EPA and GSA Webinar: E Scrap Management, Computers for Learning and the Federal Green Challenge

EPA Pesticide Factsheets

EPA and the General Services Administration (GSA) are hosting a webinar on May 2, 2018. Topics will include policies and procedures on E Scrap management, a review of the Computers For Leaning Program, and benefits of joining the Federal Green Challenge.

Software Systems for High-performance Quantum Computing

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

Humble, Travis S; Britt, Keith A

Quantum computing promises new opportunities for solving hard computational problems, but harnessing this novelty requires breakthrough concepts in the design, operation, and application of computing systems. We define some of the challenges facing the development of quantum computing systems as well as software-based approaches that can be used to overcome these challenges. Following a brief overview of the state of the art, we present models for the quantum programming and execution models, the development of architectures for hybrid high-performance computing systems, and the realization of software stacks for quantum networking. This leads to a discussion of the role that conventionalmore » computing plays in the quantum paradigm and how some of the current challenges for exascale computing overlap with those facing quantum computing.« less

A Problem Posing-Based Practicing Strategy for Facilitating Students' Computer Programming Skills in the Team-Based Learning Mode

ERIC Educational Resources Information Center

Wang, Xiao-Ming; Hwang, Gwo-Jen

2017-01-01

Computer programming is a subject that requires problem-solving strategies and involves a great number of programming logic activities which pose challenges for learners. Therefore, providing learning support and guidance is important. Collaborative learning is widely believed to be an effective teaching approach; it can enhance learners' social…

Evaluating the Effectiveness of Self-Created Student Screencasts as a Tool to Increase Student Learning Outcomes in a Hands-On Computer Programming Course

ERIC Educational Resources Information Center

Powell, Loreen M.; Wimmer, Hayden

2015-01-01

Computer programming is challenging to teach and difficult for students to learn. Instructors have searched for ways to improve student learning in programming courses. In an attempt to foster hands-on learning and to increase student learning outcomes in a programming course, the authors conducted an exploratory study to examine student created…

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

Heroux, Michael; Lethin, Richard

Programming models and environments play the essential roles in high performance computing of enabling the conception, design, implementation and execution of science and engineering application codes. Programmer productivity is strongly influenced by the effectiveness of our programming models and environments, as is software sustainability since our codes have lifespans measured in decades, so the advent of new computing architectures, increased concurrency, concerns for resilience, and the increasing demands for high-fidelity, multi-physics, multi-scale and data-intensive computations mean that we have new challenges to address as part of our fundamental R&D requirements. Fortunately, we also have new tools and environments that makemore » design, prototyping and delivery of new programming models easier than ever. The combination of new and challenging requirements and new, powerful toolsets enables significant synergies for the next generation of programming models and environments R&D. This report presents the topics discussed and results from the 2014 DOE Office of Science Advanced Scientific Computing Research (ASCR) Programming Models & Environments Summit, and subsequent discussions among the summit participants and contributors to topics in this report.« less

From Numerical Problem Solving to Model-Based Experimentation Incorporating Computer-Based Tools of Various Scales into the ChE Curriculum

ERIC Educational Resources Information Center

Shacham, Mordechai; Cutlip, Michael B.; Brauner, Neima

2009-01-01

A continuing challenge to the undergraduate chemical engineering curriculum is the time-effective incorporation and use of computer-based tools throughout the educational program. Computing skills in academia and industry require some proficiency in programming and effective use of software packages for solving 1) single-model, single-algorithm…

Computer aided reliability, availability, and safety modeling for fault-tolerant computer systems with commentary on the HARP program

NASA Technical Reports Server (NTRS)

Shooman, Martin L.

