properties of gases, materials, and their interactions can be determined from solutions of the governing equations. In the case of gases, for example, radiative transition probabilites per particle, bond-dissociation energies, and rates of simple chemical reactions can be determined computationally as reliably as from experiment. The data are proving to be quite valuable in providing inputs to real-gas flow simulation codes used to compute aerothermodynamic loads on NASA's aeroassist orbital transfer vehicles and a host of problems related to the National Aerospace Plane Program. Although more approximate, similar solutions can be obtained for ensembles of atoms simulating small particles of materials with and without the presence of gases. Computational chemistry has application in studying catalysis, properties of polymers, all of interest to various NASA missions, including those previously mentioned. In addition to discussing these applications of computational chemistry within NASA, the governing equations and the need for supercomputers for their solution is outlined.

IDEAS: A multidisciplinary computer-aided conceptual design system for spacecraft

NASA Technical Reports Server (NTRS)

Ferebee, M. J., Jr.

1984-01-01

During the conceptual development of advanced aerospace vehicles, many compromises must be considered to balance economy and performance of the total system. Subsystem tradeoffs may need to be made in order to satisfy system-sensitive attributes. Due to the increasingly complex nature of aerospace systems, these trade studies have become more difficult and time-consuming to complete and involve interactions of ever-larger numbers of subsystems, components, and performance parameters. The current advances of computer-aided synthesis, modeling and analysis techniques have greatly helped in the evaluation of competing design concepts. Langley Research Center's Space Systems Division is currently engaged in trade studies for a variety of systems which include advanced ground-launched space transportation systems, space-based orbital transfer vehicles, large space antenna concepts and space stations. The need for engineering analysis tools to aid in the rapid synthesis and evaluation of spacecraft has led to the development of the Interactive Design and Evaluation of Advanced Spacecraft (IDEAS) computer-aided design system. The ADEAS system has been used to perform trade studies of competing technologies and requirements in order to pinpoint possible beneficial areas for research and development. IDEAS is presented as a multidisciplinary tool for the analysis of advanced space systems. Capabilities range from model generation and structural and thermal analysis to subsystem synthesis and performance analysis.

Strategy and gaps for modeling, simulation, and control of hybrid systems

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

Rabiti, Cristian; Garcia, Humberto E.; Hovsapian, Rob

2015-04-01

The purpose of this report is to establish a strategy for modeling and simulation of candidate hybrid energy systems. Modeling and simulation is necessary to design, evaluate, and optimize the system technical and economic performance. Accordingly, this report first establishes the simulation requirements to analysis candidate hybrid systems. Simulation fidelity levels are established based on the temporal scale, real and synthetic data availability or needs, solution accuracy, and output parameters needed to evaluate case-specific figures of merit. Accordingly, the associated computational and co-simulation resources needed are established; including physical models when needed, code assembly and integrated solutions platforms, mathematical solvers,more » and data processing. This report first attempts to describe the figures of merit, systems requirements, and constraints that are necessary and sufficient to characterize the grid and hybrid systems behavior and market interactions. Loss of Load Probability (LOLP) and effective cost of Effective Cost of Energy (ECE), as opposed to the standard Levelized Cost of Electricty (LCOE), are introduced as technical and economical indices for integrated energy system evaluations. Financial assessment methods are subsequently introduced for evaluation of non-traditional, hybrid energy systems. Algorithms for coupled and iterative evaluation of the technical and economic performance are subsequently discussed. This report further defines modeling objectives, computational tools, solution approaches, and real-time data collection and processing (in some cases using real test units) that will be required to model, co-simulate, and optimize; (a) an energy system components (e.g., power generation unit, chemical process, electricity management unit), (b) system domains (e.g., thermal, electrical or chemical energy generation, conversion, and transport), and (c) systems control modules. Co-simulation of complex, tightly coupled, dynamic energy systems requires multiple simulation tools, potentially developed in several programming languages and resolved on separate time scales. Whereas further investigation and development of hybrid concepts will provide a more complete understanding of the joint computational and physical modeling needs, this report highlights areas in which co-simulation capabilities are warranted. The current development status, quality assurance, availability and maintainability of simulation tools that are currently available for hybrid systems modeling is presented. Existing gaps in the modeling and simulation toolsets and development needs are subsequently discussed. This effort will feed into a broader Roadmap activity for designing, developing, and demonstrating hybrid energy systems.« less

Parallel computing for automated model calibration

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

Burke, John S.; Danielson, Gary R.; Schulz, Douglas A.

2002-07-29

Natural resources model calibration is a significant burden on computing and staff resources in modeling efforts. Most assessments must consider multiple calibration objectives (for example magnitude and timing of stream flow peak). An automated calibration process that allows real time updating of data/models, allowing scientists to focus effort on improving models is needed. We are in the process of building a fully featured multi objective calibration tool capable of processing multiple models cheaply and efficiently using null cycle computing. Our parallel processing and calibration software routines have been generically, but our focus has been on natural resources model calibration. Somore » far, the natural resources models have been friendly to parallel calibration efforts in that they require no inter-process communication, only need a small amount of input data and only output a small amount of statistical information for each calibration run. A typical auto calibration run might involve running a model 10,000 times with a variety of input parameters and summary statistical output. In the past model calibration has been done against individual models for each data set. The individual model runs are relatively fast, ranging from seconds to minutes. The process was run on a single computer using a simple iterative process. We have completed two Auto Calibration prototypes and are currently designing a more feature rich tool. Our prototypes have focused on running the calibration in a distributed computing cross platform environment. They allow incorporation of?smart? calibration parameter generation (using artificial intelligence processing techniques). Null cycle computing similar to SETI@Home has also been a focus of our efforts. This paper details the design of the latest prototype and discusses our plans for the next revision of the software.« less

Examples of Effective Data Sharing in Scientific Publishing

DOE PAGES

Kitchin, John R.

2015-05-11

Here, we present a perspective on an approach to data sharing in scientific publications we have been developing in our group. The essence of the approach is that data can be embedded in a human-readable and machine-addressable way within the traditional publishing environment. We show this by example for both computational and experimental data. We articulate a need for new authoring tools to facilitate data sharing, and we discuss the tools we have been developing for this purpose. With these tools, data generation, analysis, and manuscript preparation can be deeply integrated, resulting in easier and better data sharing in scientificmore » publications.« less

Application of modern tools and techniques to maximize engineering productivity in the development of orbital operations plans for the space station progrm

NASA Technical Reports Server (NTRS)

Manford, J. S.; Bennett, G. R.

1985-01-01

The Space Station Program will incorporate analysis of operations constraints and considerations in the early design phases to avoid the need for later modifications to the Space Station for operations. The application of modern tools and administrative techniques to minimize the cost of performing effective orbital operations planning and design analysis in the preliminary design phase of the Space Station Program is discussed. Tools and techniques discussed include: approach for rigorous analysis of operations functions, use of the resources of a large computer network, and providing for efficient research and access to information.

3D Graphics Through the Internet: A "Shoot-Out"

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

3D graphics through the Internet needs to move beyond the current lowest common denominator of pre-computed movies, which consume bandwidth and are non-interactive. Panelists will demonstrate and compare 3D graphical tools for accessing, analyzing, and collaborating on information through the Internet and World-wide web. The "shoot-out" will illustrate which tools are likely to be the best for the various types of information, including dynamic scientific data, 3-D objects, and virtual environments. The goal of the panel is to encourage more effective use of the Internet by encouraging suppliers and users of information to adopt the next generation of graphical tools.

Open-source tools for data mining.

PubMed

Zupan, Blaz; Demsar, Janez

2008-03-01

With a growing volume of biomedical databases and repositories, the need to develop a set of tools to address their analysis and support knowledge discovery is becoming acute. The data mining community has developed a substantial set of techniques for computational treatment of these data. In this article, we discuss the evolution of open-source toolboxes that data mining researchers and enthusiasts have developed over the span of a few decades and review several currently available open-source data mining suites. The approaches we review are diverse in data mining methods and user interfaces and also demonstrate that the field and its tools are ready to be fully exploited in biomedical research.

Examples of Effective Data Sharing in Scientific Publishing

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

Kitchin, John R.

Here, we present a perspective on an approach to data sharing in scientific publications we have been developing in our group. The essence of the approach is that data can be embedded in a human-readable and machine-addressable way within the traditional publishing environment. We show this by example for both computational and experimental data. We articulate a need for new authoring tools to facilitate data sharing, and we discuss the tools we have been developing for this purpose. With these tools, data generation, analysis, and manuscript preparation can be deeply integrated, resulting in easier and better data sharing in scientificmore » publications.« less

Synergies and Distinctions between Computational Disciplines in Biomedical Research: Perspective from the Clinical and Translational Science Award Programs

PubMed Central

Bernstam, Elmer V.; Hersh, William R.; Johnson, Stephen B.; Chute, Christopher G.; Nguyen, Hien; Sim, Ida; Nahm, Meredith; Weiner, Mark; Miller, Perry; DiLaura, Robert P.; Overcash, Marc; Lehmann, Harold P.; Eichmann, David; Athey, Brian D.; Scheuermann, Richard H.; Anderson, Nick; Starren, Justin B.; Harris, Paul A.; Smith, Jack W.; Barbour, Ed; Silverstein, Jonathan C.; Krusch, David A.; Nagarajan, Rakesh; Becich, Michael J.

2010-01-01

Clinical and translational research increasingly requires computation. Projects may involve multiple computationally-oriented groups including information technology (IT) professionals, computer scientists and biomedical informaticians. However, many biomedical researchers are not aware of the distinctions among these complementary groups, leading to confusion, delays and sub-optimal results. Although written from the perspective of clinical and translational science award (CTSA) programs within academic medical centers, the paper addresses issues that extend beyond clinical and translational research. The authors describe the complementary but distinct roles of operational IT, research IT, computer science and biomedical informatics using a clinical data warehouse as a running example. In general, IT professionals focus on technology. The authors distinguish between two types of IT groups within academic medical centers: central or administrative IT (supporting the administrative computing needs of large organizations) and research IT (supporting the computing needs of researchers). Computer scientists focus on general issues of computation such as designing faster computers or more efficient algorithms, rather than specific applications. In contrast, informaticians are concerned with data, information and knowledge. Biomedical informaticians draw on a variety of tools, including but not limited to computers, to solve information problems in health care and biomedicine. The paper concludes with recommendations regarding administrative structures that can help to maximize the benefit of computation to biomedical research within academic health centers. PMID:19550198

Integrating Reconfigurable Hardware-Based Grid for High Performance Computing

PubMed Central

Dondo Gazzano, Julio; Sanchez Molina, Francisco; Rincon, Fernando; López, Juan Carlos

2015-01-01

FPGAs have shown several characteristics that make them very attractive for high performance computing (HPC). The impressive speed-up factors that they are able to achieve, the reduced power consumption, and the easiness and flexibility of the design process with fast iterations between consecutive versions are examples of benefits obtained with their use. However, there are still some difficulties when using reconfigurable platforms as accelerator that need to be addressed: the need of an in-depth application study to identify potential acceleration, the lack of tools for the deployment of computational problems in distributed hardware platforms, and the low portability of components, among others. This work proposes a complete grid infrastructure for distributed high performance computing based on dynamically reconfigurable FPGAs. Besides, a set of services designed to facilitate the application deployment is described. An example application and a comparison with other hardware and software implementations are shown. Experimental results show that the proposed architecture offers encouraging advantages for deployment of high performance distributed applications simplifying development process. PMID:25874241

A service-based BLAST command tool supported by cloud infrastructures.

PubMed

Carrión, Abel; Blanquer, Ignacio; Hernández, Vicente

2012-01-01

Notwithstanding the benefits of distributed-computing infrastructures for empowering bioinformatics analysis tools with the needed computing and storage capability, the actual use of these infrastructures is still low. Learning curves and deployment difficulties have reduced the impact on the wide research community. This article presents a porting strategy of BLAST based on a multiplatform client and a service that provides the same interface as sequential BLAST, thus reducing learning curve and with minimal impact on their integration on existing workflows. The porting has been done using the execution and data access components from the EC project Venus-C and the Windows Azure infrastructure provided in this project. The results obtained demonstrate a low overhead on the global execution framework and reasonable speed-up and cost-efficiency with respect to a sequential version.

The use of elearning in medical education: a review of the current situation.

PubMed

Choules, A P

2007-04-01

Computers are increasingly used in medical education. Electronic learning (elearning) is moving from textbooks in electronic format (that are increasingly enhanced by the use of multimedia adjuncts) to a truly interactive medium that can be delivered to meet the educational needs of students and postgraduate learners. Computer technology can present reliable, reusable content in a format that is convenient to the learner. It can be used to transcend geographical boundaries and time zones. It is a valuable tool to add to the medical teacher's toolkit, but like all tools it must be used appropriately. This article endeavours to review the current "state of the art2 in use of elearning and its role in medical education alongside non-electronic methods-a combination that is currently referred to as "blended" learning.

Thermal Analysis of Magnetically-Coupled Pump for Cryogenic Applications

NASA Technical Reports Server (NTRS)

Senocak, Inanc; Udaykumar, H. S.; Ndri, Narcisse; Francois, Marianne; Shyy, Wei

1999-01-01

Magnetically-coupled pump is under evaluation at Kennedy Space Center for possible cryogenic applications. A major concern is the impact of low temperature fluid flows on the pump performance. As a first step toward addressing this and related issues, a computational fluid dynamics and heat transfer tool has been adopted in a pump geometry. The computational tool includes (i) a commercial grid generator to handle multiple grid blocks and complicated geometric definitions, and (ii) an in-house computational fluid dynamics and heat transfer software developed in the Principal Investigator's group at the University of Florida. Both pure-conduction and combined convection-conduction computations have been conducted. A pure-conduction analysis gives insufficient information about the overall thermal distribution. Combined convection-conduction analysis indicates the significant influence of the coolant over the entire flow path. Since 2-D simulation is of limited help, future work on full 3-D modeling of the pump using multi-materials is needed. A comprehensive and accurate model can be developed to take into account the effect of multi-phase flow in the cooling flow loop, and the magnetic interactions.

Addressing Unmet Need for HIV Testing in Emergency Care Settings: A Role for Computer-facilitated Rapid HIV Testing?

PubMed Central

Kurth, Ann E.; Severynen, Anneleen; Spielberg, Freya

2014-01-01

HIV testing in emergency departments (EDs) remains underutilized. We evaluated a computer tool to facilitate rapid HIV testing in an urban ED. Randomly assigned non-acute adult ED patients to computer tool (‘CARE’) and rapid HIV testing before standard visit (n=258) or to standard visit (n=259) with chart access. Assessed intervention acceptability and compared noted HIV risks. Participants were 56% non-white, 58% male; median age 37 years. In the CARE arm nearly all (251/258) completed the session and received HIV results; 4 declined test consent. HIV risks were reported by 54% of users and there was one confirmed HIV-positive and 2 false-positives (seroprevalence 0.4%, 95% CI 0.01–2.2%). Half (55%) preferred computerized, over face-to-face, counseling for future HIV testing. In standard arm, one HIV test and 2 referrals for testing occurred. Computer-facilitated HIV testing appears acceptable to ED patients. Future research should assess cost-effectiveness compared with staff-delivered approaches. PMID:23837807

Enhancing reading abilities of learners with intellectual impairments through computer technology

PubMed Central

Warnick, Albert M.

2017-01-01

Background Developments in the teaching of children with disabilities support pedagogy that emphasises learners’ strengths as opposed to their assumed deficiencies. Educators and mediators who advocate this view continually strive for tools and methodologies that enhance learner participation in academic environments. Computer technology is one of the tools recognised for its potential to enrich learning experiences of learners with an intellectual impairment. Objectives We sought to assess the influence of text-to-speech stories on the reading ability of intellectually challenged learners. Method A qualitative action research study that involves learners at a special school in Cape Town, South Africa. Pre- and post-test data of the reading performance of learners are analysed with a focus on how they demonstrate change. Results Although no claims can be made about the explicit influence on reading performance, computer-assisted learning has the potential in isolating reading processes that classroom-based interventions can address. In addition, computers enhance motivation and enthusiasm to learn. Conclusion A need for education based on inclusion and positive differentiation remains the key driver in any educational interventions. PMID:28951849

VisRseq: R-based visual framework for analysis of sequencing data

PubMed Central

2015-01-01

Background Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. Results We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. We achieve this aim by providing R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, our framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows. Conclusions To validate the usability of VisRseq for analysis of sequencing data, we present two case studies performed by our collaborators and report their workflow and insights. PMID:26328469

VisRseq: R-based visual framework for analysis of sequencing data.

PubMed

Younesy, Hamid; Möller, Torsten; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

2015-01-01

Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. We achieve this aim by providing R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, our framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows. To validate the usability of VisRseq for analysis of sequencing data, we present two case studies performed by our collaborators and report their workflow and insights.

S-MART, a software toolbox to aid RNA-Seq data analysis.

PubMed

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci.

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

PubMed Central

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci. PMID:21998740

Adaptation of a Control Center Development Environment for Industrial Process Control

NASA Technical Reports Server (NTRS)

Killough, Ronnie L.; Malik, James M.

1994-01-01

In the control center, raw telemetry data is received for storage, display, and analysis. This raw data must be combined and manipulated in various ways by mathematical computations to facilitate analysis, provide diversified fault detection mechanisms, and enhance display readability. A development tool called the Graphical Computation Builder (GCB) has been implemented which provides flight controllers with the capability to implement computations for use in the control center. The GCB provides a language that contains both general programming constructs and language elements specifically tailored for the control center environment. The GCB concept allows staff who are not skilled in computer programming to author and maintain computer programs. The GCB user is isolated from the details of external subsystem interfaces and has access to high-level functions such as matrix operators, trigonometric functions, and unit conversion macros. The GCB provides a high level of feedback during computation development that improves upon the often cryptic errors produced by computer language compilers. An equivalent need can be identified in the industrial data acquisition and process control domain: that of an integrated graphical development tool tailored to the application to hide the operating system, computer language, and data acquisition interface details. The GCB features a modular design which makes it suitable for technology transfer without significant rework. Control center-specific language elements can be replaced by elements specific to industrial process control.

Simulation of the Physics of Flight

ERIC Educational Resources Information Center

Lane, W. Brian

2013-01-01

Computer simulations continue to prove to be a valuable tool in physics education. Based on the needs of an Aviation Physics course, we developed the PHYSics of FLIght Simulator (PhysFliS), which numerically solves Newton's second law for an airplane in flight based on standard aerodynamics relationships. The simulation can be used to pique…

The PLATO System: A Study in the Diffusion of an Innovation.

ERIC Educational Resources Information Center

Driscoll, Francis D.; Wolf, W. C., Jr.

This study was designed to ascertain the relationships between the steps of a tool designed to link knowledge production and the needs of knowledge users (the Wolf-Welsh Linkage Methodology or WWLM) with milestones in the evolution of an innovative computer-assisted instructional system called PLATO (Programming Logic for Advanced Teaching…

Exploring Cloud Computing Tools to Enhance Team-Based Problem Solving for Challenging Behavior

ERIC Educational Resources Information Center

Johnson, LeAnne D.

2017-01-01

Data-driven decision making is central to improving success of children. Actualizing the use of data is challenging when addressing the social, emotional, and behavioral needs of children across different types of early childhood programs (i.e., early childhood special education, early childhood family education, Head Start, and childcare).…

Modeling of the Global Water Cycle - Analytical Models

Treesearch

Yongqiang Liu; Roni Avissar

2005-01-01

Both numerical and analytical models of coupled atmosphere and its underlying ground components (land, ocean, ice) are useful tools for modeling the global and regional water cycle. Unlike complex three-dimensional climate models, which need very large computing resources and involve a large number of complicated interactions often difficult to interpret, analytical...

QR Codes in Higher Ed: Fad or Functional Tool?

ERIC Educational Resources Information Center

Gradel, Kathleen; Edson, Alden J.

2013-01-01

As higher education grapples with addressing the 21st century needs of learners, technology is a pervasive concern. Waters (2012) painted a picture of three historical "screens," namely the television screen, the computer monitor, and today's mobile device screen. As mobile devices become increasingly commonplace in the workplace and on the…

Readerbench: Automated Evaluation of Collaboration Based on Cohesion and Dialogism

ERIC Educational Resources Information Center

Dascalu, Mihai; Trausan-Matu, Stefan; McNamara, Danielle S.; Dessus, Philippe

2015-01-01

As Computer-Supported Collaborative Learning (CSCL) gains a broader usage, the need for automated tools capable of supporting tutors in the time-consuming process of analyzing conversations becomes more pressing. Moreover, collaboration, which presumes the intertwining of ideas or points of view among participants, is a central element of dialogue…

Using Computer Simulations for Promoting Model-Based Reasoning: Epistemological and Educational Dimensions

ERIC Educational Resources Information Center

Develaki, Maria

2017-01-01

Scientific reasoning is particularly pertinent to science education since it is closely related to the content and methodologies of science and contributes to scientific literacy. Much of the research in science education investigates the appropriate framework and teaching methods and tools needed to promote students' ability to reason and…

User friendly tools to target vulnerable areas at watershed scale: evaluation of the soil vulnerability and conductivity claypan indices

USDA-ARS?s Scientific Manuscript database

One finding of the Conservation Effects Assessment Program (CEAP) watershed studies was that Best Management practices (BMPs) were not always installed where most needed: in many watersheds, only a fraction of BMPs were implemented in the most vulnerable areas. While complex computer simulation mode...

Models, Databases, and Simulation Tools Needed for the Realization of Integrated Computational Materials Engineering. Proceedings of the Symposium Held at Materials Science and Technology 2010

NASA Technical Reports Server (NTRS)

Arnold, Steven M. (Editor); Wong, Terry T. (Editor)

2011-01-01

Topics covered include: An Annotative Review of Multiscale Modeling and its Application to Scales Inherent in the Field of ICME; and A Multiscale, Nonlinear, Modeling Framework Enabling the Design and Analysis of Composite Materials and Structures.

Exposure to Phthalate Emitted from Vinyl Flooring and Sorbed to Interior Surfaces, Dust, Airborne Particles and Human Skin

EPA Science Inventory

There is an urgent need to characterize potential risk to human health and the environment that arises from the manufacture and use of tens of thousands of chemicals. Computational tools and approaches for characterizing and prioritizing exposure are required: to provide input f...

Personal Computer-less (PC-less) Microcontroller Training Kit

NASA Astrophysics Data System (ADS)

Somantri, Y.; Wahyudin, D.; Fushilat, I.

2018-02-01

The need of microcontroller training kit is necessary for practical work of students of electrical engineering education. However, to use available training kit not only costly but also does not meet the need of laboratory requirements. An affordable and portable microcontroller kit could answer such problem. This paper explains the design and development of Personal Computer Less (PC-Less) Microcontroller Training Kit. It was developed based on Lattepanda processor and Arduino microcontroller as target. The training kit equipped with advanced input-output interfaces that adopted the concept of low cost and low power system. The preliminary usability testing proved this device can be used as a tool for microcontroller programming and industrial automation training. By adopting the concept of portability, the device could be operated in the rural area which electricity and computer infrastructure are limited. Furthermore, the training kit is suitable for student of electrical engineering student from university and vocational high school.

Development of computational small animal models and their applications in preclinical imaging and therapy research.

PubMed

Xie, Tianwu; Zaidi, Habib

2016-01-01

The development of multimodality preclinical imaging techniques and the rapid growth of realistic computer simulation tools have promoted the construction and application of computational laboratory animal models in preclinical research. Since the early 1990s, over 120 realistic computational animal models have been reported in the literature and used as surrogates to characterize the anatomy of actual animals for the simulation of preclinical studies involving the use of bioluminescence tomography, fluorescence molecular tomography, positron emission tomography, single-photon emission computed tomography, microcomputed tomography, magnetic resonance imaging, and optical imaging. Other applications include electromagnetic field simulation, ionizing and nonionizing radiation dosimetry, and the development and evaluation of new methodologies for multimodality image coregistration, segmentation, and reconstruction of small animal images. This paper provides a comprehensive review of the history and fundamental technologies used for the development of computational small animal models with a particular focus on their application in preclinical imaging as well as nonionizing and ionizing radiation dosimetry calculations. An overview of the overall process involved in the design of these models, including the fundamental elements used for the construction of different types of computational models, the identification of original anatomical data, the simulation tools used for solving various computational problems, and the applications of computational animal models in preclinical research. The authors also analyze the characteristics of categories of computational models (stylized, voxel-based, and boundary representation) and discuss the technical challenges faced at the present time as well as research needs in the future.