1991-01-01

Many of the most challenging reliability problems of our present decade involve complex distributed systems such as interconnected telephone switching computers, air traffic control centers, aircraft and space vehicles, and local area and wide area computer networks. In addition to the challenge of complexity, modern fault-tolerant computer systems require very high levels of reliability, e.g., avionic computers with MTTF goals of one billion hours. Most analysts find that it is too difficult to model such complex systems without computer aided design programs. In response to this need, NASA has developed a suite of computer aided reliability modeling programs beginning with CARE 3 and including a group of new programs such as: HARP, HARP-PC, Reliability Analysts Workbench (Combination of model solvers SURE, STEM, PAWS, and common front-end model ASSIST), and the Fault Tree Compiler. The HARP program is studied and how well the user can model systems using this program is investigated. One of the important objectives will be to study how user friendly this program is, e.g., how easy it is to model the system, provide the input information, and interpret the results. The experiences of the author and his graduate students who used HARP in two graduate courses are described. Some brief comparisons were made with the ARIES program which the students also used. Theoretical studies of the modeling techniques used in HARP are also included. Of course no answer can be any more accurate than the fidelity of the model, thus an Appendix is included which discusses modeling accuracy. A broad viewpoint is taken and all problems which occurred in the use of HARP are discussed. Such problems include: computer system problems, installation manual problems, user manual problems, program inconsistencies, program limitations, confusing notation, long run times, accuracy problems, etc.

Using Arduino to Teach Programming to First-Year Computer Science Students

ERIC Educational Resources Information Center

Tan, Wee Lum; Venema, Sven; Gonzalez, Ruben

2017-01-01

Transitioning to university is recognised as a challenging endeavour for commencing students. For commencing Computer Science students specifically, evidence suggests a link between poor performance in introductory technical courses, such as programming, and high attrition rates. Building resilience in students, particularly at the start of their…

Business aspects of cardiovascular computed tomography: tackling the challenges.

PubMed

Bateman, Timothy M

2008-01-01

The purpose of this article is to provide a comprehensive understanding of the business issues surrounding provision of dedicated cardiovascular computed tomographic imaging. Some of the challenges include high up-front costs, current low utilization relative to scanner capability, and inadequate payments. Cardiovascular computed tomographic imaging is a valuable clinical modality that should be offered by cardiovascular centers-of-excellence. With careful consideration of the business aspects, moderate-to-large size cardiology programs should be able to implement an economically viable cardiovascular computed tomographic service.

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

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.

Quantum Accelerators for High-performance Computing Systems

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

Humble, Travis S.; Britt, Keith A.; Mohiyaddin, Fahd A.

We define some of the programming and system-level challenges facing the application of quantum processing to high-performance computing. Alongside barriers to physical integration, prominent differences in the execution of quantum and conventional programs challenges the intersection of these computational models. Following a brief overview of the state of the art, we discuss recent advances in programming and execution models for hybrid quantum-classical computing. We discuss a novel quantum-accelerator framework that uses specialized kernels to offload select workloads while integrating with existing computing infrastructure. We elaborate on the role of the host operating system to manage these unique accelerator resources, themore » prospects for deploying quantum modules, and the requirements placed on the language hierarchy connecting these different system components. We draw on recent advances in the modeling and simulation of quantum computing systems with the development of architectures for hybrid high-performance computing systems and the realization of software stacks for controlling quantum devices. Finally, we present simulation results that describe the expected system-level behavior of high-performance computing systems composed from compute nodes with quantum processing units. We describe performance for these hybrid systems in terms of time-to-solution, accuracy, and energy consumption, and we use simple application examples to estimate the performance advantage of quantum acceleration.« less

Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles.

PubMed

Lampa, Samuel; Alvarsson, Jonathan; Spjuth, Ola

2016-01-01

Predictive modelling in drug discovery is challenging to automate as it often contains multiple analysis steps and might involve cross-validation and parameter tuning that create complex dependencies between tasks. With large-scale data or when using computationally demanding modelling methods, e-infrastructures such as high-performance or cloud computing are required, adding to the existing challenges of fault-tolerant automation. Workflow management systems can aid in many of these challenges, but the currently available systems are lacking in the functionality needed to enable agile and flexible predictive modelling. We here present an approach inspired by elements of the flow-based programming paradigm, implemented as an extension of the Luigi system which we name SciLuigi. We also discuss the experiences from using the approach when modelling a large set of biochemical interactions using a shared computer cluster.Graphical abstract.

Making Advanced Computer Science Topics More Accessible through Interactive Technologies

ERIC Educational Resources Information Center

Shao, Kun; Maher, Peter

2012-01-01

Purpose: Teaching advanced technical concepts in a computer science program to students of different technical backgrounds presents many challenges. The purpose of this paper is to present a detailed experimental pedagogy in teaching advanced computer science topics, such as computer networking, telecommunications and data structures using…

The NASA Computational Fluid Dynamics (CFD) program - Building technology to solve future challenges

NASA Technical Reports Server (NTRS)

Richardson, Pamela F.; Dwoyer, Douglas L.; Kutler, Paul; Povinelli, Louis A.

1993-01-01

This paper presents the NASA Computational Fluid Dynamics program in terms of a strategic vision and goals as well as NASA's financial commitment and personnel levels. The paper also identifies the CFD program customers and the support to those customers. In addition, the paper discusses technical emphasis and direction of the program and some recent achievements. NASA's Ames, Langley, and Lewis Research Centers are the research hubs of the CFD program while the NASA Headquarters Office of Aeronautics represents and advocates the program.

Satellite Tasking via a Tablet Computer

DTIC Science & Technology

2015-09-01

connectivity have helped to overcome the challenges of information delivery , but there remains the challenge of real-time information. This thesis...have helped to overcome the challenges of information delivery , but there remains the challenge of real-time information. This thesis examines the...76  3.  Integration with Existing Programs for Access and Dissemination of Imagery

Robotic Challenges: Robots Bring New Life to Gifted Classes, Teach Students Hands-On Problem Solving, Computer Skills.

ERIC Educational Resources Information Center

Smith, Ruth Baynard

1994-01-01

Intermediate level academically talented students learn essential elements of computer programming by working with robots at enrichment workshops at Dwight-Englewood School in Englewood, New Jersey. The children combine creative thinking and problem-solving skills to program the robots' microcomputers to perform a variety of movements. (JDD)

Imagine, Invent, Program, Share: A Library-Hosted Computer Club Promotes 21st Century Skills

ERIC Educational Resources Information Center

Myers, Brian

2009-01-01

During at least one afternoon each month, Wilmette (Illinois) Public Library (WPL) hosts a local group of computer programmers, designers, and artists, who meet to discuss digital projects and resources, technical challenges, and successful design or programming strategies. WPL's Game Design Club, now in its third year, owes its existence to a…

Designing a Versatile Dedicated Computing Lab to Support Computer Network Courses: Insights from a Case Study

ERIC Educational Resources Information Center

Gercek, Gokhan; Saleem, Naveed

2006-01-01

Providing adequate computing lab support for Management Information Systems (MIS) and Computer Science (CS) programs is a perennial challenge for most academic institutions in the US and abroad. Factors, such as lack of physical space, budgetary constraints, conflicting needs of different courses, and rapid obsolescence of computing technology,…

An Integrated Development Environment for Adiabatic Quantum Programming

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

Humble, Travis S; McCaskey, Alex; Bennink, Ryan S

2014-01-01

Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware raises the question of how well quantum programs perform. Benchmarking behavior is challenging since the multiple steps to synthesize an adiabatic quantum program are highly tunable. We present an adiabatic quantum programming environment called JADE that provides control over all the steps taken during program development. JADE captures the workflow needed to rigorously benchmark performance while also allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation enginemore » that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its use for benchmarking adiabatic quantum programs.« less

Use of Failure in IS Development Statistics: Lessons for IS Curriculum Design

ERIC Educational Resources Information Center

Longenecker, Herbert H., Jr.; Babb, Jeffry; Waguespack, Leslie; Tastle, William; Landry, Jeff

2016-01-01

The evolution of computing education reflects the history of the professional practice of computing. Keeping computing education current has been a major challenge due to the explosive advances in technologies. Academic programs in Information Systems, a long-standing computing discipline, develop and refine the theory and practice of computing…

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele; Biegel, Bryan (Technical Monitor)

2001-01-01

This viewgraph presentation provides information on the technical aspects of debugging computer code that has been automatically converted for use in a parallel computing system. Shared memory parallelization and distributed memory parallelization entail separate and distinct challenges for a debugging program. A prototype system has been developed which integrates various tools for the debugging of automatically parallelized programs including the CAPTools Database which provides variable definition information across subroutines as well as array distribution information.