Instability Mechanisms of Thermally-Driven Interfacial Flows in Liquid-Encapsulated Crystal Growth

NASA Technical Reports Server (NTRS)

Haj-Hariri, Hossein; Borhan, Ali

1997-01-01

During the past year, a great deal of effort was focused on the enhancement and refinement of the computational tools developed as part of our previous NASA grant. In particular, the interface mollification algorithm developed earlier was extended to incorporate the effects of surface-rheological properties in order to allow the study of thermocapillary flows in the presence of surface contamination. These tools will be used in the computational component of the proposed research in the remaining years of this grant. A detailed description of the progress made in this area is provided elsewhere. Briefly, the method developed allows for the convection and diffusion of bulk-insoluble surfactants on a moving and deforming interface. The novelty of the method is its grid independence: there is no need for front tracking, surface reconstruction, body-fitted grid generation, or metric evaluations; these are all very expensive computational tasks in three dimensions. For small local radii of curvature there is a need for local grid adaption so that the smearing thickness remains a small fraction of the radius of curvature. A special Neumann boundary condition was devised and applied so that the calculated surfactant concentration has no variations normal to the interface, and it is hence truly a surface-defined quantity. The discretized governing equations are solved subsequently using a time-split integration scheme which updates the concentration and the shape successively. Results demonstrate excellent agreement between the computed and exact solutions.

CANARY Risk Management of Adenocarcinoma: The Future of Imaging?

PubMed Central

Foley, Finbar; Rajagopalan, Srinivasan; Raghunath, Sushravya M; Boland, Jennifer M; Karwoski, Ronald A.; Maldonado, Fabien; Bartholmai, Brian J; Peikert, Tobias

2016-01-01

Increased clinical utilization of chest high resolution computed tomography results in increased identification of lung adenocarcinomas and persistent sub-solid opacities. However, these lesions range from very indolent to extremely aggressive tumors. Clinically relevant diagnostic tools to non-invasively risk stratify and guide individualized management of these lesions are lacking. Research efforts investigating semi-quantitative measures to decrease inter- and intra-rater variability are emerging, and in some cases steps have been taken to automate this process. However, many such methods currently are still sub-optimal, require validation and are not yet clinically applicable. The Computer-Aided Nodule Assessment and Risk Yield (CANARY) software application represents a validated tool for the automated, quantitative, non-invasive tool for risk stratification of adenocarcinoma lung nodules. CANARY correlates well with consensus histology and post-surgical patient outcomes and therefore may help to guide individualized patient management e.g. in identification of nodules amenable to radiological surveillance, or in need of adjunctive therapy. PMID:27568149

Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library Design.

PubMed

Huang, Wenkang; Nussinov, Ruth; Zhang, Jian

2017-01-01

Allostery is an intrinsic phenomenon of biological macromolecules involving regulation and/or signal transduction induced by a ligand binding to an allosteric site distinct from a molecule's active site. Allosteric drugs are currently receiving increased attention in drug discovery because drugs that target allosteric sites can provide important advantages over the corresponding orthosteric drugs including specific subtype selectivity within receptor families. Consequently, targeting allosteric sites, instead of orthosteric sites, can reduce drug-related side effects and toxicity. On the down side, allosteric drug discovery can be more challenging than traditional orthosteric drug discovery due to difficulties associated with determining the locations of allosteric sites and designing drugs based on these sites and the need for the allosteric effects to propagate through the structure, reach the ligand binding site and elicit a conformational change. In this study, we present computational tools ranging from the identification of potential allosteric sites to the design of "allosteric-like" modulator libraries. These tools may be particularly useful for allosteric drug discovery.

RF Models for Plasma-Surface Interactions in VSim

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, D. N.; Pankin, A. Y.; Roark, C. M.; Zhou, C. D.; Stoltz, P. H.; Kruger, S. E.

2014-10-01

An overview of ongoing enhancements to the Plasma Discharge (PD) module of Tech-X's VSim software tool is presented. A sub-grid kinetic sheath model, developed for the accurate computation of sheath potentials near metal and dielectric-coated walls, enables the physical effects of DC and RF sheath physics to be included in macroscopic-scale plasma simulations that need not explicitly resolve sheath scale lengths. Sheath potential evolution, together with particle behavior near the sheath, can thus be simulated in complex geometries. Generalizations of the model to include sputtering, secondary electron emission, and effects from multiple ion species and background magnetic fields are summarized; related numerical results are also presented. In addition, improved tools for plasma chemistry and IEDF/EEDF visualization and modeling are discussed, as well as our initial efforts toward the development of hybrid fluid/kinetic transition capabilities within VSim. Ultimately, we aim to establish VSimPD as a robust, efficient computational tool for modeling industrial plasma processes. Supported by US DoE SBIR-I/II Award DE-SC0009501.

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data.

PubMed

Parker, Nicolas J; Parker, Andrew G

2008-04-18

The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, Glossina pallidipes, we found the need for tools to search quickly a set of reads for near exact text matches. A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads. Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension. The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.

Tools and resources for neuroanatomy education: a systematic review.

PubMed

Arantes, M; Arantes, J; Ferreira, M A

2018-05-03

The aim of this review was to identify studies exploring neuroanatomy teaching tools and their impact in learning, as a basis towards the implementation of a neuroanatomy program in the context of a curricular reform in medical education. Computer-assisted searches were conducted through March 2017 in the PubMed, Web of Science, Medline, Current Contents Connect, KCI and Scielo Citation Index databases. Four sets of keywords were used, combining "neuroanatomy" with "education", "teaching", "learning" and "student*". Studies were reviewed independently by two readers, and data collected were confirmed by a third reader. Of the 214 studies identified, 29 studies reported data on the impact of using specific neuroanatomy teaching tools. Most of them (83%) were published in the last 8 years and were conducted in the United States of America (65.52%). Regarding the participants, medical students were the most studied sample (37.93%) and the majority of the studies (65.52%) had less than 100 participants. Approximately half of the studies included in this review used digital teaching tools (e.g., 3D computer neuroanatomy models), whereas the remaining used non-digital learning tools (e.g., 3D physical models). Our work highlight the progressive interest in the study of neuroanatomy teaching tools over the last years, as evidenced from the number of publications and highlight the need to consider new tools, coping with technological development in medical education.

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

Architecture independent environment for developing engineering software on MIMD computers

NASA Technical Reports Server (NTRS)

Valimohamed, Karim A.; Lopez, L. A.

1990-01-01

Engineers are constantly faced with solving problems of increasing complexity and detail. Multiple Instruction stream Multiple Data stream (MIMD) computers have been developed to overcome the performance limitations of serial computers. The hardware architectures of MIMD computers vary considerably and are much more sophisticated than serial computers. Developing large scale software for a variety of MIMD computers is difficult and expensive. There is a need to provide tools that facilitate programming these machines. First, the issues that must be considered to develop those tools are examined. The two main areas of concern were architecture independence and data management. Architecture independent software facilitates software portability and improves the longevity and utility of the software product. It provides some form of insurance for the investment of time and effort that goes into developing the software. The management of data is a crucial aspect of solving large engineering problems. It must be considered in light of the new hardware organizations that are available. Second, the functional design and implementation of a software environment that facilitates developing architecture independent software for large engineering applications are described. The topics of discussion include: a description of the model that supports the development of architecture independent software; identifying and exploiting concurrency within the application program; data coherence; engineering data base and memory management.

Health Literacy Assessment of the STOFHLA: Paper versus electronic administration continuation study.

PubMed

Chesser, Amy K; Keene Woods, Nikki; Wipperman, Jennifer; Wilson, Rachel; Dong, Frank

2014-02-01

Low health literacy is associated with poor health outcomes. Research is needed to understand the mechanisms and pathways of its effects. Computer-based assessment tools may improve efficiency and cost-effectiveness of health literacy research. The objective of this preliminary study was to assess if administration of the Short Test of Functional Health Literacy in Adults (STOFHLA) through a computer-based medium was comparable to the paper-based test in terms of accuracy and time to completion. A randomized, crossover design was used to compare computer versus paper format of the STOFHLA at a Midwestern family medicine residency program. Eighty participants were initially randomized to either computer (n = 42) or paper (n = 38) format of the STOFHLA. After a 30-day washout period, participants returned to complete the other version of the STOFHLA. Data analysis revealed no significant difference between paper- and computer-based surveys (p = .9401; N = 57). The majority of participants showed "adequate" health literacy via paper- and computer-based surveys (100% and 97% of participants, respectively). Electronic administration of STOFHLA results were equivalent to the paper administration results for evaluation of adult health literacy. Future investigations should focus on expanded populations in multiple health care settings and validation of other health literacy screening tools in a clinical setting.

Access and visualization using clusters and other parallel computers

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Bergou, Attila; Berriman, Bruce; Block, Gary; Collier, Jim; Curkendall, Dave; Good, John; Husman, Laura; Jacob, Joe; Laity, Anastasia;

Paranoia.Ada: A diagnostic program to evaluate Ada floating-point arithmetic

NASA Technical Reports Server (NTRS)

Hjermstad, Chris

1986-01-01

Many essential software functions in the mission critical computer resource application domain depend on floating point arithmetic. Numerically intensive functions associated with the Space Station project, such as emphemeris generation or the implementation of Kalman filters, are likely to employ the floating point facilities of Ada. Paranoia.Ada appears to be a valuabe program to insure that Ada environments and their underlying hardware exhibit the precision and correctness required to satisfy mission computational requirements. As a diagnostic tool, Paranoia.Ada reveals many essential characteristics of an Ada floating point implementation. Equipped with such knowledge, programmers need not tremble before the complex task of floating point computation.

High-resolution PET [Positron Emission Tomography] for Medical Science Studies

DOE R&D Accomplishments Database

Budinger, T. F.; Derenzo, S. E.; Huesman, R. H.; Jagust, W. J.; Valk, P. E.

1989-09-01

One of the unexpected fruits of basic physics research and the computer revolution is the noninvasive imaging power available to today's physician. Technologies that were strictly the province of research scientists only a decade or two ago now serve as the foundations for such standard diagnostic tools as x-ray computer tomography (CT), magnetic resonance imaging (MRI), magnetic resonance spectroscopy (MRS), ultrasound, single photon emission computed tomography (SPECT), and positron emission tomography (PET). Furthermore, prompted by the needs of both the practicing physician and the clinical researcher, efforts to improve these technologies continue. This booklet endeavors to describe the advantages of achieving high resolution in PET imaging.

Visualization and Analytics Tools for Infectious Disease Epidemiology: A Systematic Review

PubMed Central

Carroll, Lauren N.; Au, Alan P.; Detwiler, Landon Todd; Fu, Tsung-chieh; Painter, Ian S.; Abernethy, Neil F.

2014-01-01

Background A myriad of new tools and algorithms have been developed to help public health professionals analyze and visualize the complex data used in infectious disease control. To better understand approaches to meet these users' information needs, we conducted a systematic literature review focused on the landscape of infectious disease visualization tools for public health professionals, with a special emphasis on geographic information systems (GIS), molecular epidemiology, and social network analysis. The objectives of this review are to: (1) Identify public health user needs and preferences for infectious disease information visualization tools; (2) Identify existing infectious disease information visualization tools and characterize their architecture and features; (3) Identify commonalities among approaches applied to different data types; and (4) Describe tool usability evaluation efforts and barriers to the adoption of such tools. Methods We identified articles published in English from January 1, 1980 to June 30, 2013 from five bibliographic databases. Articles with a primary focus on infectious disease visualization tools, needs of public health users, or usability of information visualizations were included in the review. Results A total of 88 articles met our inclusion criteria. Users were found to have diverse needs, preferences and uses for infectious disease visualization tools, and the existing tools are correspondingly diverse. The architecture of the tools was inconsistently described, and few tools in the review discussed the incorporation of usability studies or plans for dissemination. Many studies identified concerns regarding data sharing, confidentiality and quality. Existing tools offer a range of features and functions that allow users to explore, analyze, and visualize their data, but the tools are often for siloed applications. Commonly cited barriers to widespread adoption included lack of organizational support, access issues, and misconceptions about tool use. Discussion and Conclusion As the volume and complexity of infectious disease data increases, public health professionals must synthesize highly disparate data to facilitate communication with the public and inform decisions regarding measures to protect the public's health. Our review identified several themes: consideration of users' needs, preferences, and computer literacy; integration of tools into routine workflow; complications associated with understanding and use of visualizations; and the role of user trust and organizational support in the adoption of these tools. Interoperability also emerged as a prominent theme, highlighting challenges associated with the increasingly collaborative and interdisciplinary nature of infectious disease control and prevention. Future work should address methods for representing uncertainty and missing data to avoid misleading users as well as strategies to minimize cognitive overload. PMID:24747356

Visualization and analytics tools for infectious disease epidemiology: a systematic review.

PubMed

Carroll, Lauren N; Au, Alan P; Detwiler, Landon Todd; Fu, Tsung-Chieh; Painter, Ian S; Abernethy, Neil F

2014-10-01

A myriad of new tools and algorithms have been developed to help public health professionals analyze and visualize the complex data used in infectious disease control. To better understand approaches to meet these users' information needs, we conducted a systematic literature review focused on the landscape of infectious disease visualization tools for public health professionals, with a special emphasis on geographic information systems (GIS), molecular epidemiology, and social network analysis. The objectives of this review are to: (1) identify public health user needs and preferences for infectious disease information visualization tools; (2) identify existing infectious disease information visualization tools and characterize their architecture and features; (3) identify commonalities among approaches applied to different data types; and (4) describe tool usability evaluation efforts and barriers to the adoption of such tools. We identified articles published in English from January 1, 1980 to June 30, 2013 from five bibliographic databases. Articles with a primary focus on infectious disease visualization tools, needs of public health users, or usability of information visualizations were included in the review. A total of 88 articles met our inclusion criteria. Users were found to have diverse needs, preferences and uses for infectious disease visualization tools, and the existing tools are correspondingly diverse. The architecture of the tools was inconsistently described, and few tools in the review discussed the incorporation of usability studies or plans for dissemination. Many studies identified concerns regarding data sharing, confidentiality and quality. Existing tools offer a range of features and functions that allow users to explore, analyze, and visualize their data, but the tools are often for siloed applications. Commonly cited barriers to widespread adoption included lack of organizational support, access issues, and misconceptions about tool use. As the volume and complexity of infectious disease data increases, public health professionals must synthesize highly disparate data to facilitate communication with the public and inform decisions regarding measures to protect the public's health. Our review identified several themes: consideration of users' needs, preferences, and computer literacy; integration of tools into routine workflow; complications associated with understanding and use of visualizations; and the role of user trust and organizational support in the adoption of these tools. Interoperability also emerged as a prominent theme, highlighting challenges associated with the increasingly collaborative and interdisciplinary nature of infectious disease control and prevention. Future work should address methods for representing uncertainty and missing data to avoid misleading users as well as strategies to minimize cognitive overload. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Cloud computing approaches to accelerate drug discovery value chain.

PubMed

Garg, Vibhav; Arora, Suchir; Gupta, Chitra

2011-12-01

Continued advancements in the area of technology have helped high throughput screening (HTS) evolve from a linear to parallel approach by performing system level screening. Advanced experimental methods used for HTS at various steps of drug discovery (i.e. target identification, target validation, lead identification and lead validation) can generate data of the order of terabytes. As a consequence, there is pressing need to store, manage, mine and analyze this data to identify informational tags. This need is again posing challenges to computer scientists to offer the matching hardware and software infrastructure, while managing the varying degree of desired computational power. Therefore, the potential of "On-Demand Hardware" and "Software as a Service (SAAS)" delivery mechanisms cannot be denied. This on-demand computing, largely referred to as Cloud Computing, is now transforming the drug discovery research. Also, integration of Cloud computing with parallel computing is certainly expanding its footprint in the life sciences community. The speed, efficiency and cost effectiveness have made cloud computing a 'good to have tool' for researchers, providing them significant flexibility, allowing them to focus on the 'what' of science and not the 'how'. Once reached to its maturity, Discovery-Cloud would fit best to manage drug discovery and clinical development data, generated using advanced HTS techniques, hence supporting the vision of personalized medicine.

Regulatory Technology Development Plan - Sodium Fast Reactor. Mechanistic Source Term - Trial Calculation. Work Plan

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

Grabaskas, David; Bucknor, Matthew; Jerden, James

2016-02-01

The overall objective of the SFR Regulatory Technology Development Plan (RTDP) effort is to identify and address potential impediments to the SFR regulatory licensing process. In FY14, an analysis by Argonne identified the development of an SFR-specific MST methodology as an existing licensing gap with high regulatory importance and a potentially long lead-time to closure. This work was followed by an initial examination of the current state-of-knowledge regarding SFR source term development (ANLART-3), which reported several potential gaps. Among these were the potential inadequacies of current computational tools to properly model and assess the transport and retention of radionuclides duringmore » a metal fuel pool-type SFR core damage incident. The objective of the current work is to determine the adequacy of existing computational tools, and the associated knowledge database, for the calculation of an SFR MST. To accomplish this task, a trial MST calculation will be performed using available computational tools to establish their limitations with regard to relevant radionuclide release/retention/transport phenomena. The application of existing modeling tools will provide a definitive test to assess their suitability for an SFR MST calculation, while also identifying potential gaps in the current knowledge base and providing insight into open issues regarding regulatory criteria/requirements. The findings of this analysis will assist in determining future research and development needs.« less

Computational Modeling in Structural Materials Processing

NASA Technical Reports Server (NTRS)

Meyyappan, Meyya; Arnold, James O. (Technical Monitor)

1997-01-01

High temperature materials such as silicon carbide, a variety of nitrides, and ceramic matrix composites find use in aerospace, automotive, machine tool industries and in high speed civil transport applications. Chemical vapor deposition (CVD) is widely used in processing such structural materials. Variations of CVD include deposition on substrates, coating of fibers, inside cavities and on complex objects, and infiltration within preforms called chemical vapor infiltration (CVI). Our current knowledge of the process mechanisms, ability to optimize processes, and scale-up for large scale manufacturing is limited. In this regard, computational modeling of the processes is valuable since a validated model can be used as a design tool. The effort is similar to traditional chemically reacting flow modeling with emphasis on multicomponent diffusion, thermal diffusion, large sets of homogeneous reactions, and surface chemistry. In the case of CVI, models for pore infiltration are needed. In the present talk, examples of SiC nitride, and Boron deposition from the author's past work will be used to illustrate the utility of computational process modeling.

A PICKSC Science Gateway for enabling the common plasma physicist to run kinetic software

NASA Astrophysics Data System (ADS)

Hu, Q.; Winjum, B. J.; Zonca, A.; Youn, C.; Tsung, F. S.; Mori, W. B.

2017-10-01

Computer simulations offer tremendous opportunities for studying plasmas, ranging from simulations for students that illuminate fundamental educational concepts to research-level simulations that advance scientific knowledge. Nevertheless, there is a significant hurdle to using simulation tools. Users must navigate codes and software libraries, determine how to wrangle output into meaningful plots, and oftentimes confront a significant cyberinfrastructure with powerful computational resources. Science gateways offer a Web-based environment to run simulations without needing to learn or manage the underlying software and computing cyberinfrastructure. We discuss our progress on creating a Science Gateway for the Particle-in-Cell and Kinetic Simulation Software Center that enables users to easily run and analyze kinetic simulations with our software. We envision that this technology could benefit a wide range of plasma physicists, both in the use of our simulation tools as well as in its adaptation for running other plasma simulation software. Supported by NSF under Grant ACI-1339893 and by the UCLA Institute for Digital Research and Education.

Exploring Midwives' Need and Intention to Adopt Electronic Integrated Antenatal Care.

PubMed

Markam, Hosizah; Hochheiser, Harry; Kuntoro, Kuntoro; Notobroto, Hari Basuki

2018-01-01

Documentation requirements for the Indonesian integrated antenatal care (ANC) program suggest the need for electronic systems to address gaps in existing paper documentation practices. Our goals were to quantify midwives' documentation completeness in a primary healthcare center, understand documentation challenges, develop a tool, and assess intention to use the tool. We analyzed existing ANC records in a primary healthcare center in Bangkalan, East Java, and conducted interviews with stakeholders to understand needs for an electronic system in support of ANC. Development of the web-based Electronic Integrated ANC (e-iANC) system used the System Development Life Cycle method. Training on the use of the system was held in the computer laboratory for 100 midwives chosen from four primary healthcare centers in each of five regions. The Unified Theory of Acceptance and Use of Technology (UTAUT) questionnaire was used to assess their intention to adopt e-iANC. The midwives' intention to adopt e-iANC was significantly influenced by performance expectancy, effort expectancy and facilitating conditions. Age, education level, and computer literacy did not significantly moderate the effects of performance expectancy and effort expectancy on adoption intention. The UTAUT results indicated that the factors that might influence intention to adopt e-iANC are potentially addressable. Results suggest that e-iANC might well be accepted by midwives.

AccuRT: A versatile tool for radiative transfer simulations in the coupled atmosphere-ocean system

NASA Astrophysics Data System (ADS)

Hamre, Børge; Stamnes, Snorre; Stamnes, Knut; Stamnes, Jakob

2017-02-01

Reliable, accurate, and efficient modeling of the transport of electromagnetic radiation in turbid media has important applications in the study of the Earth's climate by remote sensing. For example, such modeling is needed to develop forward-inverse methods used to quantify types and concentrations of aerosol and cloud particles in the atmosphere, the dissolved organic and particulate biogeochemical matter in lakes, rivers, coastal, and open-ocean waters. It is also needed to simulate the performance of remote sensing detectors deployed on aircraft, balloons, and satellites as well as radiometric detectors deployed on buoys, gliders and other aquatic observing systems. Accurate radiative transfer modeling is also required to compute irradiances and scalar irradiances that are used to compute warming/cooling and photolysis rates in the atmosphere and primary production and warming/cooling rates in the water column. AccuRT is a radiative transfer model for the coupled atmosphere-water system that is designed to be a versatile tool for researchers in the ocean optics and remote sensing communities. It addresses the needs of researchers interested in analyzing irradiance and radiance measurements in the field and laboratory as well as those interested in making simulations of the top-of-the-atmosphere radiance in support of remote sensing algorithm development.

Designing and Implementing an OVERFLOW Reader for ParaView and Comparing Performance Between Central Processing Units and Graphical Processing Units

NASA Technical Reports Server (NTRS)

Chawner, David M.; Gomez, Ray J.

2010-01-01

In the Applied Aerosciences and CFD branch at Johnson Space Center, computational simulations are run that face many challenges. Two of which are the ability to customize software for specialized needs and the need to run simulations as fast as possible. There are many different tools that are used for running these simulations and each one has its own pros and cons. Once these simulations are run, there needs to be software capable of visualizing the results in an appealing manner. Some of this software is called open source, meaning that anyone can edit the source code to make modifications and distribute it to all other users in a future release. This is very useful, especially in this branch where many different tools are being used. File readers can be written to load any file format into a program, to ease the bridging from one tool to another. Programming such a reader requires knowledge of the file format that is being read as well as the equations necessary to obtain the derived values after loading. When running these CFD simulations, extremely large files are being loaded and having values being calculated. These simulations usually take a few hours to complete, even on the fastest machines. Graphics processing units (GPUs) are usually used to load the graphics for computers; however, in recent years, GPUs are being used for more generic applications because of the speed of these processors. Applications run on GPUs have been known to run up to forty times faster than they would on normal central processing units (CPUs). If these CFD programs are extended to run on GPUs, the amount of time they would require to complete would be much less. This would allow more simulations to be run in the same amount of time and possibly perform more complex computations.

Retrieval and management of medical information from heterogeneous sources, for its integration in a medical record visualisation tool.