Predictive Models and Computational Toxicology

EPA Science Inventory

Understanding the potential health risks posed by environmental chemicals is a significant challenge elevated by the large number of diverse chemicals with generally uncharacterized exposures, mechanisms, and toxicities. The ToxCast computational toxicology research program was l...

Immersive, Interactive, Web-Enabled Computer Simulation as a Trigger for Learning: The next Generation of Problem-Based Learning in Educational Leadership

ERIC Educational Resources Information Center

Mann, Dale; Reardon, R. M.; Becker, J. D.; Shakeshaft, C.; Bacon, Nicholas

2011-01-01

This paper describes the use of advanced computer technology in an innovative educational leadership program. This program integrates full-motion video scenarios that simulate the leadership challenges typically faced by principals over the course of a full school year. These scenarios require decisions that are then coupled to consequences and…

Benefits and Challenges in Using Computers and the Internet with Adult English Learners.

ERIC Educational Resources Information Center

Terrill, Lynda

Although resources and training vary from program to program, adult English as a Second or Other Language (ESOL) teachers and English learners across the country are integrating computers and Internet use with ESOL instruction. This can be seen in the growing number of ESOL resources available on the World Wide Web. There are very good reasons for…

A Computer Science Educational Program for Establishing an Entry Point into the Computing Community of Practice

ERIC Educational Resources Information Center

Haberman, Bruria; Yehezkel, Cecile

2008-01-01

The rapid evolvement of the computing domain has posed challenges in attempting to bridge the gap between school and the contemporary world of computing, which is related to content, learning culture, and professional norms. We believe that the interaction of high-school students who major in computer science or software engineering with leading…

Playing by Programming: Making Gameplay a Programming Activity

ERIC Educational Resources Information Center

Weintrop, David; Wilensky, Uri

2016-01-01

Video games are an oft-cited reason for young learners getting interested in programming and computer science. As such, many learning opportunities build on this interest by having kids program their own video games. This approach, while sometimes successful, has its drawbacks stemming from the fact that the challenge of programming and game…

The Instrument of the Future: Computers in Education.

ERIC Educational Resources Information Center

Leonard, Rex; LeCroy, Barbara

Before computers will be able to fulfill their potential in education, two major challenges must be overcome--the lack of well-trained teachers and a lack of general knowledge about software and its capabilities. Teachers must acquire some computer literacy skills, including programming, word processing, materials generation and record keeping. In…

Tools and techniques for computational reproducibility.

PubMed

Piccolo, Stephen R; Frampton, Michael B

2016-07-11

When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced because of complexities in how software is packaged, installed, and executed-and because of limitations associated with how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges; here we describe seven such strategies. With a broad scientific audience in mind, we describe the strengths and limitations of each approach, as well as the circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.

Changing the Paradigm: Preparing Students for the Computing Profession in the 21st Century

NASA Technical Reports Server (NTRS)

Robbins, Kay A.

2003-01-01

The dramatic technological developments of the past decade have led to a tremendous growth in the demand for computer science professionals well-versed in advanced technology and techniques. NASA, traditionally a haven for cutting-edge innovators, is now competing with every industrial and government sector for computer science talent. The computer science program at University of Texas at San Antonio (UTSA) faces challenges beyond those intrinsically presented by rapid technological change, because a significant number of UTSA students come from low-income families with no Internet or computer access at home. An examination of enrollment statistics for the computer science program at UTSA showed that very few students who entered as freshmen successfully graduated. The upper division courses appeared to be populated by graduate students removing deficiencies and by transfer students. The faculty was also concerned that the students who did graduate from the program did not have the strong technical and programming skills that the CS program had been noted for in the community during the 1980's.

Tailored program evaluation: Past, present, future.

PubMed

Suggs, L Suzanne; Cowdery, Joan E; Carroll, Jennifer B

2006-11-01

This paper discusses measurement issues related to the evaluation of computer-tailored health behavior change programs. As the first generation of commercially available tailored products is utilized in health promotion programming, programmers and researchers are becoming aware of the unique challenges that the evaluation of these programs presents. A project is presented that used an online tailored health behavior assessment (HBA) in a worksite setting. Process and outcome evaluation methods are described and include the challenges faced, and strategies proposed and implemented, for meeting them. Implications for future research in tailored program development, implementation, and evaluation are also discussed.