PubMed

Cabarcos, Alba; Sanchez, Tamara; Seoane, Jose A; Aguiar-Pulido, Vanessa; Freire, Ana; Dorado, Julian; Pazos, Alejandro

2010-01-01

Nowadays, medical practice needs, at the patient Point-of-Care (POC), personalised knowledge adjustable in each moment to the clinical needs of each patient, in order to provide support to decision-making processes, taking into account personalised information. To achieve this, adapting the hospital information systems is necessary. Thus, there is a need of computational developments capable of retrieving and integrating the large amount of biomedical information available today, managing the complexity and diversity of these systems. Hence, this paper describes a prototype which retrieves biomedical information from different sources, manages it to improve the results obtained and to reduce response time and, finally, integrates it so that it is useful for the clinician, providing all the information available about the patient at the POC. Moreover, it also uses tools which allow medical staff to communicate and share knowledge.

Best behaviour? Ontologies and the formal description of animal behaviour.

PubMed

Gkoutos, Georgios V; Hoehndorf, Robert; Tsaprouni, Loukia; Schofield, Paul N

2015-10-01

The development of ontologies for describing animal behaviour has proved to be one of the most difficult of all scientific knowledge domains. Ranging from neurological processes to human emotions, the range and scope needed for such ontologies is highly challenging, but if data integration and computational tools such as automated reasoning are to be fully applied in this important area the underlying principles of these ontologies need to be better established and development needs detailed coordination. Whilst the state of scientific knowledge is always paramount in ontology and formal description framework design, this is a particular problem with neurobehavioural ontologies where our understanding of the relationship between behaviour and its underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain.

NASA Enterprise Visual Analysis

NASA Technical Reports Server (NTRS)

Lopez-Tellado, Maria; DiSanto, Brenda; Humeniuk, Robert; Bard, Richard, Jr.; Little, Mia; Edwards, Robert; Ma, Tien-Chi; Hollifield, Kenneith; White, Chuck

2007-01-01

NASA Enterprise Visual Analysis (NEVA) is a computer program undergoing development as a successor to Launch Services Analysis Tool (LSAT), formerly known as Payload Carrier Analysis Tool (PCAT). NEVA facilitates analyses of proposed configurations of payloads and packing fixtures (e.g. pallets) in a space shuttle payload bay for transport to the International Space Station. NEVA reduces the need to use physical models, mockups, and full-scale ground support equipment in performing such analyses. Using NEVA, one can take account of such diverse considerations as those of weight distribution, geometry, collision avoidance, power requirements, thermal loads, and mechanical loads.

SuML: A Survey Markup Language for Generalized Survey Encoding

PubMed Central

Barclay, MW; Lober, WB; Karras, BT

2002-01-01

There is a need in clinical and research settings for a sophisticated, generalized, web based survey tool that supports complex logic, separation of content and presentation, and computable guidelines. There are many commercial and open source survey packages available that provide simple logic; few provide sophistication beyond “goto” statements; none support the use of guidelines. These tools are driven by databases, static web pages, and structured documents using markup languages such as eXtensible Markup Language (XML). We propose a generalized, guideline aware language and an implementation architecture using open source standards.

Geocoded data structures and their applications to Earth science investigations

NASA Technical Reports Server (NTRS)

Goldberg, M.

1984-01-01

A geocoded data structure is a means for digitally representing a geographically referenced map or image. The characteristics of representative cellular, linked, and hybrid geocoded data structures are reviewed. The data processing requirements of Earth science projects at the Goddard Space Flight Center and the basic tools of geographic data processing are described. Specific ways that new geocoded data structures can be used to adapt these tools to scientists' needs are presented. These include: expanding analysis and modeling capabilities; simplifying the merging of data sets from diverse sources; and saving computer storage space.

A parallel-processing approach to computing for the geographic sciences

USGS Publications Warehouse

Crane, Michael; Steinwand, Dan; Beckmann, Tim; Krpan, Greg; Haga, Jim; Maddox, Brian; Feller, Mark

2001-01-01

The overarching goal of this project is to build a spatially distributed infrastructure for information science research by forming a team of information science researchers and providing them with similar hardware and software tools to perform collaborative research. Four geographically distributed Centers of the U.S. Geological Survey (USGS) are developing their own clusters of low-cost personal computers into parallel computing environments that provide a costeffective way for the USGS to increase participation in the high-performance computing community. Referred to as Beowulf clusters, these hybrid systems provide the robust computing power required for conducting research into various areas, such as advanced computer architecture, algorithms to meet the processing needs for real-time image and data processing, the creation of custom datasets from seamless source data, rapid turn-around of products for emergency response, and support for computationally intense spatial and temporal modeling.

Using the Eclipse Parallel Tools Platform to Assist Earth Science Model Development and Optimization on High Performance Computers

NASA Astrophysics Data System (ADS)

Alameda, J. C.

2011-12-01

Development and optimization of computational science models, particularly on high performance computers, and with the advent of ubiquitous multicore processor systems, practically on every system, has been accomplished with basic software tools, typically, command-line based compilers, debuggers, performance tools that have not changed substantially from the days of serial and early vector computers. However, model complexity, including the complexity added by modern message passing libraries such as MPI, and the need for hybrid code models (such as openMP and MPI) to be able to take full advantage of high performance computers with an increasing core count per shared memory node, has made development and optimization of such codes an increasingly arduous task. Additional architectural developments, such as many-core processors, only complicate the situation further. In this paper, we describe how our NSF-funded project, "SI2-SSI: A Productive and Accessible Development Workbench for HPC Applications Using the Eclipse Parallel Tools Platform" (WHPC) seeks to improve the Eclipse Parallel Tools Platform, an environment designed to support scientific code development targeted at a diverse set of high performance computing systems. Our WHPC project to improve Eclipse PTP takes an application-centric view to improve PTP. We are using a set of scientific applications, each with a variety of challenges, and using PTP to drive further improvements to both the scientific application, as well as to understand shortcomings in Eclipse PTP from an application developer perspective, to drive our list of improvements we seek to make. We are also partnering with performance tool providers, to drive higher quality performance tool integration. We have partnered with the Cactus group at Louisiana State University to improve Eclipse's ability to work with computational frameworks and extremely complex build systems, as well as to develop educational materials to incorporate into computational science and engineering codes. Finally, we are partnering with the lead PTP developers at IBM, to ensure we are as effective as possible within the Eclipse community development. We are also conducting training and outreach to our user community, including conference BOF sessions, monthly user calls, and an annual user meeting, so that we can best inform the improvements we make to Eclipse PTP. With these activities we endeavor to encourage use of modern software engineering practices, as enabled through the Eclipse IDE, with computational science and engineering applications. These practices include proper use of source code repositories, tracking and rectifying issues, measuring and monitoring code performance changes against both optimizations as well as ever-changing software stacks and configurations on HPC systems, as well as ultimately encouraging development and maintenance of testing suites -- things that have become commonplace in many software endeavors, but have lagged in the development of science applications. We view that the challenge with the increased complexity of both HPC systems and science applications demands the use of better software engineering methods, preferably enabled by modern tools such as Eclipse PTP, to help the computational science community thrive as we evolve the HPC landscape.

The Development of an eHealth Tool Suite for Prostate Cancer Patients and Their Partners

PubMed Central

Van Bogaert, Donna; Hawkins, Robert; Pingree, Suzanne; Jarrard, David

2013-01-01

Background eHealth resources for people facing health crises must balance the expert knowledge and perspective of developers and clinicians against the very different needs and perspectives of prospective users. This formative study explores the information and support needs of posttreatment prostate cancer patients and their partners as a way to improve an existing eHealth information and support system called CHESS (Comprehensive Health Enhancement Support System). Methods Focus groups with patient survivors and their partners were used to identify information gaps and information-seeking milestones. Results Both patients and partners expressed a need for assistance in decision making, connecting with experienced patients, and making sexual adjustments. Female partners of patients are more active in searching for cancer information. All partners have information and support needs distinct from those of the patient. Conclusions Findings were used to develop a series of interactive tools and navigational features for the CHESS prostate cancer computer-mediated system. PMID:22591675

Short-term Forecasting Tools for Agricultural Nutrient Management.

PubMed

Easton, Zachary M; Kleinman, Peter J A; Buda, Anthony R; Goering, Dustin; Emberston, Nichole; Reed, Seann; Drohan, Patrick J; Walter, M Todd; Guinan, Pat; Lory, John A; Sommerlot, Andrew R; Sharpley, Andrew

2017-11-01

The advent of real-time, short-term farm management tools is motivated by the need to protect water quality above and beyond the general guidance offered by existing nutrient management plans. Advances in high-performance computing and hydrologic or climate modeling have enabled rapid dissemination of real-time information that can assist landowners and conservation personnel with short-term management planning. This paper reviews short-term decision support tools for agriculture that are under various stages of development and implementation in the United States: (i) Wisconsin's Runoff Risk Advisory Forecast (RRAF) System, (ii) New York's Hydrologically Sensitive Area Prediction Tool, (iii) Virginia's Saturated Area Forecast Model, (iv) Pennsylvania's Fertilizer Forecaster, (v) Washington's Application Risk Management (ARM) System, and (vi) Missouri's Design Storm Notification System. Although these decision support tools differ in their underlying model structure, the resolution at which they are applied, and the hydroclimates to which they are relevant, all provide forecasts (range 24-120 h) of runoff risk or soil moisture saturation derived from National Weather Service Forecast models. Although this review highlights the need for further development of robust and well-supported short-term nutrient management tools, their potential for adoption and ultimate utility requires an understanding of the appropriate context of application, the strategic and operational needs of managers, access to weather forecasts, scales of application (e.g., regional vs. field level), data requirements, and outreach communication structure. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Current status of computational methods for transonic unsteady aerodynamics and aeroelastic applications

NASA Technical Reports Server (NTRS)

Edwards, John W.; Malone, John B.

1992-01-01

The current status of computational methods for unsteady aerodynamics and aeroelasticity is reviewed. The key features of challenging aeroelastic applications are discussed in terms of the flowfield state: low-angle high speed flows and high-angle vortex-dominated flows. The critical role played by viscous effects in determining aeroelastic stability for conditions of incipient flow separation is stressed. The need for a variety of flow modeling tools, from linear formulations to implementations of the Navier-Stokes equations, is emphasized. Estimates of computer run times for flutter calculations using several computational methods are given. Applications of these methods for unsteady aerodynamic and transonic flutter calculations for airfoils, wings, and configurations are summarized. Finally, recommendations are made concerning future research directions.

Exemplar for simulation challenges: Large-deformation micromechanics of Sylgard 184/glass microballoon syntactic foams.

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

Brown, Judith Alice; Long, Kevin Nicholas

2018-05-01

Sylgard® 184/Glass Microballoon (GMB) potting material is currently used in many NW systems. Analysts need a macroscale constitutive model that can predict material behavior under complex loading and damage evolution. To address this need, ongoing modeling and experimental efforts have focused on study of damage evolution in these materials. Micromechanical finite element simulations that resolve individual GMB and matrix components promote discovery and better understanding of the material behavior. With these simulations, we can study the role of the GMB volume fraction, time-dependent damage, behavior under confined vs. unconfined compression, and the effects of partial damage. These simulations are challengingmore » and push the boundaries of capability even with the high performance computing tools available at Sandia. We summarize the major challenges and the current state of this modeling effort, as an exemplar of micromechanical modeling needs that can motivate advances in future computing efforts.« less

Nurses and computers. An international perspective on nurses' requirements.

PubMed

Bond, Carol S

2007-01-01

This paper reports the findings from a Florence Nightingale Foundation Travel Scholarship undertaken by the author in the spring of 2006. The aim of the visit was to explore nurses' attitudes towards, and experiences of, using computers in their practice, and the requirements that they have to encourage, promote and support them in using ICT. Nurses were found to be using computers mainly for carrying out administrative tasks, such as updating records, rather than as information tools to support evidence based practice, or patient information needs. Nurses discussed the systems they used, the equipment provided, and their skills, or more often their lack of skills. The need for support was a frequent comment, most nurses feeling that it was essential that help was available at the point of need, and that it was provided by someone, preferably a nurse, who understood the work context. Three groups of nurses were identified. Engagers; Worried Willing and Resisters. The report concludes that pre-registration education has a responsibility to seek to ensure that newly qualified nurses enter practice as engagers.

Computational Prediction of Pressure and Thermal Environments in the Flame Trench With Launch Vehicles

NASA Technical Reports Server (NTRS)

Brehm, Christoph; Sozer, Emre; Barad, Michael F.; Housman, Jeffrey A.; Kiris, Cetin C.; Moini-Yekta, Shayan; Vu, Bruce T.; Parlier, Christopher R.

2014-01-01

One of the key objectives for the development of the 21st Century Space Launch Com- plex is to provide the exibility needed to support evolving launch vehicles and spacecrafts with enhanced range capacity. The launch complex needs to support various proprietary and commercial vehicles with widely di erent needs. The design of a multi-purpose main ame de ector supporting many di erent launch vehicles becomes a very challenging task when considering that even small geometric changes may have a strong impact on the pressure and thermal environment. The physical and geometric complexity encountered at the launch site require the use of state-of-the-art Computational Fluid Dynamics (CFD) tools to predict the pressure and thermal environments. Due to harsh conditions encountered in the launch environment, currently available CFD methods which are frequently employed for aerodynamic and ther- mal load predictions in aerospace applications, reach their limits of validity. This paper provides an in-depth discussion on the computational and physical challenges encountered when attempting to provide a detailed description of the ow eld in the launch environ- ment. Several modeling aspects, such as viscous versus inviscid calculations, single-species versus multiple-species ow models, and calorically perfect gas versus thermally perfect gas, are discussed. The Space Shuttle and the Falcon Heavy launch vehicles are used to study di erent engine and geometric con gurations. Finally, we provide a discussion on traditional analytical tools which have been used to provide estimates on the expected pressure and thermal loads.

Heavy Lift Vehicle (HLV) Avionics Flight Computing Architecture Study

NASA Technical Reports Server (NTRS)

Hodson, Robert F.; Chen, Yuan; Morgan, Dwayne R.; Butler, A. Marc; Sdhuh, Joseph M.; Petelle, Jennifer K.; Gwaltney, David A.; Coe, Lisa D.; Koelbl, Terry G.; Nguyen, Hai D.

2011-01-01

A NASA multi-Center study team was assembled from LaRC, MSFC, KSC, JSC and WFF to examine potential flight computing architectures for a Heavy Lift Vehicle (HLV) to better understand avionics drivers. The study examined Design Reference Missions (DRMs) and vehicle requirements that could impact the vehicles avionics. The study considered multiple self-checking and voting architectural variants and examined reliability, fault-tolerance, mass, power, and redundancy management impacts. Furthermore, a goal of the study was to develop the skills and tools needed to rapidly assess additional architectures should requirements or assumptions change.

Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions

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

Song, Hyun-Seob; Nelson, William C.; Lee, Joon-Yong

Interest in applying microbial communities to biotechnology continues to increase. Successful engineering of microbial communities requires a fundamental shift in focus from enhancing metabolic capabilities in individual organisms to promoting synergistic interspecies interactions. This goal necessitates in silico tools that provide a predictive understanding of how microorganisms interact with each other and their environments. In this regard, we highlight a need for a new concept that we have termed biological computer-aided design of interactions (BioCADi). We ground this discussion within the context of metabolic network modeling.

Optical Micromachining

NASA Technical Reports Server (NTRS)

1998-01-01

Under an SBIR (Small Business Innovative Research) with Marshall Space Flight Center, Potomac Photonics, Inc., constructed and demonstrated a unique tool that fills a need in the area of diffractive and refractive micro-optics. It is an integrated computer-aided design and computer-aided micro-machining workstation that will extend the benefits of diffractive and micro-optic technology to optical designers. Applications of diffractive optics include sensors and monitoring equipment, analytical instruments, and fiber optic distribution and communication. The company has been making diffractive elements with the system as a commercial service for the last year.

Touchfree medical interfaces.

PubMed

Rossol, Nathaniel; Cheng, Irene; Rui Shen; Basu, Anup

2014-01-01

Real-time control of visual display systems via mid-air hand gestures offers many advantages over traditional interaction modalities. In medicine, for example, it allows a practitioner to adjust display values, e.g. contrast or zoom, on a medical visualization interface without the need to re-sterilize the interface. However, when users are holding a small tool (such as a pen, surgical needle, or computer stylus) the need to constantly put the tool down in order to make hand gesture interactions is not ideal. This work presents a novel interface that automatically adjusts for gesturing with hands and hand-held tools to precisely control medical displays. The novelty of our interface is that it uses a single set of gestures designed to be equally effective for fingers and hand-held tools without using markers. This type of interface was previously not feasible with low-resolution depth sensors such as Kinect, but is now achieved by using the recently released Leap Motion controller. Our interface is validated through a user study on a group of people given the task of adjusting parameters on a medical image.

FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies.

PubMed

Wilson, Carolyn A; Simonyan, Vahan

2014-01-01

Applications of next-generation sequencing (NGS) technologies require availability and access to an information technology (IT) infrastructure and bioinformatics tools for large amounts of data storage and analyses. The U.S. Food and Drug Administration (FDA) anticipates that the use of NGS data to support regulatory submissions will continue to increase as the scientific and clinical communities become more familiar with the technologies and identify more ways to apply these advanced methods to support development and evaluation of new biomedical products. FDA laboratories are conducting research on different NGS platforms and developing the IT infrastructure and bioinformatics tools needed to enable regulatory evaluation of the technologies and the data sponsors will submit. A High-performance Integrated Virtual Environment, or HIVE, has been launched, and development and refinement continues as a collaborative effort between the FDA and George Washington University to provide the tools to support these needs. The use of a highly parallelized environment facilitated by use of distributed cloud storage and computation has resulted in a platform that is both rapid and responsive to changing scientific needs. The FDA plans to further develop in-house capacity in this area, while also supporting engagement by the external community, by sponsoring an open, public workshop to discuss NGS technologies and data formats standardization, and to promote the adoption of interoperability protocols in September 2014. Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and bioinformatics tools to be able to store and analyze large amounts of data. To address this need, we have developed the High-performance Integrated Virtual Environment, or HIVE. HIVE uses a combination of distributed cloud storage and distributed cloud computations to provide a platform that is both rapid and responsive to support the growing and increasingly diverse scientific and regulatory needs of FDA scientists in their evaluation of NGS in research and ultimately for evaluation of NGS data in regulatory submissions. © PDA, Inc. 2014.

RNA-Seq Analysis to Measure the Expression of SINE Retroelements.

PubMed

Román, Ángel Carlos; Morales-Hernández, Antonio; Fernández-Salguero, Pedro M

2016-01-01

The intrinsic features of retroelements, like their repetitive nature and disseminated presence in their host genomes, demand the use of advanced methodologies for their bioinformatic and functional study. The short length of SINE (short interspersed elements) retrotransposons makes such analyses even more complex. Next-generation sequencing (NGS) technologies are currently one of the most widely used tools to characterize the whole repertoire of gene expression in a specific tissue. In this chapter, we will review the molecular and computational methods needed to perform NGS analyses on SINE elements. We will also describe new methods of potential interest for researchers studying repetitive elements. We intend to outline the general ideas behind the computational analyses of NGS data obtained from SINE elements, and to stimulate other scientists to expand our current knowledge on SINE biology using RNA-seq and other NGS tools.

The use of elearning in medical education: a review of the current situation

PubMed Central

Choules, A P

2007-01-01

Computers are increasingly used in medical education. Electronic learning (elearning) is moving from textbooks in electronic format (that are increasingly enhanced by the use of multimedia adjuncts) to a truly interactive medium that can be delivered to meet the educational needs of students and postgraduate learners. Computer technology can present reliable, reusable content in a format that is convenient to the learner. It can be used to transcend geographical boundaries and time zones. It is a valuable tool to add to the medical teacher's toolkit, but like all tools it must be used appropriately. This article endeavours to review the current “state of the art2 in use of elearning and its role in medical education alongside non‐electronic methods—a combination that is currently referred to as “blended” learning. PMID:17403945

DNA-binding specificity prediction with FoldX.

PubMed

Nadra, Alejandro D; Serrano, Luis; Alibés, Andreu

2011-01-01

With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. In this chapter, we present a simple and powerful method to either know the DNA specificity of a wild-type protein or design new specificities by using the protein design algorithm FoldX. The only basic requirement is having a good resolution structure of the complex. Protein-DNA interaction design may aid the development of new parts designed to be orthogonal, decoupled, and precise in its target. Further, it could help to fine-tune the systems in terms of specificity, discrimination, and binding constants. In the age of newly developed devices and invented systems, computer-aided engineering promises to be an invaluable tool. Copyright © 2011 Elsevier Inc. All rights reserved.

A Development Architecture for Serious Games Using BCI (Brain Computer Interface) Sensors

PubMed Central

Sung, Yunsick; Cho, Kyungeun; Um, Kyhyun

2012-01-01

Games that use brainwaves via brain–computer interface (BCI) devices, to improve brain functions are known as BCI serious games. Due to the difficulty of developing BCI serious games, various BCI engines and authoring tools are required, and these reduce the development time and cost. However, it is desirable to reduce the amount of technical knowledge of brain functions and BCI devices needed by game developers. Moreover, a systematic BCI serious game development process is required. In this paper, we present a methodology for the development of BCI serious games. We describe an architecture, authoring tools, and development process of the proposed methodology, and apply it to a game development approach for patients with mild cognitive impairment as an example. This application demonstrates that BCI serious games can be developed on the basis of expert-verified theories. PMID:23202227

A development architecture for serious games using BCI (brain computer interface) sensors.

PubMed

Sung, Yunsick; Cho, Kyungeun; Um, Kyhyun

2012-11-12

Games that use brainwaves via brain-computer interface (BCI) devices, to improve brain functions are known as BCI serious games. Due to the difficulty of developing BCI serious games, various BCI engines and authoring tools are required, and these reduce the development time and cost. However, it is desirable to reduce the amount of technical knowledge of brain functions and BCI devices needed by game developers. Moreover, a systematic BCI serious game development process is required. In this paper, we present a methodology for the development of BCI serious games. We describe an architecture, authoring tools, and development process of the proposed methodology, and apply it to a game development approach for patients with mild cognitive impairment as an example. This application demonstrates that BCI serious games can be developed on the basis of expert-verified theories.

Characterizing and Supporting Change in Algebra Students' Representational Fluency in a CAS/Paper-and-Pencil Environment

ERIC Educational Resources Information Center

Fonger, Nicole L.

2012-01-01

Representational fluency (RF) includes an ability to interpret, create, move within and among, and connect tool-based representations of mathematical objects. Taken as an indicator of conceptual understanding, there is a need to better support school algebra students' RF in learning environments that utilize both computer algebra systems…

2015 Army Science Planning and Strategy Meeting Series: Outcomes and Conclusions

DTIC Science & Technology

2017-12-21

modeling and nanoscale characterization tools to enable efficient design of hybridized manufacturing ; realtime, multiscale computational capability...to enable predictive analytics for expeditionary on-demand manufacturing • Discovery of design principles to enable programming advanced genetic...goals, significant research is needed to mature the fundamental materials science, processing and manufacturing sciences, design methodologies, data

Advantages of Computer Simulation in Enhancing Students' Learning about Landform Evolution: A Case Study Using the Grand Canyon

ERIC Educational Resources Information Center

Luo, Wei; Pelletier, Jon; Duffin, Kirk; Ormand, Carol; Hung, Wei-chen; Shernoff, David J.; Zhai, Xiaoming; Iverson, Ellen; Whalley, Kyle; Gallaher, Courtney; Furness, Walter

2016-01-01

The long geological time needed for landform development and evolution poses a challenge for understanding and appreciating the processes involved. The Web-based Interactive Landform Simulation Model--Grand Canyon (WILSIM-GC, http://serc.carleton.edu/landform/) is an educational tool designed to help students better understand such processes,…

Computer-based tools for decision support in agroforestry: Current state and future needs

Treesearch

E.A. Ellis; G. Bentrup; Michelle M. Schoeneberger

2004-01-01

Successful design of agroforestry practices hinges on the ability to pull together very diverse and sometimes large sets of information (i.e., biophysical, economic and social factors), and then implementing the synthesis of this information across several spatial scales from site to landscape. Agroforestry, by its very nature, creates complex systems with impacts...

Health Literacy Assessment of the STOFHLA: Paper versus Electronic Administration Continuation Study

ERIC Educational Resources Information Center

Chesser, Amy K.; Keene Woods, Nikki; Wipperman, Jennifer; Wilson, Rachel; Dong, Frank

2014-01-01

Low health literacy is associated with poor health outcomes. Research is needed to understand the mechanisms and pathways of its effects. Computer-based assessment tools may improve efficiency and cost-effectiveness of health literacy research. The objective of this preliminary study was to assess if administration of the Short Test of Functional…

New directions for Artificial Intelligence (AI) methods in optimum design

NASA Technical Reports Server (NTRS)

Hajela, Prabhat

1989-01-01

Developments and applications of artificial intelligence (AI) methods in the design of structural systems is reviewed. Principal shortcomings in the current approach are emphasized, and the need for some degree of formalism in the development environment for such design tools is underscored. Emphasis is placed on efforts to integrate algorithmic computations in expert systems.

CAM Highlights (FY 80)

DTIC Science & Technology

1980-10-01

industrialized nations in almost every manufacturing market place. Many foreign nation’s manu- facturing advancements have resulted from...towards planning a computerized data storage and retrieval system based on Group Technology (GT) principles . The data storage and re- trieval...several computer languages available on the market to program numerically controlled machine tools. However, there was a need for a docu- ment showing

Serious Games as a Malleable Learning Medium: The Effects of Narrative, Gameplay, and Making on Students' Performance and Attitudes

ERIC Educational Resources Information Center

Garneli, Varvara; Giannakos, Michail; Chorianopoulos, Konstantinos

2017-01-01

Research into educational technology has evaluated new computer-based systems as tools for improving students' academic performance and engagement. Serious games should also be considered as an alternative pedagogical medium for attracting students with different needs and expectations. In this field study, we empirically examined different forms…

How to Find Good Apps: An Evaluation Rubric for Instructional Apps for Teaching Students with Learning Disabilities

ERIC Educational Resources Information Center

Ok, Min Wook; Kim, Min Kyung; Kang, Eun Young; Bryant, Brian R.

2016-01-01

Computers can be an effective teaching method for students with learning disabilities (LD). The use of mobile devices as education tools for students with disabilities has received considerable attention in special education recently. Parents, teachers, and professionals look for effective applications (i.e., apps) that meet the needs of their…

From Newton to Gates--Digital Principia

ERIC Educational Resources Information Center

Beckwith, E. George; Cunniff, Daniel T.

2008-01-01

Computers are becoming the norm for teaching and learning. The Internet gives people ready access to text, visual and audio messages from around the world. For teachers, content is critical and the future dictates the need for major changes in the role of the teacher and learner. Today's digital tools and video games have proven to be well known…

Measuring Astronomical Distances with Linear Programming

ERIC Educational Resources Information Center

Narain, Akshar

2015-01-01

A few years ago it was suggested that the distance to celestial bodies could be computed by tracking their position over about 24 hours and then solving a regression problem. One only needed to use inexpensive telescopes, cameras, and astrometry tools, and the experiment could be done from one's backyard. However, it is not obvious to an amateur…

International Bibliography of Computer-Assisted Terminology.

ERIC Educational Resources Information Center

Krommer-Benz, Magdalena, Comp.

Because of the need for adequate reference tools in the new area of data banks for the field of terminology (there are currently 25 term banks in existence and more are planned), this bibliography lists some 350 references selected from a large number of both primary and secondary sources. It includes some entries selected from a list of…

FunRich proteomics software analysis, let the fun begin!

PubMed

Benito-Martin, Alberto; Peinado, Héctor

2015-08-01

Protein MS analysis is the preferred method for unbiased protein identification. It is normally applied to a large number of both small-scale and high-throughput studies. However, user-friendly computational tools for protein analysis are still needed. In this issue, Mathivanan and colleagues (Proteomics 2015, 15, 2597-2601) report the development of FunRich software, an open-access software that facilitates the analysis of proteomics data, providing tools for functional enrichment and interaction network analysis of genes and proteins. FunRich is a reinterpretation of proteomic software, a standalone tool combining ease of use with customizable databases, free access, and graphical representations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Towards a publicly available, map-based regional software tool to estimate unregulated daily streamflow at ungauged rivers

USGS Publications Warehouse

Archfield, Stacey A.; Steeves, Peter A.; Guthrie, John D.; Ries, Kernell G.

2013-01-01

Streamflow information is critical for addressing any number of hydrologic problems. Often, streamflow information is needed at locations that are ungauged and, therefore, have no observations on which to base water management decisions. Furthermore, there has been increasing need for daily streamflow time series to manage rivers for both human and ecological functions. To facilitate negotiation between human and ecological demands for water, this paper presents the first publicly available, map-based, regional software tool to estimate historical, unregulated, daily streamflow time series (streamflow not affected by human alteration such as dams or water withdrawals) at any user-selected ungauged river location. The map interface allows users to locate and click on a river location, which then links to a spreadsheet-based program that computes estimates of daily streamflow for the river location selected. For a demonstration region in the northeast United States, daily streamflow was, in general, shown to be reliably estimated by the software tool. Estimating the highest and lowest streamflows that occurred in the demonstration region over the period from 1960 through 2004 also was accomplished but with more difficulty and limitations. The software tool provides a general framework that can be applied to other regions for which daily streamflow estimates are needed.

Systems biology driven software design for the research enterprise.

PubMed

Boyle, John; Cavnor, Christopher; Killcoyne, Sarah; Shmulevich, Ilya

2008-06-25

In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

PubMed

Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

Planform: an application and database of graph-encoded planarian regenerative experiments.

PubMed

Lobo, Daniel; Malone, Taylor J; Levin, Michael

2013-04-15

Understanding the mechanisms governing the regeneration capabilities of many organisms is a fundamental interest in biology and medicine. An ever-increasing number of manipulation and molecular experiments are attempting to discover a comprehensive model for regeneration, with the planarian flatworm being one of the most important model species. Despite much effort, no comprehensive, constructive, mechanistic models exist yet, and it is now clear that computational tools are needed to mine this huge dataset. However, until now, there is no database of regenerative experiments, and the current genotype-phenotype ontologies and databases are based on textual descriptions, which are not understandable by computers. To overcome these difficulties, we present here Planform (Planarian formalization), a manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. The database contains more than a thousand experiments from the main publications in the planarian literature. The software tool provides the user with a graphical interface to easily interact with and mine the database. The presented system is a valuable resource for the regeneration community and, more importantly, will pave the way for the application of novel artificial intelligence tools to extract knowledge from this dataset. The database and software tool are freely available at http://planform.daniel-lobo.com.

The effect of introducing computers into an introductory physics problem-solving laboratory

NASA Astrophysics Data System (ADS)

McCullough, Laura Ellen

2000-10-01

Computers are appearing in every type of classroom across the country. Yet they often appear without benefit of studying their effects. The research that is available on computer use in classrooms has found mixed results, and often ignores the theoretical and instructional contexts of the computer in the classroom. The University of Minnesota's physics department employs a cooperative-group problem solving pedagogy, based on a cognitive apprenticeship instructional model, in its calculus-based introductory physics course. This study was designed to determine possible negative effects of introducing a computerized data-acquisition and analysis tool into this pedagogy as a problem-solving tool for students to use in laboratory. To determine the effects of the computer tool, two quasi-experimental treatment groups were selected. The computer-tool group (N = 170) used a tool, designed for this study (VideoTool), to collect and analyze motion data in the laboratory. The control group (N = 170) used traditional non-computer equipment (spark tapes and Polaroid(TM) film). The curriculum was kept as similar as possible for the two groups. During the ten week academic quarter, groups were examined for effects on performance on conceptual tests and grades, attitudes towards the laboratory and the laboratory tools, and behaviors within cooperative groups. Possible interactions with gender were also examined. Few differences were found between the control and computer-tool groups. The control group received slightly higher scores on one conceptual test, but this difference was not educationally significant. The computer-tool group had slightly more positive attitudes towards using the computer tool than their counterparts had towards the traditional tools. The computer-tool group also perceived that they spoke more frequently about physics misunderstandings, while the control group felt that they discussed equipment difficulties more often. This perceptual difference interacted with gender, with the men in the control group more likely to discuss equipment difficulties than any other group. Overall, the differences between the control and quasi-experimental groups were minimal. It was concluded that carefully replacing traditional data collection and analysis tools with a computer tool had no negative effects on achievement, attitude, group behavior, and did not interact with gender.

Effectiveness of a Technology-Based Intervention to Teach Evidence-Based Practice: The EBR Tool.

PubMed

Long, JoAnn D; Gannaway, Paula; Ford, Cindy; Doumit, Rita; Zeeni, Nadine; Sukkarieh-Haraty, Ola; Milane, Aline; Byers, Beverly; Harrison, LaNell; Hatch, Daniel; Brown, Justin; Proper, Sharlan; White, Patricia; Song, Huaxin

2016-02-01

As the world becomes increasingly digital, advances in technology have changed how students access evidence-based information. Research suggests that students overestimate their ability to locate quality online research and lack the skills needed to evaluate the scientific literature. Clinical nurses report relying on personal experience to answer clinical questions rather than searching evidence-based sources. To address the problem, a web-based, evidence-based research (EBR) tool that is usable from a computer, smartphone, or iPad was developed and tested. The purpose of the EBR tool is to guide students through the basic steps needed to locate and critically appraise the online scientific literature while linking users to quality electronic resources to support evidence-based practice (EBP). Testing of the tool took place in a mixed-method, quasi-experimental, and two-population randomized controlled trial (RCT) design in a U.S. and Middle East university. A statistically significant improvement in overall research skills was supported in the quasi-experimental nursing student group and RCT nutrition student group using the EBR tool. A statistically significant proportional difference was supported in the RCT nutrition and PharmD intervention groups in participants' ability to distinguish the credibility of online source materials compared with controls. The majority of participants could correctly apply PICOTS to a case study when using the tool. The data from this preliminary study suggests that the EBR tool enhanced student overall research skills and selected EBP skills while generating data for assessment of learning outcomes. The EBR tool places evidence-based resources at the fingertips of users by addressing some of the most commonly cited barriers to research utilization while exposing users to information and online literacy standards of practice, meeting a growing need within nursing curricula. © 2016 Sigma Theta Tau International.

Build It: Will They Come?

NASA Astrophysics Data System (ADS)

Corrie, Brian; Zimmerman, Todd

Scientific research is fundamentally collaborative in nature, and many of today's complex scientific problems require domain expertise in a wide range of disciplines. In order to create research groups that can effectively explore such problems, research collaborations are often formed that involve colleagues at many institutions, sometimes spanning a country and often spanning the world. An increasingly common manifestation of such a collaboration is the collaboratory (Bos et al., 2007), a “…center without walls in which the nation's researchers can perform research without regard to geographical location — interacting with colleagues, accessing instrumentation, sharing data and computational resources, and accessing information from digital libraries.” In order to bring groups together on such a scale, a wide range of components need to be available to researchers, including distributed computer systems, remote instrumentation, data storage, collaboration tools, and the financial and human resources to operate and run such a system (National Research Council, 1993). Media Spaces, as both a technology and a social facilitator, have the potential to meet many of these needs. In this chapter, we focus on the use of scientific media spaces (SMS) as a tool for supporting collaboration in scientific research. In particular, we discuss the design, deployment, and use of a set of SMS environments deployed by WestGrid and one of its collaborating organizations, the Centre for Interdisciplinary Research in the Mathematical and Computational Sciences (IRMACS) over a 5-year period.

CMS Connect

NASA Astrophysics Data System (ADS)

Balcas, J.; Bockelman, B.; Gardner, R., Jr.; Hurtado Anampa, K.; Jayatilaka, B.; Aftab Khan, F.; Lannon, K.; Larson, K.; Letts, J.; Marra Da Silva, J.; Mascheroni, M.; Mason, D.; Perez-Calero Yzquierdo, A.; Tiradani, A.

2017-10-01

The CMS experiment collects and analyzes large amounts of data coming from high energy particle collisions produced by the Large Hadron Collider (LHC) at CERN. This involves a huge amount of real and simulated data processing that needs to be handled in batch-oriented platforms. The CMS Global Pool of computing resources provide +100K dedicated CPU cores and another 50K to 100K CPU cores from opportunistic resources for these kind of tasks and even though production and event processing analysis workflows are already managed by existing tools, there is still a lack of support to submit final stage condor-like analysis jobs familiar to Tier-3 or local Computing Facilities users into these distributed resources in an integrated (with other CMS services) and friendly way. CMS Connect is a set of computing tools and services designed to augment existing services in the CMS Physics community focusing on these kind of condor analysis jobs. It is based on the CI-Connect platform developed by the Open Science Grid and uses the CMS GlideInWMS infrastructure to transparently plug CMS global grid resources into a virtual pool accessed via a single submission machine. This paper describes the specific developments and deployment of CMS Connect beyond the CI-Connect platform in order to integrate the service with CMS specific needs, including specific Site submission, accounting of jobs and automated reporting to standard CMS monitoring resources in an effortless way to their users.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

PubMed

Goff, Stephen A; Vaughn, Matthew; McKay, Sheldon; Lyons, Eric; Stapleton, Ann E; Gessler, Damian; Matasci, Naim; Wang, Liya; Hanlon, Matthew; Lenards, Andrew; Muir, Andy; Merchant, Nirav; Lowry, Sonya; Mock, Stephen; Helmke, Matthew; Kubach, Adam; Narro, Martha; Hopkins, Nicole; Micklos, David; Hilgert, Uwe; Gonzales, Michael; Jordan, Chris; Skidmore, Edwin; Dooley, Rion; Cazes, John; McLay, Robert; Lu, Zhenyuan; Pasternak, Shiran; Koesterke, Lars; Piel, William H; Grene, Ruth; Noutsos, Christos; Gendler, Karla; Feng, Xin; Tang, Chunlao; Lent, Monica; Kim, Seung-Jin; Kvilekval, Kristian; Manjunath, B S; Tannen, Val; Stamatakis, Alexandros; Sanderson, Michael; Welch, Stephen M; Cranston, Karen A; Soltis, Pamela; Soltis, Doug; O'Meara, Brian; Ane, Cecile; Brutnell, Tom; Kleibenstein, Daniel J; White, Jeffery W; Leebens-Mack, James; Donoghue, Michael J; Spalding, Edgar P; Vision, Todd J; Myers, Christopher R; Lowenthal, David; Enquist, Brian J; Boyle, Brad; Akoglu, Ali; Andrews, Greg; Ram, Sudha; Ware, Doreen; Stein, Lincoln; Stanzione, Dan

2011-01-01

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

Computational systems chemical biology.

PubMed

Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

PubMed Central

Goff, Stephen A.; Vaughn, Matthew; McKay, Sheldon; Lyons, Eric; Stapleton, Ann E.; Gessler, Damian; Matasci, Naim; Wang, Liya; Hanlon, Matthew; Lenards, Andrew; Muir, Andy; Merchant, Nirav; Lowry, Sonya; Mock, Stephen; Helmke, Matthew; Kubach, Adam; Narro, Martha; Hopkins, Nicole; Micklos, David; Hilgert, Uwe; Gonzales, Michael; Jordan, Chris; Skidmore, Edwin; Dooley, Rion; Cazes, John; McLay, Robert; Lu, Zhenyuan; Pasternak, Shiran; Koesterke, Lars; Piel, William H.; Grene, Ruth; Noutsos, Christos; Gendler, Karla; Feng, Xin; Tang, Chunlao; Lent, Monica; Kim, Seung-Jin; Kvilekval, Kristian; Manjunath, B. S.; Tannen, Val; Stamatakis, Alexandros; Sanderson, Michael; Welch, Stephen M.; Cranston, Karen A.; Soltis, Pamela; Soltis, Doug; O'Meara, Brian; Ane, Cecile; Brutnell, Tom; Kleibenstein, Daniel J.; White, Jeffery W.; Leebens-Mack, James; Donoghue, Michael J.; Spalding, Edgar P.; Vision, Todd J.; Myers, Christopher R.; Lowenthal, David; Enquist, Brian J.; Boyle, Brad; Akoglu, Ali; Andrews, Greg; Ram, Sudha; Ware, Doreen; Stein, Lincoln; Stanzione, Dan

2011-01-01

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services. PMID:22645531

Computational Systems Chemical Biology

PubMed Central

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2013-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007). The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology / systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology. PMID:20838980

Toward a VPH/Physiome ToolKit.

PubMed

Garny, Alan; Cooper, Jonathan; Hunter, Peter J

2010-01-01

The Physiome Project was officially launched in 1997 and has since brought together teams from around the world to work on the development of a computational framework for the modeling of the human body. At the European level, this effort is focused around patient-specific solutions and is known as the Virtual Physiological Human (VPH) Initiative.Such modeling is both multiscale (in space and time) and multiphysics. This, therefore, requires careful interaction and collaboration between the teams involved in the VPH/Physiome effort, if we are to produce computer models that are not only quantitative, but also integrative and predictive.In that context, several technologies and solutions are already available, developed both by groups involved in the VPH/Physiome effort, and by others. They address areas such as data handling/fusion, markup languages, model repositories, ontologies, tools (for simulation, imaging, data fitting, etc.), as well as grid, middleware, and workflow.Here, we provide an overview of resources that should be considered for inclusion in the VPH/Physiome ToolKit (i.e., the set of tools that addresses the needs and requirements of the Physiome Project and VPH Initiative) and discuss some of the challenges that we are still facing.

Modeling RF-induced Plasma-Surface Interactions with VSim

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, David N.; Pankin, Alexei Y.; Roark, Christine M.; Stoltz, Peter H.; Zhou, Sean C.-D.; Kruger, Scott E.

2014-10-01

An overview of ongoing enhancements to the Plasma Discharge (PD) module of Tech-X's VSim software tool is presented. A sub-grid kinetic sheath model, developed for the accurate computation of sheath potentials near metal and dielectric-coated walls, enables the physical effects of DC and RF sheath dynamics to be included in macroscopic-scale plasma simulations that need not explicitly resolve sheath scale lengths. Sheath potential evolution, together with particle behavior near the sheath (e.g. sputtering), can thus be simulated in complex, experimentally relevant geometries. Simulations of RF sheath-enhanced impurity production near surfaces of the C-Mod field-aligned ICRF antenna are presented to illustrate the model; impurity mitigation techniques are also explored. Model extensions to capture the physics of secondary electron emission and of multispecies plasmas are summarized, together with a discussion of improved tools for plasma chemistry and IEDF/EEDF visualization and modeling. The latter tools are also highly relevant for commercial plasma processing applications. Ultimately, we aim to establish VSimPD as a robust, efficient computational tool for modeling fusion and industrial plasma processes. Supported by U.S. DoE SBIR Phase I/II Award DE-SC0009501.

Advanced Simulation and Computing Fiscal Year 14 Implementation Plan, Rev. 0.5

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

Meisner, Robert; McCoy, Michel; Archer, Bill

2013-09-11

The Stockpile Stewardship Program (SSP) is a single, highly integrated technical program for maintaining the surety and reliability of the U.S. nuclear stockpile. The SSP uses nuclear test data, computational modeling and simulation, and experimental facilities to advance understanding of nuclear weapons. It includes stockpile surveillance, experimental research, development and engineering programs, and an appropriately scaled production capability to support stockpile requirements. This integrated national program requires the continued use of experimental facilities and programs, and the computational enhancements to support these programs. The Advanced Simulation and Computing Program (ASC) is a cornerstone of the SSP, providing simulation capabilities andmore » computational resources that support annual stockpile assessment and certification, study advanced nuclear weapons design and manufacturing processes, analyze accident scenarios and weapons aging, and provide the tools to enable stockpile Life Extension Programs (LEPs) and the resolution of Significant Finding Investigations (SFIs). This requires a balanced resource, including technical staff, hardware, simulation software, and computer science solutions. In its first decade, the ASC strategy focused on demonstrating simulation capabilities of unprecedented scale in three spatial dimensions. In its second decade, ASC is now focused on increasing predictive capabilities in a three-dimensional (3D) simulation environment while maintaining support to the SSP. The program continues to improve its unique tools for solving progressively more difficult stockpile problems (sufficient resolution, dimensionality, and scientific details), quantify critical margins and uncertainties, and resolve increasingly difficult analyses needed for the SSP. Moreover, ASC’s business model is integrated and focused on requirements-driven products that address long-standing technical questions related to enhanced predictive capability in the simulation tools.« less

Distributed geospatial model sharing based on open interoperability standards

USGS Publications Warehouse

Feng, Min; Liu, Shuguang; Euliss, Ned H.; Fang, Yin

2009-01-01

Numerous geospatial computational models have been developed based on sound principles and published in journals or presented in conferences. However modelers have made few advances in the development of computable modules that facilitate sharing during model development or utilization. Constraints hampering development of model sharing technology includes limitations on computing, storage, and connectivity; traditional stand-alone and closed network systems cannot fully support sharing and integrating geospatial models. To address this need, we have identified methods for sharing geospatial computational models using Service Oriented Architecture (SOA) techniques and open geospatial standards. The service-oriented model sharing service is accessible using any tools or systems compliant with open geospatial standards, making it possible to utilize vast scientific resources available from around the world to solve highly sophisticated application problems. The methods also allow model services to be empowered by diverse computational devices and technologies, such as portable devices and GRID computing infrastructures. Based on the generic and abstract operations and data structures required for Web Processing Service (WPS) standards, we developed an interactive interface for model sharing to help reduce interoperability problems for model use. Geospatial computational models are shared on model services, where the computational processes provided by models can be accessed through tools and systems compliant with WPS. We developed a platform to help modelers publish individual models in a simplified and efficient way. Finally, we illustrate our technique using wetland hydrological models we developed for the prairie pothole region of North America.

Parallel, distributed and GPU computing technologies in single-particle electron microscopy

PubMed Central

Schmeisser, Martin; Heisen, Burkhard C.; Luettich, Mario; Busche, Boris; Hauer, Florian; Koske, Tobias; Knauber, Karl-Heinz; Stark, Holger

2009-01-01

Most known methods for the determination of the structure of macromolecular complexes are limited or at least restricted at some point by their computational demands. Recent developments in information technology such as multicore, parallel and GPU processing can be used to overcome these limitations. In particular, graphics processing units (GPUs), which were originally developed for rendering real-time effects in computer games, are now ubiquitous and provide unprecedented computational power for scientific applications. Each parallel-processing paradigm alone can improve overall performance; the increased computational performance obtained by combining all paradigms, unleashing the full power of today’s technology, makes certain applications feasible that were previously virtually impossible. In this article, state-of-the-art paradigms are introduced, the tools and infrastructure needed to apply these paradigms are presented and a state-of-the-art infrastructure and solution strategy for moving scientific applications to the next generation of computer hardware is outlined. PMID:19564686

Methods for Prediction of High-Speed Reacting Flows in Aerospace Propulsion

NASA Technical Reports Server (NTRS)

Drummond, J. Philip

2014-01-01

Research to develop high-speed airbreathing aerospace propulsion systems was underway in the late 1950s. A major part of the effort involved the supersonic combustion ramjet, or scramjet, engine. Work had also begun to develop computational techniques for solving the equations governing the flow through a scramjet engine. However, scramjet technology and the computational methods to assist in its evolution would remain apart for another decade. The principal barrier was that the computational methods needed for engine evolution lacked the computer technology required for solving the discrete equations resulting from the numerical methods. Even today, computer resources remain a major pacing item in overcoming this barrier. Significant advances have been made over the past 35 years, however, in modeling the supersonic chemically reacting flow in a scramjet combustor. To see how scramjet development and the required computational tools finally merged, we briefly trace the evolution of the technology in both areas.

Computational materials science and engineering education: A survey of trends and needs

NASA Astrophysics Data System (ADS)

Thornton, K.; Nola, Samanthule; Edwin Garcia, R.; Asta, Mark; Olson, G. B.

2009-10-01

Results from a recent reassessment of the state of computational materials science and engineering (CMSE) education are reported. Surveys were distributed to the chairs and heads of materials programs, faculty members engaged in computational research, and employers of materials scientists and engineers, mainly in the United States. The data was compiled to assess current course offerings related to CMSE, the general climate for introducing computational methods in MSE curricula, and the requirements from the employers’ viewpoint. Furthermore, the available educational resources and their utilization by the community are examined. The surveys show a general support for integrating computational content into MSE education. However, they also reflect remaining issues with implementation, as well as a gap between the tools being taught in courses and those that are used by employers. Overall, the results suggest the necessity for a comprehensively developed vision and plans to further the integration of computational methods into MSE curricula.

Parallel, distributed and GPU computing technologies in single-particle electron microscopy.

PubMed

Schmeisser, Martin; Heisen, Burkhard C; Luettich, Mario; Busche, Boris; Hauer, Florian; Koske, Tobias; Knauber, Karl-Heinz; Stark, Holger

2009-07-01

Most known methods for the determination of the structure of macromolecular complexes are limited or at least restricted at some point by their computational demands. Recent developments in information technology such as multicore, parallel and GPU processing can be used to overcome these limitations. In particular, graphics processing units (GPUs), which were originally developed for rendering real-time effects in computer games, are now ubiquitous and provide unprecedented computational power for scientific applications. Each parallel-processing paradigm alone can improve overall performance; the increased computational performance obtained by combining all paradigms, unleashing the full power of today's technology, makes certain applications feasible that were previously virtually impossible. In this article, state-of-the-art paradigms are introduced, the tools and infrastructure needed to apply these paradigms are presented and a state-of-the-art infrastructure and solution strategy for moving scientific applications to the next generation of computer hardware is outlined.

Advances in Cross-Cutting Ideas for Computational Climate Science

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

Ng, Esmond; Evans, Katherine J.; Caldwell, Peter

This report presents results from the DOE-sponsored workshop titled, ``Advancing X-Cutting Ideas for Computational Climate Science Workshop,'' known as AXICCS, held on September 12--13, 2016 in Rockville, MD. The workshop brought together experts in climate science, computational climate science, computer science, and mathematics to discuss interesting but unsolved science questions regarding climate modeling and simulation, promoted collaboration among the diverse scientists in attendance, and brainstormed about possible tools and capabilities that could be developed to help address them. Emerged from discussions at the workshop were several research opportunities that the group felt could advance climate science significantly. These include (1)more » process-resolving models to provide insight into important processes and features of interest and inform the development of advanced physical parameterizations, (2) a community effort to develop and provide integrated model credibility, (3) including, organizing, and managing increasingly connected model components that increase model fidelity yet complexity, and (4) treating Earth system models as one interconnected organism without numerical or data based boundaries that limit interactions. The group also identified several cross-cutting advances in mathematics, computer science, and computational science that would be needed to enable one or more of these big ideas. It is critical to address the need for organized, verified, and optimized software, which enables the models to grow and continue to provide solutions in which the community can have confidence. Effectively utilizing the newest computer hardware enables simulation efficiency and the ability to handle output from increasingly complex and detailed models. This will be accomplished through hierarchical multiscale algorithms in tandem with new strategies for data handling, analysis, and storage. These big ideas and cross-cutting technologies for enabling breakthrough climate simulation advancements also need the "glue" of outreach and learning across the scientific domains to be successful. The workshop identified several strategies to allow productive, continuous engagement across those who have a broad knowledge of the various angles of the problem. Specific ideas to foster education and tools to make material progress were discussed. Examples include follow-on cross-cutting meetings that enable unstructured discussions of the types this workshop fostered. A concerted effort to recruit undergraduate and graduate students from all relevant domains and provide them experience, training, and networking across their immediate expertise is needed. This will broaden and expand their exposure to the future needs and solutions, and provide a pipeline of scientists with a diversity of knowledge and know-how. Providing real-world experience with subject matter experts from multiple angles may also motivate the students to attack these problems and even come up with the missing solutions.« less

Advances in Cross-Cutting Ideas for Computational Climate Science

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

Ng, E.; Evans, K.; Caldwell, P.

This report presents results from the DOE-sponsored workshop titled, Advancing X-Cutting Ideas for Computational Climate Science Workshop,'' known as AXICCS, held on September 12--13, 2016 in Rockville, MD. The workshop brought together experts in climate science, computational climate science, computer science, and mathematics to discuss interesting but unsolved science questions regarding climate modeling and simulation, promoted collaboration among the diverse scientists in attendance, and brainstormed about possible tools and capabilities that could be developed to help address them. Emerged from discussions at the workshop were several research opportunities that the group felt could advance climate science significantly. These include (1)more » process-resolving models to provide insight into important processes and features of interest and inform the development of advanced physical parameterizations, (2) a community effort to develop and provide integrated model credibility, (3) including, organizing, and managing increasingly connected model components that increase model fidelity yet complexity, and (4) treating Earth system models as one interconnected organism without numerical or data based boundaries that limit interactions. The group also identified several cross-cutting advances in mathematics, computer science, and computational science that would be needed to enable one or more of these big ideas. It is critical to address the need for organized, verified, and optimized software, which enables the models to grow and continue to provide solutions in which the community can have confidence. Effectively utilizing the newest computer hardware enables simulation efficiency and the ability to handle output from increasingly complex and detailed models. This will be accomplished through hierarchical multiscale algorithms in tandem with new strategies for data handling, analysis, and storage. These big ideas and cross-cutting technologies for enabling breakthrough climate simulation advancements also need the "glue" of outreach and learning across the scientific domains to be successful. The workshop identified several strategies to allow productive, continuous engagement across those who have a broad knowledge of the various angles of the problem. Specific ideas to foster education and tools to make material progress were discussed. Examples include follow-on cross-cutting meetings that enable unstructured discussions of the types this workshop fostered. A concerted effort to recruit undergraduate and graduate students from all relevant domains and provide them experience, training, and networking across their immediate expertise is needed. This will broaden and expand their exposure to the future needs and solutions, and provide a pipeline of scientists with a diversity of knowledge and know-how. Providing real-world experience with subject matter experts from multiple angles may also motivate the students to attack these problems and even come up with the missing solutions.« less

Development of computational small animal models and their applications in preclinical imaging and therapy research

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

Xie, Tianwu; Zaidi, Habib, E-mail: habib.zaidi@hcuge.ch; Geneva Neuroscience Center, Geneva University, Geneva CH-1205

The development of multimodality preclinical imaging techniques and the rapid growth of realistic computer simulation tools have promoted the construction and application of computational laboratory animal models in preclinical research. Since the early 1990s, over 120 realistic computational animal models have been reported in the literature and used as surrogates to characterize the anatomy of actual animals for the simulation of preclinical studies involving the use of bioluminescence tomography, fluorescence molecular tomography, positron emission tomography, single-photon emission computed tomography, microcomputed tomography, magnetic resonance imaging, and optical imaging. Other applications include electromagnetic field simulation, ionizing and nonionizing radiation dosimetry, and themore » development and evaluation of new methodologies for multimodality image coregistration, segmentation, and reconstruction of small animal images. This paper provides a comprehensive review of the history and fundamental technologies used for the development of computational small animal models with a particular focus on their application in preclinical imaging as well as nonionizing and ionizing radiation dosimetry calculations. An overview of the overall process involved in the design of these models, including the fundamental elements used for the construction of different types of computational models, the identification of original anatomical data, the simulation tools used for solving various computational problems, and the applications of computational animal models in preclinical research. The authors also analyze the characteristics of categories of computational models (stylized, voxel-based, and boundary representation) and discuss the technical challenges faced at the present time as well as research needs in the future.« less

Comparing student performance on paper- and computer-based math curriculum-based measures.

PubMed

Hensley, Kiersten; Rankin, Angelica; Hosp, John

2017-01-01

As the number of computerized curriculum-based measurement (CBM) tools increases, it is necessary to examine whether or not student performance can generalize across a variety of test administration modes (i.e., paper or computer). The purpose of this study is to compare math fact fluency on paper versus computer for 197 upper elementary students. Students completed identical sets of probes on paper and on the computer, which were then scored for digits correct, problems correct, and accuracy. Results showed a significant difference in performance between the two sets of probes, with higher fluency rates on the paper probes. Because decisions about levels of student support and interventions often rely on measures such as these, more research in this area is needed to examine the potential differences in student performance between paper-based and computer-based CBMs.

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

McCoy, Michel; Archer, Bill; Hendrickson, Bruce

The Stockpile Stewardship Program (SSP) is an integrated technical program for maintaining the safety, surety, and reliability of the U.S. nuclear stockpile. The SSP uses nuclear test data, computational modeling and simulation, and experimental facilities to advance understanding of nuclear weapons. It includes stockpile surveillance, experimental research, development and engineering programs, and an appropriately scaled production capability to support stockpile requirements. This integrated national program requires the continued use of experimental facilities and programs, and the computational capabilities to support these programs. The Advanced Simulation and Computing Program (ASC) is a cornerstone of the SSP, providing simulation capabilities and computationalmore » resources that support annual stockpile assessment and certification, study advanced nuclear weapons design and manufacturing processes, analyze accident scenarios and weapons aging, and provide the tools to enable stockpile Life Extension Programs (LEPs) and the resolution of Significant Finding Investigations (SFIs). This requires a balance of resource, including technical staff, hardware, simulation software, and computer science solutions. ASC is now focused on increasing predictive capabilities in a three-dimensional (3D) simulation environment while maintaining support to the SSP. The program continues to improve its unique tools for solving progressively more difficult stockpile problems (sufficient resolution, dimensionality, and scientific details), and quantifying critical margins and uncertainties. Resolving each issue requires increasingly difficult analyses because the aging process has progressively moved the stockpile further away from the original test base. Where possible, the program also enables the use of high performance computing (HPC) and simulation tools to address broader national security needs, such as foreign nuclear weapon assessments and counter nuclear terrorism.« less

Enabling a Scientific Cloud Marketplace: VGL (Invited)

NASA Astrophysics Data System (ADS)

Fraser, R.; Woodcock, R.; Wyborn, L. A.; Vote, J.; Rankine, T.; Cox, S. J.

2013-12-01

The Virtual Geophysics Laboratory (VGL) provides a flexible, web based environment where researchers can browse data and use a variety of scientific software packaged into tool kits that run in the Cloud. Both data and tool kits are published by multiple researchers and registered with the VGL infrastructure forming a data and application marketplace. The VGL provides the basic work flow of Discovery and Access to the disparate data sources and a Library for tool kits and scripting to drive the scientific codes. Computation is then performed on the Research or Commercial Clouds. Provenance information is collected throughout the work flow and can be published alongside the results allowing for experiment comparison and sharing with other researchers. VGL's "mix and match" approach to data, computational resources and scientific codes, enables a dynamic approach to scientific collaboration. VGL allows scientists to publish their specific contribution, be it data, code, compute or work flow, knowing the VGL framework will provide other components needed for a complete application. Other scientists can choose the pieces that suit them best to assemble an experiment. The coarse grain workflow of the VGL framework combined with the flexibility of the scripting library and computational toolkits allows for significant customisation and sharing amongst the community. The VGL utilises the cloud computational and storage resources from the Australian academic research cloud provided by the NeCTAR initiative and a large variety of data accessible from national and state agencies via the Spatial Information Services Stack (SISS - http://siss.auscope.org). VGL v1.2 screenshot - http://vgl.auscope.org

Cielo Computational Environment Usage Model With Mappings to ACE Requirements for the General Availability User Environment Capabilities Release Version 1.1

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

Vigil,Benny Manuel; Ballance, Robert; Haskell, Karen

Cielo is a massively parallel supercomputer funded by the DOE/NNSA Advanced Simulation and Computing (ASC) program, and operated by the Alliance for Computing at Extreme Scale (ACES), a partnership between Los Alamos National Laboratory (LANL) and Sandia National Laboratories (SNL). The primary Cielo compute platform is physically located at Los Alamos National Laboratory. This Cielo Computational Environment Usage Model documents the capabilities and the environment to be provided for the Q1 FY12 Level 2 Cielo Capability Computing (CCC) Platform Production Readiness Milestone. This document describes specific capabilities, tools, and procedures to support both local and remote users. The model ismore » focused on the needs of the ASC user working in the secure computing environments at Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory, or Sandia National Laboratories, but also addresses the needs of users working in the unclassified environment. The Cielo Computational Environment Usage Model maps the provided capabilities to the tri-Lab ASC Computing Environment (ACE) Version 8.0 requirements. The ACE requirements reflect the high performance computing requirements for the Production Readiness Milestone user environment capabilities of the ASC community. A description of ACE requirements met, and those requirements that are not met, are included in each section of this document. The Cielo Computing Environment, along with the ACE mappings, has been issued and reviewed throughout the tri-Lab community.« less

A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits.

PubMed

Mahjani, Behrang; Toor, Salman; Nettelblad, Carl; Holmgren, Sverker

2017-01-01

In quantitative trait locus (QTL) mapping significance of putative QTL is often determined using permutation testing. The computational needs to calculate the significance level are immense, 10 4 up to 10 8 or even more permutations can be needed. We have previously introduced the PruneDIRECT algorithm for multiple QTL scan with epistatic interactions. This algorithm has specific strengths for permutation testing. Here, we present a flexible, parallel computing framework for identifying multiple interacting QTL using the PruneDIRECT algorithm which uses the map-reduce model as implemented in Hadoop. The framework is implemented in R, a widely used software tool among geneticists. This enables users to rearrange algorithmic steps to adapt genetic models, search algorithms, and parallelization steps to their needs in a flexible way. Our work underlines the maturity of accessing distributed parallel computing for computationally demanding bioinformatics applications through building workflows within existing scientific environments. We investigate the PruneDIRECT algorithm, comparing its performance to exhaustive search and DIRECT algorithm using our framework on a public cloud resource. We find that PruneDIRECT is vastly superior for permutation testing, and perform 2 ×10 5 permutations for a 2D QTL problem in 15 hours, using 100 cloud processes. We show that our framework scales out almost linearly for a 3D QTL search.

Defining a Computational Framework for the Assessment of ...

EPA Pesticide Factsheets

The Adverse Outcome Pathway (AOP) framework describes the effects of environmental stressors across multiple scales of biological organization and function. This includes an evaluation of the potential for each key event to occur across a broad range of species in order to determine the taxonomic applicability of each AOP. Computational tools are needed to facilitate this process. Recently, we developed a tool that uses sequence homology to evaluate the applicability of molecular initiating events across species (Lalone et al., Toxicol. Sci., 2016). To extend our ability to make computational predictions at higher levels of biological organization, we have created the AOPdb. This database links molecular targets identified associated with key events in the AOPwiki to publically available data (e.g. gene-protein, pathway, species orthology, ontology, chemical, disease) including ToxCast assay information. The AOPdb combines different data types in order to characterize the impacts of chemicals to human health and the environment and serves as a decision support tool for case study development in the area of taxonomic applicability. As a proof of concept, the AOPdb allows identification of relevant molecular targets, biological pathways, and chemical and disease associations across species for four AOPs from the AOP-Wiki (https://aopwiki.org): Estrogen receptor antagonism leading to reproductive dysfunction (Aop:30); Aromatase inhibition leading to reproductive d

SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data.

PubMed

Woodhouse, Steven; Piterman, Nir; Wintersteiger, Christoph M; Göttgens, Berthold; Fisher, Jasmin

2018-05-25

Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease processes. New ambitious efforts like the Human Cell Atlas will soon lead to an explosion of data with potential for uncovering and understanding the regulatory networks which underlie the behaviour of all human cells. In order to take advantage of this data, however, there is a need for general-purpose, user-friendly and efficient computational tools that can be readily used by biologists who do not have specialist computer science knowledge. The Single Cell Network Synthesis toolkit (SCNS) is a general-purpose computational tool for the reconstruction and analysis of executable models from single-cell gene expression data. Through a graphical user interface, SCNS takes single-cell qPCR or RNA-sequencing data taken across a time course, and searches for logical rules that drive transitions from early cell states towards late cell states. Because the resulting reconstructed models are executable, they can be used to make predictions about the effect of specific gene perturbations on the generation of specific lineages. SCNS should be of broad interest to the growing number of researchers working in single-cell genomics and will help further facilitate the generation of valuable mechanistic insights into developmental, homeostatic and disease processes.

Enhancements in medicine by integrating content based image retrieval in computer-aided diagnosis

NASA Astrophysics Data System (ADS)

Aggarwal, Preeti; Sardana, H. K.

2010-02-01

Computer-aided diagnosis (CAD) has become one of the major research subjects in medical imaging and diagnostic radiology. With cad, radiologists use the computer output as a "second opinion" and make the final decisions. Retrieving images is a useful tool to help radiologist to check medical image and diagnosis. The impact of contentbased access to medical images is frequently reported but existing systems are designed for only a particular context of diagnosis. The challenge in medical informatics is to develop tools for analyzing the content of medical images and to represent them in a way that can be efficiently searched and compared by the physicians. CAD is a concept established by taking into account equally the roles of physicians and computers. To build a successful computer aided diagnostic system, all the relevant technologies, especially retrieval need to be integrated in such a manner that should provide effective and efficient pre-diagnosed cases with proven pathology for the current case at the right time. In this paper, it is suggested that integration of content-based image retrieval (CBIR) in cad can bring enormous results in medicine especially in diagnosis. This approach is also compared with other approaches by highlighting its advantages over those approaches.

A comparative study of the Unified System for Orbit Computation and the Flight Design System. [computer programs for mission planning tasks associated with space shuttle

NASA Technical Reports Server (NTRS)

Maag, W.

1977-01-01

The Flight Design System (FDS) and the Unified System for Orbit Computation (USOC) are compared and described in relation to mission planning for the shuttle transportation system (STS). The FDS is designed to meet the requirements of a standardized production tool and the USOC is designed for rapid generation of particular application programs. The main emphasis in USOC is put on adaptability to new types of missions. It is concluded that a software system having a USOC-like structure, adapted to the specific needs of MPAD, would be appropriate to support planning tasks in the area unique to STS missions.

New insights into faster computation of uncertainties

NASA Astrophysics Data System (ADS)

Bhattacharya, Atreyee

2012-11-01

Heavy computation power, lengthy simulations, and an exhaustive number of model runs—often these seem like the only statistical tools that scientists have at their disposal when computing uncertainties associated with predictions, particularly in cases of environmental processes such as groundwater movement. However, calculation of uncertainties need not be as lengthy, a new study shows. Comparing two approaches—the classical Bayesian “credible interval” and a less commonly used regression-based “confidence interval” method—Lu et al. show that for many practical purposes both methods provide similar estimates of uncertainties. The advantage of the regression method is that it demands 10-1000 model runs, whereas the classical Bayesian approach requires 10,000 to millions of model runs.

Crashworthiness: Planes, trains, and automobiles

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

Logan, R.W.; Tokarz, F.J.; Whirley, R.G.

A powerful DYNA3D computer code simulates the dynamic effects of stress traveling through structures. It is the most advanced modeling tool available to study crashworthiness problems and to analyze impacts. Now used by some 1000 companies, government research laboratories, and universities in the U.S. and abroad, DYNA3D is also a preeminent example of successful technology transfer. The initial interest in such a code was to simulate the structural response of weapons systems. The need was to model not the explosive or nuclear events themselves but rather the impacts of weapons systems with the ground, tracking the stress waves as theymore » move through the object. This type of computer simulation augmented or, in certain cases, reduced the need for expensive and time-consuming crash testing.« less

Use of application containers and workflows for genomic data analysis.

PubMed

Schulz, Wade L; Durant, Thomas J S; Siddon, Alexa J; Torres, Richard

2016-01-01

The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.

Galileo Teacher Training Program - GTTP Days

NASA Astrophysics Data System (ADS)

Heenatigala, T.; Doran, R.

2012-09-01

Despite the vast availability of teaching resources on the internet, finding a quality and user-friendly materials is a challenge. Many teachers are not trained with proper computing skills to search for the right materials. With years of expertise training teachers globally, Galileo Teacher Training Program (GTTP) [1] recognize the need of having a go-to place for teachers to access resources. To fill this need GTTP developed - GTTP Days - a program creating resource guides for planetary, lunar and solar fields. Avoiding the imbalance in science resources between the developed and undeveloped world, GTTP Days is available both online and offline as a printable version. Each resource guide covers areas such as scientific knowledge, exploration, observation, photography, art & culture and web tools. The lesson plans of each guide include hands-on activities, web tools, software tools, and activities for people with disabilities [2]. Each activity indicate the concepts used, the skills required and age level which guides the teachers and educators to select the correct content suitable for local curriculum.

Digital interactive learning of oral radiographic anatomy.

PubMed

Vuchkova, J; Maybury, T; Farah, C S

2012-02-01

Studies reporting high number of diagnostic errors made from radiographs suggest the need to improve the learning of radiographic interpretation in the dental curriculum. Given studies that show student preference for computer-assisted or digital technologies, the purpose of this study was to develop an interactive digital tool and to determine whether it was more successful than a conventional radiology textbook in assisting dental students with the learning of radiographic anatomy. Eighty-eight dental students underwent a learning phase of radiographic anatomy using an interactive digital tool alongside a conventional radiology textbook. The success of the digital tool, when compared to the textbook, was assessed by quantitative means using a radiographic interpretation test and by qualitative means using a structured Likert scale survey, asking students to evaluate their own learning outcomes from the digital tool. Student evaluations of the digital tool showed that almost all participants (95%) indicated that the tool positively enhanced their learning of radiographic anatomy and interpretation. The success of the digital tool in assisting the learning of radiographic interpretation is discussed in the broader context of learning and teaching curricula, and preference (by students) for the use of this digital form when compared to the conventional literate form of the textbook. Whilst traditional textbooks are still valued in the dental curriculum, it is evident that the preference for computer-assisted learning of oral radiographic anatomy enhances the learning experience by enabling students to interact and better engage with the course material. © 2011 John Wiley & Sons A/S.

Addressing unmet need for HIV testing in emergency care settings: a role for computer-facilitated rapid HIV testing?

PubMed

Kurth, Ann E; Severynen, Anneleen; Spielberg, Freya

2013-08-01

HIV testing in emergency departments (EDs) remains underutilized. The authors evaluated a computer tool to facilitate rapid HIV testing in an urban ED. Randomly assigned nonacute adult ED patients were randomly assigned to a computer tool (CARE) and rapid HIV testing before a standard visit (n = 258) or to a standard visit (n = 259) with chart access. The authors assessed intervention acceptability and compared noted HIV risks. Participants were 56% nonWhite and 58% male; median age was 37 years. In the CARE arm, nearly all (251/258) of the patients completed the session and received HIV results; four declined to consent to the test. HIV risks were reported by 54% of users; one participant was confirmed HIV-positive, and two were confirmed false-positive (seroprevalence 0.4%, 95% CI [0.01, 2.2]). Half (55%) of the patients preferred computerized rather than face-to-face counseling for future HIV testing. In the standard arm, one HIV test and two referrals for testing occurred. Computer-facilitated HIV testing appears acceptable to ED patients. Future research should assess cost-effectiveness compared with staff-delivered approaches.

Overview of the SAMSI year-long program on Statistical, Mathematical and Computational Methods for Astronomy

NASA Astrophysics Data System (ADS)

Jogesh Babu, G.

2017-01-01

A year-long research (Aug 2016- May 2017) program on `Statistical, Mathematical and Computational Methods for Astronomy (ASTRO)’ is well under way at Statistical and Applied Mathematical Sciences Institute (SAMSI), a National Science Foundation research institute in Research Triangle Park, NC. This program has brought together astronomers, computer scientists, applied mathematicians and statisticians. The main aims of this program are: to foster cross-disciplinary activities; to accelerate the adoption of modern statistical and mathematical tools into modern astronomy; and to develop new tools needed for important astronomical research problems. The program provides multiple avenues for cross-disciplinary interactions, including several workshops, long-term visitors, and regular teleconferences, so participants can continue collaborations, even if they can only spend limited time in residence at SAMSI. The main program is organized around five working groups:i) Uncertainty Quantification and Astrophysical Emulationii) Synoptic Time Domain Surveysiii) Multivariate and Irregularly Sampled Time Seriesiv) Astrophysical Populationsv) Statistics, computation, and modeling in cosmology.A brief description of each of the work under way by these groups will be given. Overlaps among various working groups will also be highlighted. How the wider astronomy community can both participate and benefit from the activities, will be briefly mentioned.

Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery

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

Nugent, Peter E.; Simonson, J. Michael

2011-10-24

This report is based on the Department of Energy (DOE) Workshop on “Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery” that was held at the Bethesda Marriott in Maryland on October 24-25, 2011. The workshop brought together leading researchers from the Basic Energy Sciences (BES) facilities and Advanced Scientific Computing Research (ASCR). The workshop was co-sponsored by these two Offices to identify opportunities and needs for data analysis, ownership, storage, mining, provenance and data transfer at light sources, neutron sources, microscopy centers and other facilities. Their charge was to identify current and anticipated issues inmore » the acquisition, analysis, communication and storage of experimental data that could impact the progress of scientific discovery, ascertain what knowledge, methods and tools are needed to mitigate present and projected shortcomings and to create the foundation for information exchanges and collaboration between ASCR and BES supported researchers and facilities. The workshop was organized in the context of the impending data tsunami that will be produced by DOE’s BES facilities. Current facilities, like SLAC National Accelerator Laboratory’s Linac Coherent Light Source, can produce up to 18 terabytes (TB) per day, while upgraded detectors at Lawrence Berkeley National Laboratory’s Advanced Light Source will generate ~10TB per hour. The expectation is that these rates will increase by over an order of magnitude in the coming decade. The urgency to develop new strategies and methods in order to stay ahead of this deluge and extract the most science from these facilities was recognized by all. The four focus areas addressed in this workshop were: Workflow Management - Experiment to Science: Identifying and managing the data path from experiment to publication. Theory and Algorithms: Recognizing the need for new tools for computation at scale, supporting large data sets and realistic theoretical models. Visualization and Analysis: Supporting near-real-time feedback for experiment optimization and new ways to extract and communicate critical information from large data sets. Data Processing and Management: Outlining needs in computational and communication approaches and infrastructure needed to handle unprecedented data volume and information content. It should be noted that almost all participants recognized that there were unlikely to be any turn-key solutions available due to the unique, diverse nature of the BES community, where research at adjacent beamlines at a given light source facility often span everything from biology to materials science to chemistry using scattering, imaging and/or spectroscopy. However, it was also noted that advances supported by other programs in data research, methodologies, and tool development could be implemented on reasonable time scales with modest effort. Adapting available standard file formats, robust workflows, and in-situ analysis tools for user facility needs could pay long-term dividends. Workshop participants assessed current requirements as well as future challenges and made the following recommendations in order to achieve the ultimate goal of enabling transformative science in current and future BES facilities: Theory and analysis components should be integrated seamlessly within experimental workflow. Develop new algorithms for data analysis based on common data formats and toolsets. Move analysis closer to experiment. Move the analysis closer to the experiment to enable real-time (in-situ) streaming capabilities, live visualization of the experiment and an increase of the overall experimental efficiency. Match data management access and capabilities with advancements in detectors and sources. Remove bottlenecks, provide interoperability across different facilities/beamlines and apply forefront mathematical techniques to more efficiently extract science from the experiments. This workshop report examines and reviews the status of several BES facilities and highlights the successes and shortcomings of the current data and communication pathways for scientific discovery. It then ascertains what methods and tools are needed to mitigate present and projected data bottlenecks to science over the next 10 years. The goal of this report is to create the foundation for information exchanges and collaborations among ASCR and BES supported researchers, the BES scientific user facilities, and ASCR computing and networking facilities. To jumpstart these activities, there was a strong desire to see a joint effort between ASCR and BES along the lines of the highly successful Scientific Discovery through Advanced Computing (SciDAC) program in which integrated teams of engineers, scientists and computer scientists were engaged to tackle a complete end-to-end workflow solution at one or more beamlines, to ascertain what challenges will need to be addressed in order to handle future increases in data« less

Health literacy screening instruments for eHealth applications: a systematic review.

PubMed

Collins, Sarah A; Currie, Leanne M; Bakken, Suzanne; Vawdrey, David K; Stone, Patricia W

2012-06-01

To systematically review current health literacy (HL) instruments for use in consumer-facing and mobile health information technology screening and evaluation tools. The databases, PubMed, OVID, Google Scholar, Cochrane Library and Science Citation Index, were searched for health literacy assessment instruments using the terms "health", "literacy", "computer-based," and "psychometrics". All instruments identified by this method were critically appraised according to their reported psychometric properties and clinical feasibility. Eleven different health literacy instruments were found. Screening questions, such as asking a patient about his/her need for assistance in navigating health information, were evaluated in seven different studies and are promising for use as a valid, reliable, and feasible computer-based approach to identify patients that struggle with low health literacy. However, there was a lack of consistency in the types of screening questions proposed. There is also a lack of information regarding the psychometric properties of computer-based health literacy instruments. Only English language health literacy assessment instruments were reviewed and analyzed. Current health literacy screening tools demonstrate varying benefits depending on the context of their use. In many cases, it seems that a single screening question may be a reliable, valid, and feasible means for establishing health literacy. A combination of screening questions that assess health literacy and technological literacy may enable tailoring eHealth applications to user needs. Further research should determine the best screening question(s) and the best synthesis of various instruments' content and methodologies for computer-based health literacy screening and assessment. Copyright © 2012 Elsevier Inc. All rights reserved.

Health Literacy Screening Instruments for eHealth Applications: A Systematic Review

PubMed Central

Collins, Sarah A.; Currie, Leanne M.; Bakken, Suzanne; Vawdrey, David K.; Stone, Patricia W.

2012-01-01

Objective To systematically review current health literacy (HL) instruments for use in consumer-facing and mobile health information technology screening and evaluation tools. Design The databases, PubMed, OVID, Google Scholar, Cochrane Library and Science Citation Index, were searched for health literacy assessment instruments using the terms “health”, “literacy”, “computer-based,” and “psychometrics”. All instruments identified by this method were critically appraised according to their reported psychometric properties and clinical feasibility. Results Eleven different health literacy instruments were found. Screening questions, such as asking a patient about his/her need for assistance in navigating health information, were evaluated in 7 different studies and are promising for use as a valid, reliable, and feasible computer-based approach to identify patients that struggle with low health literacy. However, there was a lack of consistency in the types of screening questions proposed. There is also a lack of information regarding the psychometric properties of computer-based health literacy instruments. Limitations Only English language health literacy assessment instruments were reviewed and analyzed. Conclusions Current health literacy screening tools demonstrate varying benefits depending on the context of their use. In many cases, it seems that a single screening question may be a reliable, valid, and feasible means for establishing health literacy. A combination of screening questions that assess health literacy and technological literacy may enable tailoring eHealth applications to user needs. Further research should determine the best screening question(s) and the best synthesis of various instruments’ content and methodologies for computer-based health literacy screening and assessment. PMID:22521719

Computational materials chemistry for carbon capture using porous materials

NASA Astrophysics Data System (ADS)

Sharma, Abhishek; Huang, Runhong; Malani, Ateeque; Babarao, Ravichandar

2017-11-01

Control over carbon dioxide (CO2) release is extremely important to decrease its hazardous effects on the environment such as global warming, ocean acidification, etc. For CO2 capture and storage at industrial point sources, nanoporous materials offer an energetically viable and economically feasible approach compared to chemisorption in amines. There is a growing need to design and synthesize new nanoporous materials with enhanced capability for carbon capture. Computational materials chemistry offers tools to screen and design cost-effective materials for CO2 separation and storage, and it is less time consuming compared to trial and error experimental synthesis. It also provides a guide to synthesize new materials with better properties for real world applications. In this review, we briefly highlight the various carbon capture technologies and the need of computational materials design for carbon capture. This review discusses the commonly used computational chemistry-based simulation methods for structural characterization and prediction of thermodynamic properties of adsorbed gases in porous materials. Finally, simulation studies reported on various potential porous materials, such as zeolites, porous carbon, metal organic frameworks (MOFs) and covalent organic frameworks (COFs), for CO2 capture are discussed.

Computational Fluid Dynamic Analysis of Hydrodynamic forces on inundated bridge decks

NASA Astrophysics Data System (ADS)

Afzal, Bushra; Guo, Junke; Kerenyi, Kornel

2010-11-01

The hydraulic forces experienced by an inundated bridge deck have great importance in the design of bridges. Flood flows or hurricane add significant hydrodynamic loading on bridges, possibly resulting in failure of the bridge superstructures. The objective of the study is to establish validated computational practice to address research needs of the transportation community via computational fluid dynamic simulations. The reduced scale experiments conducted at Turner-Fairbank Highway Research Center establish the foundations of validated computational practices to address the research needs of the transportation community. Three bridge deck prototypes were used: a typical six-girder highway bridge deck, a three-girder deck, and a streamlined deck designed to better withstand the hydraulic forces. Results of the study showed that the streamlined deck significantly reduces drag, lift, and moment coefficient in comparison to the other bridge deck types. The CFD results matched the experimental data in terms of the relationship between inundation ratio and force measured at the bridge. The results of the present research will provide a tool for designing new bridges and retrofitting old ones.

Computer literacy: Where are nurse educators on the continuum?

PubMed

Hanley, Elizabeth

2006-01-01

Computers are becoming ubiquitous in health and education, and it is expected that nurses from undergraduate nursing programmes are computer literate when they enter the workforce. Similarly nurse educators are expected to be computer literate to model the use of information technology in their workplace. They are expected to use email for communication and a range of computer applications for presentation of course materials and reports. Additionally, as more courses are delivered in flexible mode, educators require more comprehensive computing skills, including confidence and competence in a range of applications. A cohort of nurse educators from one tertiary institution was surveyed to assess their perceived computer literacy and how they attained this. A questionnaire that covered seven domains of computer literacy was used to assess this. The results were illuminating and identified specific training needs for this group. Their perceived lack of skill with Groupwise email and the student database program are of concern as these are essential tools for nurse educators at this polytechnic.

Computational methods in metabolic engineering for strain design.

PubMed

Long, Matthew R; Ong, Wai Kit; Reed, Jennifer L

2015-08-01

Metabolic engineering uses genetic approaches to control microbial metabolism to produce desired compounds. Computational tools can identify new biological routes to chemicals and the changes needed in host metabolism to improve chemical production. Recent computational efforts have focused on exploring what compounds can be made biologically using native, heterologous, and/or enzymes with broad specificity. Additionally, computational methods have been developed to suggest different types of genetic modifications (e.g. gene deletion/addition or up/down regulation), as well as suggest strategies meeting different criteria (e.g. high yield, high productivity, or substrate co-utilization). Strategies to improve the runtime performances have also been developed, which allow for more complex metabolic engineering strategies to be identified. Future incorporation of kinetic considerations will further improve strain design algorithms. Copyright © 2015 Elsevier Ltd. All rights reserved.

The reduced basis method for the electric field integral equation

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

Fares, M., E-mail: fares@cerfacs.f; Hesthaven, J.S., E-mail: Jan_Hesthaven@Brown.ed; Maday, Y., E-mail: maday@ann.jussieu.f

We introduce the reduced basis method (RBM) as an efficient tool for parametrized scattering problems in computational electromagnetics for problems where field solutions are computed using a standard Boundary Element Method (BEM) for the parametrized electric field integral equation (EFIE). This combination enables an algorithmic cooperation which results in a two step procedure. The first step consists of a computationally intense assembling of the reduced basis, that needs to be effected only once. In the second step, we compute output functionals of the solution, such as the Radar Cross Section (RCS), independently of the dimension of the discretization space, formore » many different parameter values in a many-query context at very little cost. Parameters include the wavenumber, the angle of the incident plane wave and its polarization.« less

An interactive tool for visualization of spike train synchronization.

PubMed

Terry, Kevin

2010-08-15

A number of studies have examined the synchronization of central and peripheral spike trains by applying signal analysis techniques in the time and frequency domains. These analyses can reveal the presence of one or more common neural inputs that produce synchronization. However, synchronization measurements can fluctuate significantly due to the inherent variability of neural discharges and a finite data record length. Moreover, the effect of these natural variations is further compounded by the number of parameters available for calculating coherence in the frequency domain and the number of indices used to quantify short-term synchronization (STS) in the time domain. The computational tool presented here provides the user with an interactive environment that dynamically calculates and displays spike train properties along with STS and coherence indices to show how these factors interact. It is intended for a broad range of users, from those who are new to synchronization to experienced researchers who want to develop more meaningful and effective computational and experimental studies. To ensure this freely available tool meets the needs of all users, there are two versions. The first is a stand-alone version for educational use that can run on any computer. The second version can be modified and expanded by researchers who want to explore more in-depth questions about synchronization. Therefore, the distribution and use of this tool should both improve the understanding of fundamental spike train synchronization dynamics and produce more efficient and meaningful synchronization studies. (c) 2010 Elsevier B.V. All rights reserved.

High School Teachers' Problem Solving Activities to Review and Extend Their Mathematical and Didactical Knowledge

ERIC Educational Resources Information Center

Santos-Trigo, Manuel; Barrera-Mora, Fernando

2011-01-01

The study documents the extent to which high school teachers reflect on their need to revise and extend their mathematical and practicing knowledge. In this context, teachers worked on a set of tasks as a part of an inquiring community that promoted the use of different computational tools in problem solving approaches. Results indicated that the…

Data needs for X-ray astronomy satellites

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

Kallman, T.

I review the current status of atomic data for X-ray astronomy satellites. This includes some of the astrophysical issues which can be addressed, current modeling and analysis techniques, computational tools, the limitations imposed by currently available atomic data, and the validity of standard assumptions. I also discuss the future: challenges associated with future missions and goals for atomic data collection.

Total System Design (TSD) Methodology Assessment.

DTIC Science & Technology

1983-01-01

hardware implementation. Author: Martin - Marietta Aerospace Title: Total System Design Methodology Source: Martin - Marietta Technical Report MCR -79-646...systematic, rational approach to computer systems design is needed. Martin - Marietta has produced a Total System Design Methodology to support such design...gathering and ordering. The purpose of the paper is to document the existing TSD methoeology at Martin - Marietta , describe the supporting tools, and

Getting It Going--Keeping It Running: A Handbook for Career Information Systems.

ERIC Educational Resources Information Center

Clyde, John S.

This handbook was designed as a tool to assist school and agency staff in management and in-service training needed in implementing a comprehensive Career Information System (CIS). The background, goals, and organization of CIS are given briefly. An explanation of the System which is computer-based yet also employs a manual needle-sort system is…

Overview of Human-Centric Space Situational Awareness Science and Technology

DTIC Science & Technology

2012-09-01

AGI), the developers of Satellite Tool Kit ( STK ), has provided demonstrations of innovative SSA visualization concepts that take advantage of the...needs inherent with SSA. RH has conducted CTAs and developed work-centered human-computer interfaces, visualizations , and collaboration technologies...all end users. RH’s Battlespace Visualization Branch researches methods to exploit the visual channel primarily to improve decision making and

Factors Affecting Students' Acceptance of Tablet PCs: A Study in Italian High Schools

ERIC Educational Resources Information Center

Cacciamani, Stefano; Villani, Daniela; Bonanomi, Andrea; Carissoli, Claudia; Olivari, Maria Giulia; Morganti, Laura; Riva, Giuseppe; Confalonieri, Emanuela

2018-01-01

To maximize the advantages of the tablet personal computer (TPC) at school, this technology needs to be accepted by students as new tool for learning. With reference to the Technology Acceptance Model and the Unified Theory of Acceptance and Use of Technology, the aims of this study were (a) to analyze factors influencing high school students'…

Development and Testing of a High School Business Game. Final Report.

ERIC Educational Resources Information Center

McNair, Douglas D.; West, Alfred P., Jr.

A computer based business game to be used as a teaching tool in high school business-related courses was designed, developed, and tested. The game is constructed in modules that can be linked together in a variety of ways to achieve a different decision configuration for different class needs and a changing configuration over time to parallel the…

Patentability aspects of computational cancer models

NASA Astrophysics Data System (ADS)

Lishchuk, Iryna

2017-07-01

Multiscale cancer models, implemented in silico, simulate tumor progression at various spatial and temporal scales. Having the innovative substance and possessing the potential of being applied as decision support tools in clinical practice, patenting and obtaining patent rights in cancer models seems prima facie possible. What legal hurdles the cancer models need to overcome for being patented we inquire from this paper.

In-Service Teachers' Self-Efficacy, Professional Development, and Web 2.0 Tools for Integration

ERIC Educational Resources Information Center

Pan, Shu Chien; Franklin, Teresa

2011-01-01

Background: The implementation and integration of computer technologies in K-12 education has seen nearly constant growth since the early 1980s (Culp, Honey, Mandinach & Bailey, 2003), in part because this trend has become synonymous with skills that students will need as participants in a competitive global economy (Culp et al., 2003). It has…

DDGui, a new and fast way to analyse DRAGON and DONJON code results

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

Chambon, R.; Marleau, G.

2012-07-01

With the largely increased performance of computer, the results from DRAGON and DONJON have increase in size and complexity. The scroll, copy and paste technique to get the result is not appropriate anymore. Many in-house script, software, macro have been developed to make the data gathering easier. However, the limit of these solutions is their specificity and the difficulty to export them from one place to another. A general tool usable and accessible by everyone was needed. The first bricks for a very fast and intuitive way to analyse the DRAGON and DONJON results have been put together in themore » graphic user interface DDGUI. Based on the extensive ROOT C++ package, the possible features are numerous. For this first version of the software, we have programmed the fundamental tools which may be the more useful on an everyday basis: view the data structures content, draw the geometry and draw the flux or power from a DONJON computation. The tests show how amazingly fast the user can get the information needed for a general overview or more precise analyses. Several other features will be implemented in the near feature. (authors)« less

Remote Sensing: A valuable tool in the Forest Service decision making process. [in Utah

NASA Technical Reports Server (NTRS)

Stanton, F. L.

1975-01-01

Forest Service studies for integrating remotely sensed data into existing information systems highlight a need to: (1) re-examine present methods of collecting and organizing data, (2) develop an integrated information system for rapidly processing and interpreting data, (3) apply existing technological tools in new ways, and (4) provide accurate and timely information for making right management decisions. The Forest Service developed an integrated information system using remote sensors, microdensitometers, computer hardware and software, and interactive accessories. Their efforts substantially reduce the time it takes for collecting and processing data.

Langley Ground Facilities and Testing in the 21st Century

NASA Technical Reports Server (NTRS)

Ambur, Damodar R.; Kegelman, Jerome T.; Kilgore, William A.

2010-01-01

A strategic approach for retaining and more efficiently operating the essential Langley Ground Testing Facilities in the 21st Century is presented. This effort takes advantage of the previously completed and ongoing studies at the Agency and National levels. This integrated approach takes into consideration the overall decline in test business base within the nation and reduced utilization in each of the Langley facilities with capabilities to test in the subsonic, transonic, supersonic, and hypersonic speed regimes. The strategy accounts for capability needs to meet the Agency programmatic requirements and strategic goals and to execute test activities in the most efficient and flexible facility operating structure. The structure currently being implemented at Langley offers agility to right-size our capability and capacity from a national perspective, to accommodate the dynamic nature of the testing needs, and will address the influence of existing and emerging analytical tools for design. The paradigm for testing in the retained facilities is to efficiently and reliably provide more accurate and high-quality test results at an affordable cost to support design information needs for flight regimes where the computational capability is not adequate and to verify and validate the existing and emerging computational tools. Each of the above goals are planned to be achieved, keeping in mind the increasing small industry customer base engaged in developing unpiloted aerial vehicles and commercial space transportation systems.

Exploring Midwives' Need and Intention to Adopt Electronic Integrated Antenatal Care

PubMed Central

Markam, Hosizah; Hochheiser, Harry; Kuntoro, Kuntoro; Notobroto, Hari Basuki

2018-01-01

Documentation requirements for the Indonesian integrated antenatal care (ANC) program suggest the need for electronic systems to address gaps in existing paper documentation practices. Our goals were to quantify midwives' documentation completeness in a primary healthcare center, understand documentation challenges, develop a tool, and assess intention to use the tool. We analyzed existing ANC records in a primary healthcare center in Bangkalan, East Java, and conducted interviews with stakeholders to understand needs for an electronic system in support of ANC. Development of the web-based Electronic Integrated ANC (e-iANC) system used the System Development Life Cycle method. Training on the use of the system was held in the computer laboratory for 100 midwives chosen from four primary healthcare centers in each of five regions. The Unified Theory of Acceptance and Use of Technology (UTAUT) questionnaire was used to assess their intention to adopt e-iANC. The midwives' intention to adopt e-iANC was significantly influenced by performance expectancy, effort expectancy and facilitating conditions. Age, education level, and computer literacy did not significantly moderate the effects of performance expectancy and effort expectancy on adoption intention. The UTAUT results indicated that the factors that might influence intention to adopt e-iANC are potentially addressable. Results suggest that e-iANC might well be accepted by midwives. PMID:29618961

Experimenter's laboratory for visualized interactive science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Klemp, Marjorie K.; Lasater, Sally W.; Szczur, Marti R.; Klemp, Joseph B.

1992-01-01

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

Experimenter's laboratory for visualized interactive science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Klemp, Marjorie K.; Lasater, Sally W.; Szczur, Marti R.; Klemp, Joseph B.

1993-01-01

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperatable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color-shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

FITSManager: Management of Personal Astronomical Data

NASA Astrophysics Data System (ADS)

Cui, Chenzhou; Fan, Dongwei; Zhao, Yongheng; Kembhavi, Ajit; He, Boliang; Cao, Zihuang; Li, Jian; Nandrekar, Deoyani

2011-07-01

With the increase of personal storage capacity, it is easy to find hundreds to thousands of FITS files in the personal computer of an astrophysicist. Because Flexible Image Transport System (FITS) is a professional data format initiated by astronomers and used mainly in the small community, data management toolkits for FITS files are very few. Astronomers need a powerful tool to help them manage their local astronomical data. Although Virtual Observatory (VO) is a network oriented astronomical research environment, its applications and related technologies provide useful solutions to enhance the management and utilization of astronomical data hosted in an astronomer's personal computer. FITSManager is such a tool to provide astronomers an efficient management and utilization of their local data, bringing VO to astronomers in a seamless and transparent way. FITSManager provides fruitful functions for FITS file management, like thumbnail, preview, type dependent icons, header keyword indexing and search, collaborated working with other tools and online services, and so on. The development of the FITSManager is an effort to fill the gap between management and analysis of astronomical data.

Big Data Approaches for the Analysis of Large-Scale fMRI Data Using Apache Spark and GPU Processing: A Demonstration on Resting-State fMRI Data from the Human Connectome Project

PubMed Central

Boubela, Roland N.; Kalcher, Klaudius; Huf, Wolfgang; Našel, Christian; Moser, Ewald

2016-01-01

Technologies for scalable analysis of very large datasets have emerged in the domain of internet computing, but are still rarely used in neuroimaging despite the existence of data and research questions in need of efficient computation tools especially in fMRI. In this work, we present software tools for the application of Apache Spark and Graphics Processing Units (GPUs) to neuroimaging datasets, in particular providing distributed file input for 4D NIfTI fMRI datasets in Scala for use in an Apache Spark environment. Examples for using this Big Data platform in graph analysis of fMRI datasets are shown to illustrate how processing pipelines employing it can be developed. With more tools for the convenient integration of neuroimaging file formats and typical processing steps, big data technologies could find wider endorsement in the community, leading to a range of potentially useful applications especially in view of the current collaborative creation of a wealth of large data repositories including thousands of individual fMRI datasets. PMID:26778951

Highlights of the Workshop

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1997-01-01

Economic stresses are forcing many industries to reduce cost and time-to-market, and to insert emerging technologies into their products. Engineers are asked to design faster, ever more complex systems. Hence, there is a need for novel design paradigms and effective design tools to reduce the design and development times. Several computational tools and facilities have been developed to support the design process. Some of these are described in subsequent presentations. The focus of the workshop is on the computational tools and facilities which have high potential for use in future design environment for aerospace systems. The outline for the introductory remarks is given. First, the characteristics and design drivers for future aerospace systems are outlined; second, simulation-based design environment, and some of its key modules are described; third, the vision for the next-generation design environment being planned by NASA, the UVA ACT Center and JPL is presented. The anticipated major benefits of the planned environment are listed; fourth, some of the government-supported programs related to simulation-based design are listed; and fifth, the objectives and format of the workshop are presented.

Modeling NIF experimental designs with adaptive mesh refinement and Lagrangian hydrodynamics

NASA Astrophysics Data System (ADS)

Koniges, A. E.; Anderson, R. W.; Wang, P.; Gunney, B. T. N.; Becker, R.; Eder, D. C.; MacGowan, B. J.; Schneider, M. B.

2006-06-01

Incorporation of adaptive mesh refinement (AMR) into Lagrangian hydrodynamics algorithms allows for the creation of a highly powerful simulation tool effective for complex target designs with three-dimensional structure. We are developing an advanced modeling tool that includes AMR and traditional arbitrary Lagrangian-Eulerian (ALE) techniques. Our goal is the accurate prediction of vaporization, disintegration and fragmentation in National Ignition Facility (NIF) experimental target elements. Although our focus is on minimizing the generation of shrapnel in target designs and protecting the optics, the general techniques are applicable to modern advanced targets that include three-dimensional effects such as those associated with capsule fill tubes. Several essential computations in ordinary radiation hydrodynamics need to be redesigned in order to allow for AMR to work well with ALE, including algorithms associated with radiation transport. Additionally, for our goal of predicting fragmentation, we include elastic/plastic flow into our computations. We discuss the integration of these effects into a new ALE-AMR simulation code. Applications of this newly developed modeling tool as well as traditional ALE simulations in two and three dimensions are applied to NIF early-light target designs.

Distributed data mining on grids: services, tools, and applications.

PubMed

Cannataro, Mario; Congiusta, Antonio; Pugliese, Andrea; Talia, Domenico; Trunfio, Paolo

2004-12-01

Data mining algorithms are widely used today for the analysis of large corporate and scientific datasets stored in databases and data archives. Industry, science, and commerce fields often need to analyze very large datasets maintained over geographically distributed sites by using the computational power of distributed and parallel systems. The grid can play a significant role in providing an effective computational support for distributed knowledge discovery applications. For the development of data mining applications on grids we designed a system called Knowledge Grid. This paper describes the Knowledge Grid framework and presents the toolset provided by the Knowledge Grid for implementing distributed knowledge discovery. The paper discusses how to design and implement data mining applications by using the Knowledge Grid tools starting from searching grid resources, composing software and data components, and executing the resulting data mining process on a grid. Some performance results are also discussed.

Overview of aerothermodynamic loads definition study

NASA Technical Reports Server (NTRS)

Gaugler, Raymond E.

1989-01-01

Over the years, NASA has been conducting the Advanced Earth-to-Orbit (AETO) Propulsion Technology Program to provide the knowledge, understanding, and design methodology that will allow the development of advanced Earth-to-orbit propulsion systems with high performance, extended service life, automated operations, and diagnostics for in-flight health monitoring. The objective of the Aerothermodynamic Loads Definition Study is to develop methods to more accurately predict the operating environment in AETO propulsion systems, such as the Space Shuttle Main Engine (SSME) powerhead. The approach taken consists of 2 parts: to modify, apply, and disseminate existing computational fluid dynamics tools in response to current needs and to develop new technology that will enable more accurate computation of the time averaged and unsteady aerothermodynamic loads in the SSME powerhead. The software tools are detailed. Significant progress was made in the area of turbomachinery, where there is an overlap between the AETO efforts and research in the aeronautical gas turbine field.

[The virtual university in medicine. Context, concepts, specifications, users' manual].

PubMed

Duvauferrier, R; Séka, L P; Rolland, Y; Rambeau, M; Le Beux, P; Morcet, N

1998-09-01

The widespread use of Web servers, with the emergence of interactive functions and the possibility of credit card payment via Internet, together with the requirement for continuing education and the subsequent need for a computer to link into the health care network have incited the development of a virtual university scheme on Internet. The Virtual University of Radiology is not only a computer-assisted teaching tool with a set of attractive features, but also a powerful engine allowing the organization, distribution and control of medical knowledge available in the www.server. The scheme provides patient access to general information, a secretary's office for enrollment and the Virtual University itself, with its library, image database, a forum for subspecialties and clinical case reports, an evaluation module and various guides and help tools for diagnosis, prescription and indexing. Currently the Virtual University of Radiology offers diagnostic imaging, but can also be used by other specialties and for general practice.

Development of Fuel Shuffling Module for PHISICS

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

Allan Mabe; Andrea Alfonsi; Cristian Rabiti

2013-06-01

PHISICS (Parallel and Highly Innovative Simulation for the INL Code System) [4] code toolkit has been in development at the Idaho National Laboratory. This package is intended to provide a modern analysis tool for reactor physics investigation. It is designed with the mindset to maximize accuracy for a given availability of computational resources and to give state of the art tools to the modern nuclear engineer. This is obtained by implementing several different algorithms and meshing approaches among which the user will be able to choose, in order to optimize his computational resources and accuracy needs. The software is completelymore » modular in order to simplify the independent development of modules by different teams and future maintenance. The package is coupled with the thermo-hydraulic code RELAP5-3D [3]. In the following the structure of the different PHISICS modules is briefly recalled, focusing on the new shuffling module (SHUFFLE), object of this paper.« less

Nonlinear Aerodynamics and the Design of Wing Tips

NASA Technical Reports Server (NTRS)

Kroo, Ilan

1991-01-01

The analysis and design of wing tips for fixed wing and rotary wing aircraft still remains part art, part science. Although the design of airfoil sections and basic planform geometry is well developed, the tip regions require more detailed consideration. This is important because of the strong impact of wing tip flow on wing drag; although the tip region constitutes a small portion of the wing, its effect on the drag can be significant. The induced drag of a wing is, for a given lift and speed, inversely proportional to the square of the wing span. Concepts are proposed as a means of reducing drag. Modern computational methods provide a tool for studying these issues in greater detail. The purpose of the current research program is to improve the understanding of the fundamental issues involved in the design of wing tips and to develop the range of computational and experimental tools needed for further study of these ideas.

Teaching Computational Thinking: Deciding to Take Small Steps in a Curriculum

NASA Astrophysics Data System (ADS)

Madoff, R. D.; Putkonen, J.

2016-12-01

While computational thinking and reasoning are not necessarily the same as computer programming, programs such as MATLAB can provide the medium through which the logical and computational thinking at the foundation of science can be taught, learned, and experienced. And while math and computer anxiety are often discussed as critical obstacles to students' progress in their geoscience curriculum, it is here suggested that an unfamiliarity with the computational and logical reasoning is what poses a first stumbling block, in addition to the hurdle of expending the effort to learn how to translate a computational problem into the appropriate computer syntax in order to achieve the intended results. Because computational thinking is so vital for all fields, there is a need to initiate many and to build support in the curriculum for it. This presentation focuses on elements to bring into the teaching of computational thinking that are intended as additions to learning MATLAB programming as a basic tool. Such elements include: highlighting a key concept, discussing a basic geoscience problem where the concept would show up, having the student draw or outline a sketch of what they think an operation needs to do in order to perform a desired result, and then finding the relevant syntax to work with. This iterative pedagogy simulates what someone with more experience in programming does, so it discloses the thinking process in the black box of a result. Intended as only a very early stage introduction, advanced applications would need to be developed as students go through an academic program. The objective would be to expose and introduce computational thinking to majors and non-majors and to alleviate some of the math and computer anxiety so that students would choose to advance on with programming or modeling, whether it is built into a 4-year curriculum or not.

PREPARING FOR EXASCALE: ORNL Leadership Computing Application Requirements and Strategy

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

Joubert, Wayne; Kothe, Douglas B; Nam, Hai Ah

2009-12-01

In 2009 the Oak Ridge Leadership Computing Facility (OLCF), a U.S. Department of Energy (DOE) facility at the Oak Ridge National Laboratory (ORNL) National Center for Computational Sciences (NCCS), elicited petascale computational science requirements from leading computational scientists in the international science community. This effort targeted science teams whose projects received large computer allocation awards on OLCF systems. A clear finding of this process was that in order to reach their science goals over the next several years, multiple projects will require computational resources in excess of an order of magnitude more powerful than those currently available. Additionally, for themore » longer term, next-generation science will require computing platforms of exascale capability in order to reach DOE science objectives over the next decade. It is generally recognized that achieving exascale in the proposed time frame will require disruptive changes in computer hardware and software. Processor hardware will become necessarily heterogeneous and will include accelerator technologies. Software must undergo the concomitant changes needed to extract the available performance from this heterogeneous hardware. This disruption portends to be substantial, not unlike the change to the message passing paradigm in the computational science community over 20 years ago. Since technological disruptions take time to assimilate, we must aggressively embark on this course of change now, to insure that science applications and their underlying programming models are mature and ready when exascale computing arrives. This includes initiation of application readiness efforts to adapt existing codes to heterogeneous architectures, support of relevant software tools, and procurement of next-generation hardware testbeds for porting and testing codes. The 2009 OLCF requirements process identified numerous actions necessary to meet this challenge: (1) Hardware capabilities must be advanced on multiple fronts, including peak flops, node memory capacity, interconnect latency, interconnect bandwidth, and memory bandwidth. (2) Effective parallel programming interfaces must be developed to exploit the power of emerging hardware. (3) Science application teams must now begin to adapt and reformulate application codes to the new hardware and software, typified by hierarchical and disparate layers of compute, memory and concurrency. (4) Algorithm research must be realigned to exploit this hierarchy. (5) When possible, mathematical libraries must be used to encapsulate the required operations in an efficient and useful way. (6) Software tools must be developed to make the new hardware more usable. (7) Science application software must be improved to cope with the increasing complexity of computing systems. (8) Data management efforts must be readied for the larger quantities of data generated by larger, more accurate science models. Requirements elicitation, analysis, validation, and management comprise a difficult and inexact process, particularly in periods of technological change. Nonetheless, the OLCF requirements modeling process is becoming increasingly quantitative and actionable, as the process becomes more developed and mature, and the process this year has identified clear and concrete steps to be taken. This report discloses (1) the fundamental science case driving the need for the next generation of computer hardware, (2) application usage trends that illustrate the science need, (3) application performance characteristics that drive the need for increased hardware capabilities, (4) resource and process requirements that make the development and deployment of science applications on next-generation hardware successful, and (5) summary recommendations for the required next steps within the computer and computational science communities.« less

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing. The PRIMA Project

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

Malony, Allen D.; Wolf, Felix G.

2014-01-31

The growing number of cores provided by today’s high-­end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-­performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensivelymore » across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-­fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-­Productivity Supercomputing (VI-­HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-­HPS training activities together within the past three years.« less

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing: the PRIMA Project

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

Malony, Allen D.; Wolf, Felix G.

2014-01-31

The growing number of cores provided by today’s high-end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensivelymore » across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-Productivity Supercomputing (VI-HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-HPS training activities together within the past three years.« less

Application of Reduced Order Transonic Aerodynamic Influence Coefficient Matrix for Design Optimization

NASA Technical Reports Server (NTRS)

Pak, Chan-gi; Li, Wesley W.

2009-01-01

Supporting the Aeronautics Research Mission Directorate guidelines, the National Aeronautics and Space Administration [NASA] Dryden Flight Research Center is developing a multidisciplinary design, analysis, and optimization [MDAO] tool. This tool will leverage existing tools and practices, and allow the easy integration and adoption of new state-of-the-art software. Today s modern aircraft designs in transonic speed are a challenging task due to the computation time required for the unsteady aeroelastic analysis using a Computational Fluid Dynamics [CFD] code. Design approaches in this speed regime are mainly based on the manual trial and error. Because of the time required for unsteady CFD computations in time-domain, this will considerably slow down the whole design process. These analyses are usually performed repeatedly to optimize the final design. As a result, there is considerable motivation to be able to perform aeroelastic calculations more quickly and inexpensively. This paper will describe the development of unsteady transonic aeroelastic design methodology for design optimization using reduced modeling method and unsteady aerodynamic approximation. The method requires the unsteady transonic aerodynamics be represented in the frequency or Laplace domain. Dynamically linear assumption is used for creating Aerodynamic Influence Coefficient [AIC] matrices in transonic speed regime. Unsteady CFD computations are needed for the important columns of an AIC matrix which corresponded to the primary modes for the flutter. Order reduction techniques, such as Guyan reduction and improved reduction system, are used to reduce the size of problem transonic flutter can be found by the classic methods, such as Rational function approximation, p-k, p, root-locus etc. Such a methodology could be incorporated into MDAO tool for design optimization at a reasonable computational cost. The proposed technique is verified using the Aerostructures Test Wing 2 actually designed, built, and tested at NASA Dryden Flight Research Center. The results from the full order model and the approximate reduced order model are analyzed and compared.

Eigenvalue Contributon Estimator for Sensitivity Calculations with TSUNAMI-3D

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

Rearden, Bradley T; Williams, Mark L

2007-01-01

Since the release of the Tools for Sensitivity and Uncertainty Analysis Methodology Implementation (TSUNAMI) codes in SCALE [1], the use of sensitivity and uncertainty analysis techniques for criticality safety applications has greatly increased within the user community. In general, sensitivity and uncertainty analysis is transitioning from a technique used only by specialists to a practical tool in routine use. With the desire to use the tool more routinely comes the need to improve the solution methodology to reduce the input and computational burden on the user. This paper reviews the current solution methodology of the Monte Carlo eigenvalue sensitivity analysismore » sequence TSUNAMI-3D, describes an alternative approach, and presents results from both methodologies.« less

The Integrated Waste Tracking System - A Flexible Waste Management Tool

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

Anderson, Robert Stephen

2001-02-01

The US Department of Energy (DOE) Idaho National Engineering and Environmental Laboratory (INEEL) has fully embraced a flexible, computer-based tool to help increase waste management efficiency and integrate multiple operational functions from waste generation through waste disposition while reducing cost. The Integrated Waste Tracking System (IWTS)provides comprehensive information management for containerized waste during generation,storage, treatment, transport, and disposal. The IWTS provides all information necessary for facilities to properly manage and demonstrate regulatory compliance. As a platformindependent, client-server and Web-based inventory and compliance system, the IWTS has proven to be a successful tracking, characterization, compliance, and reporting tool that meets themore » needs of both operations and management while providing a high level of management flexibility.« less

Using computer graphics to enhance astronaut and systems safety

NASA Technical Reports Server (NTRS)

Brown, J. W.

1985-01-01

Computer graphics is being employed at the NASA Johnson Space Center as a tool to perform rapid, efficient and economical analyses for man-machine integration, flight operations development and systems engineering. The Operator Station Design System (OSDS), a computer-based facility featuring a highly flexible and versatile interactive software package, PLAID, is described. This unique evaluation tool, with its expanding data base of Space Shuttle elements, various payloads, experiments, crew equipment and man models, supports a multitude of technical evaluations, including spacecraft and workstation layout, definition of astronaut visual access, flight techniques development, cargo integration and crew training. As OSDS is being applied to the Space Shuttle, Orbiter payloads (including the European Space Agency's Spacelab) and future space vehicles and stations, astronaut and systems safety are being enhanced. Typical OSDS examples are presented. By performing physical and operational evaluations during early conceptual phases. supporting systems verification for flight readiness, and applying its capabilities to real-time mission support, the OSDS provides the wherewithal to satisfy a growing need of the current and future space programs for efficient, economical analyses.

A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems

NASA Astrophysics Data System (ADS)

Portegies Zwart, Simon; McMillan, Steve; O'Nualláin, Breanndán; Heggie, Douglas; Lombardi, James; Hut, Piet; Banerjee, Sambaran; Belkus, Houria; Fragos, Tassos; Fregeau, John; Fuji, Michiko; Gaburov, Evghenii; Glebbeek, Evert; Groen, Derek; Harfst, Stefan; Izzard, Rob; Jurić, Mario; Justham, Stephen; Teuben, Peter; van Bever, Joris; Yaron, Ofer; Zemp, Marcel

We present MUSE, a software framework for tying together existing computational tools for different astrophysical domains into a single multiphysics, multiscale workload. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for a generalized stellar systems workload. MUSE has now reached a "Noah's Ark" milestone, with two available numerical solvers for each domain. MUSE can treat small stellar associations, galaxies and everything in between, including planetary systems, dense stellar clusters and galactic nuclei. Here we demonstrate an examples calculated with MUSE: the merger of two galaxies. In addition we demonstrate the working of MUSE on a distributed computer. The current MUSE code base is publicly available as open source at http://muse.li.

The probability estimation of the electronic lesson implementation taking into account software reliability

NASA Astrophysics Data System (ADS)

Gurov, V. V.

2017-01-01

Software tools for educational purposes, such as e-lessons, computer-based testing system, from the point of view of reliability, have a number of features. The main ones among them are the need to ensure a sufficiently high probability of their faultless operation for a specified time, as well as the impossibility of their rapid recovery by the way of replacing it with a similar running program during the classes. The article considers the peculiarities of reliability evaluation of programs in contrast to assessments of hardware reliability. The basic requirements to reliability of software used for carrying out practical and laboratory classes in the form of computer-based training programs are given. The essential requirements applicable to the reliability of software used for conducting the practical and laboratory studies in the form of computer-based teaching programs are also described. The mathematical tool based on Markov chains, which allows to determine the degree of debugging of the training program for use in the educational process by means of applying the graph of the software modules interaction, is presented.

Computational crystallization

PubMed Central

Altan, Irem; Charbonneau, Patrick; Snell, Edward H.

2016-01-01

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed. PMID:26792536

Portfolio Analysis Tool

NASA Technical Reports Server (NTRS)

Barth, Tim; Zapata, Edgar; Benjamin, Perakath; Graul, Mike; Jones, Doug

2005-01-01

Portfolio Analysis Tool (PAT) is a Web-based, client/server computer program that helps managers of multiple projects funded by different customers to make decisions regarding investments in those projects. PAT facilitates analysis on a macroscopic level, without distraction by parochial concerns or tactical details of individual projects, so that managers decisions can reflect the broad strategy of their organization. PAT is accessible via almost any Web-browser software. Experts in specific projects can contribute to a broad database that managers can use in analyzing the costs and benefits of all projects, but do not have access for modifying criteria for analyzing projects: access for modifying criteria is limited to managers according to levels of administrative privilege. PAT affords flexibility for modifying criteria for particular "focus areas" so as to enable standardization of criteria among similar projects, thereby making it possible to improve assessments without need to rewrite computer code or to rehire experts, and thereby further reducing the cost of maintaining and upgrading computer code. Information in the PAT database and results of PAT analyses can be incorporated into a variety of ready-made or customizable tabular or graphical displays.

Management and development of local area network upgrade prototype

NASA Technical Reports Server (NTRS)

Fouser, T. J.

1981-01-01

Given the situation of having management and development users accessing a central computing facility and given the fact that these same users have the need for local computation and storage, the utilization of a commercially available networking system such as CP/NET from Digital Research provides the building blocks for communicating intelligent microsystems to file and print services. The major problems to be overcome in the implementation of such a network are the dearth of intelligent communication front-ends for the microcomputers and the lack of a rich set of management and software development tools.

HyperCard to SPSS: improving data integrity.

PubMed

Gostel, R

1993-01-01

This article describes a database design that captures responses in a HyperCard stack and moves the data to SPSS for the Macintosh without the need to rekey data. Pregnant women used an interactive computer application with a touch screen to answer questions and receive educational information about fetal alcohol syndrome. A database design was created to capture survey responses through interaction with a computer by a sample of prenatal women during formative evaluation trials. The author does not compare this method of data collection to other methods. This article simply describes the method of data collection as a useful research tool.

National Facilities Study. Volume 1: Facilities Inventory

NASA Technical Reports Server (NTRS)

1994-01-01

The inventory activity was initiated to solve the critical need for a single source of site specific descriptive and parametric data on major public and privately held aeronautics and aerospace related facilities. This a challenging undertaking due to the scope of the effort and the short lead time in which to assemble the inventory and have it available to support the task group study needs. The inventory remains dynamic as sites are being added and the data is accessed and refined as the study progresses. The inventory activity also included the design and implementation of a computer database and analytical tools to simplify access to the data. This volume describes the steps which were taken to define the data requirements, select sites, and solicit and acquire data from them. A discussion of the inventory structure and analytical tools is also provided.

On the usage of ultrasound computational models for decision making under ambiguity

NASA Astrophysics Data System (ADS)

Dib, Gerges; Sexton, Samuel; Prowant, Matthew; Crawford, Susan; Diaz, Aaron

2018-04-01

Computer modeling and simulation is becoming pervasive within the non-destructive evaluation (NDE) industry as a convenient tool for designing and assessing inspection techniques. This raises a pressing need for developing quantitative techniques for demonstrating the validity and applicability of the computational models. Computational models provide deterministic results based on deterministic and well-defined input, or stochastic results based on inputs defined by probability distributions. However, computational models cannot account for the effects of personnel, procedures, and equipment, resulting in ambiguity about the efficacy of inspections based on guidance from computational models only. In addition, ambiguity arises when model inputs, such as the representation of realistic cracks, cannot be defined deterministically, probabilistically, or by intervals. In this work, Pacific Northwest National Laboratory demonstrates the ability of computational models to represent field measurements under known variabilities, and quantify the differences using maximum amplitude and power spectrum density metrics. Sensitivity studies are also conducted to quantify the effects of different input parameters on the simulation results.

High End Computing Technologies for Earth Science Applications: Trends, Challenges, and Innovations

NASA Technical Reports Server (NTRS)

Parks, John (Technical Monitor); Biswas, Rupak; Yan, Jerry C.; Brooks, Walter F.; Sterling, Thomas L.

2003-01-01

Earth science applications of the future will stress the capabilities of even the highest performance supercomputers in the areas of raw compute power, mass storage management, and software environments. These NASA mission critical problems demand usable multi-petaflops and exabyte-scale systems to fully realize their science goals. With an exciting vision of the technologies needed, NASA has established a comprehensive program of advanced research in computer architecture, software tools, and device technology to ensure that, in partnership with US industry, it can meet these demanding requirements with reliable, cost effective, and usable ultra-scale systems. NASA will exploit, explore, and influence emerging high end computing architectures and technologies to accelerate the next generation of engineering, operations, and discovery processes for NASA Enterprises. This article captures this vision and describes the concepts, accomplishments, and the potential payoff of the key thrusts that will help meet the computational challenges in Earth science applications.

Quantum Information Theory - an Invitation

NASA Astrophysics Data System (ADS)

Werner, Reinhard F.

Quantum information and quantum computers have received a lot of public attention recently. Quantum computers have been advertised as a kind of warp drive for computing, and indeed the promise of the algorithms of Shor and Grover is to perform computations which are extremely hard or even provably impossible on any merely ``classical'' computer.In this article I shall give an account of the basic concepts of quantum information theory is given, staying as much as possible in the area of general agreement.The article is divided into two parts. The first (up to the end of Sect. 2.5) is mostly in plain English, centered around the exploration of what can or cannot be done with quantum systems as information carriers. The second part, Sect. 2.6, then gives a description of the mathematical structures and of some of the tools needed to develop the theory.

Perspectives on an education in computational biology and medicine.

PubMed

Rubinstein, Jill C

2012-09-01

The mainstream application of massively parallel, high-throughput assays in biomedical research has created a demand for scientists educated in Computational Biology and Bioinformatics (CBB). In response, formalized graduate programs have rapidly evolved over the past decade. Concurrently, there is increasing need for clinicians trained to oversee the responsible translation of CBB research into clinical tools. Physician-scientists with dedicated CBB training can facilitate such translation, positioning themselves at the intersection between computational biomedical research and medicine. This perspective explores key elements of the educational path to such a position, specifically addressing: 1) evolving perceptions of the role of the computational biologist and the impact on training and career opportunities; 2) challenges in and strategies for obtaining the core skill set required of a biomedical researcher in a computational world; and 3) how the combination of CBB with medical training provides a logical foundation for a career in academic medicine and/or biomedical research.

Towards ethical decision support and knowledge management in neonatal intensive care.

PubMed

Yang, L; Frize, M; Eng, P; Walker, R; Catley, C

2004-01-01

Recent studies in neonatal medicine, clinical nursing, and cognitive psychology have indicated the need to augment current decision-making practice in neonatal intensive care units with computerized, intelligent decision support systems. Rapid progress in artificial intelligence and knowledge management facilitates the design of collaborative ethical decision-support tools that allow clinicians to provide better support for parents facing inherently difficult choices, such as when to withdraw aggressive treatment. The appropriateness of using computers to support ethical decision-making is critically analyzed through research and literature review. In ethical dilemmas, multiple diverse participants need to communicate and function as a team to select the best treatment plan. In order to do this, physicians require reliable estimations of prognosis, while parents need a highly useable tool to help them assimilate complex medical issues and address their own value system. Our goal is to improve and structuralize the ethical decision-making that has become an inevitable part of modern neonatal care units. The paper contributes to clinical decision support by outlining the needs and basis for ethical decision support and justifying the proposed development efforts.

Systems biology driven software design for the research enterprise

PubMed Central

Boyle, John; Cavnor, Christopher; Killcoyne, Sarah; Shmulevich, Ilya

2008-01-01

Background In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. Results We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. Conclusion By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data. PMID:18578887

ProCon - PROteomics CONversion tool.

PubMed

Mayer, Gerhard; Stephan, Christian; Meyer, Helmut E; Kohl, Michael; Marcus, Katrin; Eisenacher, Martin

2015-11-03

With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest™/Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x=versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015. Published by Elsevier B.V.

On aerodynamic wake analysis and its relation to total aerodynamic drag in a wind tunnel environment

NASA Astrophysics Data System (ADS)

Guterres, Rui M.

The present work was developed with the goal of advancing the state of the art in the application of three-dimensional wake data analysis to the quantification of aerodynamic drag on a body in a low speed wind tunnel environment. Analysis of the existing tools, their strengths and limitations is presented. Improvements to the existing analysis approaches were made. Software tools were developed to integrate the analysis into a practical tool. A comprehensive derivation of the equations needed for drag computations based on three dimensional separated wake data is developed. A set of complete steps ranging from the basic mathematical concept to the applicable engineering equations is presented. An extensive experimental study was conducted. Three representative body types were studied in varying ground effect conditions. A detailed qualitative wake analysis using wake imaging and two and three dimensional flow visualization was performed. Several significant features of the flow were identified and their relation to the total aerodynamic drag established. A comprehensive wake study of this type is shown to be in itself a powerful tool for the analysis of the wake aerodynamics and its relation to body drag. Quantitative wake analysis techniques were developed. Significant post processing and data conditioning tools and precision analysis were developed. The quality of the data is shown to be in direct correlation with the accuracy of the computed aerodynamic drag. Steps are taken to identify the sources of uncertainty. These are quantified when possible and the accuracy of the computed results is seen to significantly improve. When post processing alone does not resolve issues related to precision and accuracy, solutions are proposed. The improved quantitative wake analysis is applied to the wake data obtained. Guidelines are established that will lead to more successful implementation of these tools in future research programs. Close attention is paid to implementation of issues that are of crucial importance for the accuracy of the results and that are not detailed in the literature. The impact of ground effect on the flows in hand is qualitatively and quantitatively studied. Its impact on the accuracy of the computations as well as the wall drag incompatibility with the theoretical model followed are discussed. The newly developed quantitative analysis provides significantly increased accuracy. The aerodynamic drag coefficient is computed within one percent of balance measured value for the best cases.

The impact of computer self-efficacy, computer anxiety, and perceived usability and acceptability on the efficacy of a decision support tool for colorectal cancer screening

PubMed Central

Lindblom, Katrina; Gregory, Tess; Flight, Ingrid H K; Zajac, Ian

2011-01-01

Objective This study investigated the efficacy of an internet-based personalized decision support (PDS) tool designed to aid in the decision to screen for colorectal cancer (CRC) using a fecal occult blood test. We tested whether the efficacy of the tool in influencing attitudes to screening was mediated by perceived usability and acceptability, and considered the role of computer self-efficacy and computer anxiety in these relationships. Methods Eighty-one participants aged 50–76 years worked through the on-line PDS tool and completed questionnaires on computer self-efficacy, computer anxiety, attitudes to and beliefs about CRC screening before and after exposure to the PDS, and perceived usability and acceptability of the tool. Results Repeated measures ANOVA found that PDS exposure led to a significant increase in knowledge about CRC and screening, and more positive attitudes to CRC screening as measured by factors from the Preventive Health Model. Perceived usability and acceptability of the PDS mediated changes in attitudes toward CRC screening (but not CRC knowledge), and computer self-efficacy and computer anxiety were significant predictors of individuals' perceptions of the tool. Conclusion Interventions designed to decrease computer anxiety, such as computer courses and internet training, may improve the acceptability of new health information technologies including internet-based decision support tools, increasing their impact on behavior change. PMID:21857024

Boxes of Model Building and Visualization.

PubMed

Turk, Dušan

2017-01-01

Macromolecular crystallography and electron microscopy (single-particle and in situ tomography) are merging into a single approach used by the two coalescing scientific communities. The merger is a consequence of technical developments that enabled determination of atomic structures of macromolecules by electron microscopy. Technological progress in experimental methods of macromolecular structure determination, computer hardware, and software changed and continues to change the nature of model building and visualization of molecular structures. However, the increase in automation and availability of structure validation are reducing interactive manual model building to fiddling with details. On the other hand, interactive modeling tools increasingly rely on search and complex energy calculation procedures, which make manually driven changes in geometry increasingly powerful and at the same time less demanding. Thus, the need for accurate manual positioning of a model is decreasing. The user's push only needs to be sufficient to bring the model within the increasing convergence radius of the computing tools. It seems that we can now better than ever determine an average single structure. The tools work better, requirements for engagement of human brain are lowered, and the frontier of intellectual and scientific challenges has moved on. The quest for resolution of new challenges requires out-of-the-box thinking. A few issues such as model bias and correctness of structure, ongoing developments in parameters defining geometric restraints, limitations of the ideal average single structure, and limitations of Bragg spot data are discussed here, together with the challenges that lie ahead.

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications

PubMed Central

Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner. PMID:28531174

GECKO: a complete large-scale gene expression analysis platform.

PubMed

Theilhaber, Joachim; Ulyanov, Anatoly; Malanthara, Anish; Cole, Jack; Xu, Dapeng; Nahf, Robert; Heuer, Michael; Brockel, Christoph; Bushnell, Steven

2004-12-10

Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing approximately 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph), in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (approximately 100 users) and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data. The Gecko system is being made publicly available as free software http://sourceforge.net/projects/geckoe. In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

PubMed Central

Brusniak, Mi-Youn; Bodenmiller, Bernd; Campbell, David; Cooke, Kelly; Eddes, James; Garbutt, Andrew; Lau, Hollis; Letarte, Simon; Mueller, Lukas N; Sharma, Vagisha; Vitek, Olga; Zhang, Ning; Aebersold, Ruedi; Watts, Julian D

2008-01-01

Background Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. Results We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. Conclusion The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field. PMID:19087345

Methodologies and Tools for Tuning Parallel Programs: 80% Art, 20% Science, and 10% Luck

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Bailey, David (Technical Monitor)

1996-01-01

The need for computing power has forced a migration from serial computation on a single processor to parallel processing on multiprocessors. However, without effective means to monitor (and analyze) program execution, tuning the performance of parallel programs becomes exponentially difficult as program complexity and machine size increase. In the past few years, the ubiquitous introduction of performance tuning tools from various supercomputer vendors (Intel's ParAide, TMC's PRISM, CRI's Apprentice, and Convex's CXtrace) seems to indicate the maturity of performance instrumentation/monitor/tuning technologies and vendors'/customers' recognition of their importance. However, a few important questions remain: What kind of performance bottlenecks can these tools detect (or correct)? How time consuming is the performance tuning process? What are some important technical issues that remain to be tackled in this area? This workshop reviews the fundamental concepts involved in analyzing and improving the performance of parallel and heterogeneous message-passing programs. Several alternative strategies will be contrasted, and for each we will describe how currently available tuning tools (e.g. AIMS, ParAide, PRISM, Apprentice, CXtrace, ATExpert, Pablo, IPS-2) can be used to facilitate the process. We will characterize the effectiveness of the tools and methodologies based on actual user experiences at NASA Ames Research Center. Finally, we will discuss their limitations and outline recent approaches taken by vendors and the research community to address them.

Analyzing the Cohesion of English Text and Discourse with Automated Computer Tools

ERIC Educational Resources Information Center

Jeon, Moongee

2014-01-01

This article investigates the lexical and discourse features of English text and discourse with automated computer technologies. Specifically, this article examines the cohesion of English text and discourse with automated computer tools, Coh-Metrix and TEES. Coh-Metrix is a text analysis computer tool that can analyze English text and discourse…

The Implications of Cognitive Psychology for Computer-Based Learning Tools.

ERIC Educational Resources Information Center

Kozma, Robert B.

1987-01-01

Defines cognitive computer tools as software programs that use the control capabilities of computers to amplify, extend, or enhance human cognition; suggests seven ways in which computers can aid learning; and describes the "Learning Tool," a software package for the Apple Macintosh microcomputer that is designed to aid learning of…

Platform-independent software for medical image processing on the Internet

NASA Astrophysics Data System (ADS)

Mancuso, Michael E.; Pathak, Sayan D.; Kim, Yongmin

1997-05-01

We have developed a software tool for image processing over the Internet. The tool is a general purpose, easy to use, flexible, platform independent image processing software package with functions most commonly used in medical image processing.It provides for processing of medical images located wither remotely on the Internet or locally. The software was written in Java - the new programming language developed by Sun Microsystems. It was compiled and tested using Microsoft's Visual Java 1.0 and Microsoft's Just in Time Compiler 1.00.6211. The software is simple and easy to use. In order to use the tool, the user needs to download the software from our site before he/she runs it using any Java interpreter, such as those supplied by Sun, Symantec, Borland or Microsoft. Future versions of the operating systems supplied by Sun, Microsoft, Apple, IBM, and others will include Java interpreters. The software is then able to access and process any image on the iNternet or on the local computer. Using a 512 X 512 X 8-bit image, a 3 X 3 convolution took 0.88 seconds on an Intel Pentium Pro PC running at 200 MHz with 64 Mbytes of memory. A window/level operation took 0.38 seconds while a 3 X 3 median filter took 0.71 seconds. These performance numbers demonstrate the feasibility of using this software interactively on desktop computes. Our software tool supports various image processing techniques commonly used in medical image processing and can run without the need of any specialized hardware. It can become an easily accessible resource over the Internet to promote the learning and of understanding image processing algorithms. Also, it could facilitate sharing of medical image databases and collaboration amongst researchers and clinicians, regardless of location.

Trends in HFE Methods and Tools and Their Applicability to Safety Reviews

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

O'Hara, J.M.; Plott, C.; Milanski, J.

2009-09-30

The U.S. Nuclear Regulatory Commission's (NRC) conducts human factors engineering (HFE) safety reviews of applicant submittals for new plants and for changes to existing plants. The reviews include the evaluation of the methods and tools (M&T) used by applicants as part of their HFE program. The technology used to perform HFE activities has been rapidly evolving, resulting in a whole new generation of HFE M&Ts. The objectives of this research were to identify the current trends in HFE methods and tools, determine their applicability to NRC safety reviews, and identify topics for which the NRC may need additional guidance tomore » support the NRC's safety reviews. We conducted a survey that identified over 100 new HFE M&Ts. The M&Ts were assessed to identify general trends. Seven trends were identified: Computer Applications for Performing Traditional Analyses, Computer-Aided Design, Integration of HFE Methods and Tools, Rapid Development Engineering, Analysis of Cognitive Tasks, Use of Virtual Environments and Visualizations, and Application of Human Performance Models. We assessed each trend to determine its applicability to the NRC's review by considering (1) whether the nuclear industry is making use of M&Ts for each trend, and (2) whether M&Ts reflecting the trend can be reviewed using the current design review guidance. We concluded that M&T trends that are applicable to the commercial nuclear industry and are expected to impact safety reviews may be considered for review guidance development. Three trends fell into this category: Analysis of Cognitive Tasks, Use of Virtual Environments and Visualizations, and Application of Human Performance Models. The other trends do not need to be addressed at this time.« less

Virtual reality based surgical assistance and training system for long duration space missions.

PubMed

Montgomery, K; Thonier, G; Stephanides, M; Schendel, S

2001-01-01

Access to medical care during long duration space missions is extremely important. Numerous unanticipated medical problems will need to be addressed promptly and efficiently. Although telemedicine provides a convenient tool for remote diagnosis and treatment, it is impractical due to the long delay between data transmission and reception to Earth. While a well-trained surgeon-internist-astronaut would be an essential addition to the crew, the vast number of potential medical problems necessitate instant access to computerized, skill-enhancing and diagnostic tools. A functional prototype of a virtual reality based surgical training and assistance tool was created at our center, using low-power, small, lightweight components that would be easy to transport on a space mission. The system consists of a tracked, head-mounted display, a computer system, and a number of tracked surgical instruments. The software provides a real-time surgical simulation system with integrated monitoring and information retrieval and a voice input/output subsystem. Initial medical content for the system has been created, comprising craniofacial, hand, inner ear, and general anatomy, as well as information on a number of surgical procedures and techniques. One surgical specialty in particular, microsurgery, was provided as a full simulation due to its long training requirements, significant impact on result due to experience, and likelihood for need. However, the system is easily adapted to realistically simulate a large number of other surgical procedures. By providing a general system for surgical simulation and assistance, the astronaut-surgeon can maintain their skills, acquire new specialty skills, and use tools for computer-based surgical planning and assistance to minimize overall crew and mission risk.

Development of an Adaptable Display and Diagnostic System for the Evaluation of Tropical Cyclone Forecasts

NASA Astrophysics Data System (ADS)

Kucera, P. A.; Burek, T.; Halley-Gotway, J.

2015-12-01

NCAR's Joint Numerical Testbed Program (JNTP) focuses on the evaluation of experimental forecasts of tropical cyclones (TCs) with the goal of developing new research tools and diagnostic evaluation methods that can be transitioned to operations. Recent activities include the development of new TC forecast verification methods and the development of an adaptable TC display and diagnostic system. The next generation display and diagnostic system is being developed to support evaluation needs of the U.S. National Hurricane Center (NHC) and broader TC research community. The new hurricane display and diagnostic capabilities allow forecasters and research scientists to more deeply examine the performance of operational and experimental models. The system is built upon modern and flexible technology that includes OpenLayers Mapping tools that are platform independent. The forecast track and intensity along with associated observed track information are stored in an efficient MySQL database. The system provides easy-to-use interactive display system, and provides diagnostic tools to examine forecast track stratified by intensity. Consensus forecasts can be computed and displayed interactively. The system is designed to display information for both real-time and for historical TC cyclones. The display configurations are easily adaptable to meet the needs of the end-user preferences. Ongoing enhancements include improving capabilities for stratification and evaluation of historical best tracks, development and implementation of additional methods to stratify and compute consensus hurricane track and intensity forecasts, and improved graphical display tools. The display is also being enhanced to incorporate gridded forecast, satellite, and sea surface temperature fields. The presentation will provide an overview of the display and diagnostic system development and demonstration of the current capabilities.

GenomicTools: a computational platform for developing high-throughput analytics in genomics.

PubMed

Tsirigos, Aristotelis; Haiminen, Niina; Bilal, Erhan; Utro, Filippo

2012-01-15

Recent advances in sequencing technology have resulted in the dramatic increase of sequencing data, which, in turn, requires efficient management of computational resources, such as computing time, memory requirements as well as prototyping of computational pipelines. We present GenomicTools, a flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. GenomicTools implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address a wide spectrum of tasks ranging from pre-processing and quality control to meta-analyses. Additionally, the GenomicTools platform is designed to analyze large datasets of any size by minimizing memory requirements. In practical applications, where comparable, GenomicTools outperforms existing tools in terms of both time and memory usage. The GenomicTools platform (version 2.0.0) was implemented in C++. The source code, documentation, user manual, example datasets and scripts are available online at http://code.google.com/p/ibm-cbc-genomic-tools.

FRACTAL Systems & Project suite: engineering tools for improving development and operation of the systems

NASA Astrophysics Data System (ADS)

Pérez-Calpena, A.; Mujica-Alvarez, E.; Osinde-Lopez, J.; García-Vargas, M.

2008-07-01

This paper describes the FRACTAL Systems & Projects suite. This suite is composed by several tools (GECO, DOCMA and SUMO) that provide the capabilities that all organizations need to store and manage the system information generated along the project's lifetime, from the design phase to the operation phase. The amount of information that is generated in a project keeps growing in size and complexity along the project's lifetime, to an extent that it becomes impossible to manage it without the aid of specific computer-based tools. The suite described in this paper is the solution developed by FRACTAL to assist the execution of different scientific projects, mainly related with telescopes and instruments, for astronomical research centres. These tools help the system and project engineers to maintain the technical control of the systems and to ensure an optimal use of the resources. GECO eases the control of the system configuration data; DOCMA provides the means to organise and manage the documents generated in the project; SUMO allows managing and scheduling the operation, the maintenance activities and the resources during the operational phase of a system. These tools improve the project communication making the information available to the authorized users (project team, customers, Consortium's members, etc). Finally and depending on the project needs, these three tools can be used integrated or in an independent manner.

A strip chart recorder pattern recognition tool kit for Shuttle operations

NASA Technical Reports Server (NTRS)

Hammen, David G.; Moebes, Travis A.; Shelton, Robert O.; Savely, Robert T.

1993-01-01

During Space Shuttle operations, Mission Control personnel monitor numerous mission-critical systems such as electrical power; guidance, navigation, and control; and propulsion by means of paper strip chart recorders. For example, electrical power controllers monitor strip chart recorder pen traces to identify onboard electrical equipment activations and deactivations. Recent developments in pattern recognition technologies coupled with new capabilities that distribute real-time Shuttle telemetry data to engineering workstations make it possible to develop computer applications that perform some of the low-level monitoring now performed by controllers. The number of opportunities for such applications suggests a need to build a pattern recognition tool kit to reduce software development effort through software reuse. We are building pattern recognition applications while keeping such a tool kit in mind. We demonstrated the initial prototype application, which identifies electrical equipment activations, during three recent Shuttle flights. This prototype was developed to test the viability of the basic system architecture, to evaluate the performance of several pattern recognition techniques including those based on cross-correlation, neural networks, and statistical methods, to understand the interplay between an advanced automation application and human controllers to enhance utility, and to identify capabilities needed in a more general-purpose tool kit.

Users guide for information retrieval using APL

NASA Technical Reports Server (NTRS)

Shapiro, A.

1974-01-01

A Programming Language (APL) is a precise, concise, and powerful computer programming language. Several features make APL useful to managers and other potential computer users. APL is interactive; therefore, the user can communicate with his program or data base in near real-time. This, coupled with the fact that APL has excellent debugging features, reduces program checkout time to minutes or hours rather than days or months. Of particular importance is the fact that APL can be utilized as a management science tool using such techniques as operations research, statistical analysis, and forecasting. The gap between the scientist and the manager could be narrowed by showing how APL can be used to do what the scientists and the manager each need to do, retrieve information. Sometimes, the information needs to be retrieved rapidly. In this case APL is ideally suited for this challenge.

Use of application containers and workflows for genomic data analysis

PubMed Central

Schulz, Wade L.; Durant, Thomas J. S.; Siddon, Alexa J.; Torres, Richard

2016-01-01

Background: The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Methods: Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. Results: While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. Conclusions: With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia. PMID:28163975

Active Control of Fan Noise: Feasibility Study. Volume 5; Numerical Computation of Acoustic Mode Reflection Coefficients for an Unflanged Cylindrical Duct

NASA Technical Reports Server (NTRS)

Kraft, R. E.

1996-01-01

A computational method to predict modal reflection coefficients in cylindrical ducts has been developed based on the work of Homicz, Lordi, and Rehm, which uses the Wiener-Hopf method to account for the boundary conditions at the termination of a thin cylindrical pipe. The purpose of this study is to develop a computational routine to predict the reflection coefficients of higher order acoustic modes impinging on the unflanged termination of a cylindrical duct. This effort was conducted wider Task Order 5 of the NASA Lewis LET Program, Active Noise Control of aircraft Engines: Feasibility Study, and will be used as part of the development of an integrated source noise, acoustic propagation, ANC actuator coupling, and control system algorithm simulation. The reflection coefficient prediction will be incorporated into an existing cylindrical duct modal analysis to account for the reflection of modes from the duct termination. This will provide a more accurate, rapid computation design tool for evaluating the effect of reflected waves on active noise control systems mounted in the duct, as well as providing a tool for the design of acoustic treatment in inlet ducts. As an active noise control system design tool, the method can be used preliminary to more accurate but more numerically intensive acoustic propagation models such as finite element methods. The resulting computer program has been shown to give reasonable results, some examples of which are presented. Reliable data to use for comparison is scarce, so complete checkout is difficult, and further checkout is needed over a wider range of system parameters. In future efforts the method will be adapted as a subroutine to the GEAE segmented cylindrical duct modal analysis program.

Design and implementation of a UNIX based distributed computing system

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

Love, J.S.; Michael, M.W.

1994-12-31

We have designed, implemented, and are running a corporate-wide distributed processing batch queue on a large number of networked workstations using the UNIX{reg_sign} operating system. Atlas Wireline researchers and scientists have used the system for over a year. The large increase in available computer power has greatly reduced the time required for nuclear and electromagnetic tool modeling. Use of remote distributed computing has simultaneously reduced computation costs and increased usable computer time. The system integrates equipment from different manufacturers, using various CPU architectures, distinct operating system revisions, and even multiple processors per machine. Various differences between the machines have tomore » be accounted for in the master scheduler. These differences include shells, command sets, swap spaces, memory sizes, CPU sizes, and OS revision levels. Remote processing across a network must be performed in a manner that is seamless from the users` perspective. The system currently uses IBM RISC System/6000{reg_sign}, SPARCstation{sup TM}, HP9000s700, HP9000s800, and DEC Alpha AXP{sup TM} machines. Each CPU in the network has its own speed rating, allowed working hours, and workload parameters. The system if designed so that all of the computers in the network can be optimally scheduled without adversely impacting the primary users of the machines. The increase in the total usable computational capacity by means of distributed batch computing can change corporate computing strategy. The integration of disparate computer platforms eliminates the need to buy one type of computer for computations, another for graphics, and yet another for day-to-day operations. It might be possible, for example, to meet all research and engineering computing needs with existing networked computers.« less

Understanding Calculus beyond Computations: A Descriptive Study of the Parallel Meanings and Expectations of Teachers and Users of Calculus

ERIC Educational Resources Information Center

Ferguson, Leann J.

2012-01-01

Calculus is an important tool for building mathematical models of the world around us and is thus used in a variety of disciplines, such as physics and engineering. These disciplines rely on calculus courses to provide the mathematical foundation needed for success in their courses. Unfortunately, due to the basal conceptions of what it means to…

Natural language processing and the Now-or-Never bottleneck.

PubMed

Gómez-Rodríguez, Carlos

2016-01-01

Researchers, motivated by the need to improve the efficiency of natural language processing tools to handle web-scale data, have recently arrived at models that remarkably match the expected features of human language processing under the Now-or-Never bottleneck framework. This provides additional support for said framework and highlights the research potential in the interaction between applied computational linguistics and cognitive science.

Developing Tools for Assessing and Using Commercially Available Reading Software Programs to Promote the Development of Early Reading Skills in Children

ERIC Educational Resources Information Center

Wood, Eileen; Gottardo, Alexandra; Grant, Amy; Evans, Mary Ann; Phillips, Linda; Savage, Robert

2012-01-01

As computers become an increasingly ubiquitous part of young children's lives there is a need to examine how best to harness digital technologies to promote learning in early childhood education contexts. The development of emergent literacy skills is 1 domain for which numerous software programs are available for young learners. In this study, we…