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

Barrett, Brian W.; Hemmert, K. Scott; Underwood, Keith Douglas

Achieving the next three orders of magnitude performance increase to move from petascale to exascale computing will require a significant advancements in several fundamental areas. Recent studies have outlined many of the challenges in hardware and software that will be needed. In this paper, we examine these challenges with respect to high-performance networking. We describe the repercussions of anticipated changes to computing and networking hardware and discuss the impact that alternative parallel programming models will have on the network software stack. We also present some ideas on possible approaches that address some of these challenges.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

PubMed Central

Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter; Koslicki, David; Janssen, Stefan; Dröge, Johannes; Gregor, Ivan; Majda, Stephan; Fiedler, Jessika; Dahms, Eik; Bremges, Andreas; Fritz, Adrian; Garrido-Oter, Ruben; Jørgensen, Tue Sparholt; Shapiro, Nicole; Blood, Philip D.; Gurevich, Alexey; Bai, Yang; Turaev, Dmitrij; DeMaere, Matthew Z.; Chikhi, Rayan; Nagarajan, Niranjan; Quince, Christopher; Meyer, Fernando; Balvočiūtė, Monika; Hansen, Lars Hestbjerg; Sørensen, Søren J.; Chia, Burton K. H.; Denis, Bertrand; Froula, Jeff L.; Wang, Zhong; Egan, Robert; Kang, Dongwan Don; Cook, Jeffrey J.; Deltel, Charles; Beckstette, Michael; Lemaitre, Claire; Peterlongo, Pierre; Rizk, Guillaume; Lavenier, Dominique; Wu, Yu-Wei; Singer, Steven W.; Jain, Chirag; Strous, Marc; Klingenberg, Heiner; Meinicke, Peter; Barton, Michael; Lingner, Thomas; Lin, Hsin-Hung; Liao, Yu-Chieh; Silva, Genivaldo Gueiros Z.; Cuevas, Daniel A.; Edwards, Robert A.; Saha, Surya; Piro, Vitor C.; Renard, Bernhard Y.; Pop, Mihai; Klenk, Hans-Peter; Göker, Markus; Kyrpides, Nikos C.; Woyke, Tanja; Vorholt, Julia A.; Schulze-Lefert, Paul; Rubin, Edward M.; Darling, Aaron E.; Rattei, Thomas; McHardy, Alice C.

2018-01-01

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions. PMID:28967888

Computing, Information and Communications Technology (CICT) Website

NASA Technical Reports Server (NTRS)

Hardman, John; Tu, Eugene (Technical Monitor)

2002-01-01

The Computing, Information and Communications Technology Program (CICT) was established in 2001 to ensure NASA's Continuing leadership in emerging technologies. It is a coordinated, Agency-wide effort to develop and deploy key enabling technologies for a broad range of mission-critical tasks. The NASA CICT program is designed to address Agency-specific computing, information, and communications technology requirements beyond the projected capabilities of commercially available solutions. The areas of technical focus have been chosen for their impact on NASA's missions, their national importance, and the technical challenge they provide to the Program. In order to meet its objectives, the CICT Program is organized into the following four technology focused projects: 1) Computing, Networking and Information Systems (CNIS); 2) Intelligent Systems (IS); 3) Space Communications (SC); 4) Information Technology Strategic Research (ITSR).

An interactive parallel programming environment applied in atmospheric science

NASA Technical Reports Server (NTRS)

vonLaszewski, G.

1996-01-01

This article introduces an interactive parallel programming environment (IPPE) that simplifies the generation and execution of parallel programs. One of the tasks of the environment is to generate message-passing parallel programs for homogeneous and heterogeneous computing platforms. The parallel programs are represented by using visual objects. This is accomplished with the help of a graphical programming editor that is implemented in Java and enables portability to a wide variety of computer platforms. In contrast to other graphical programming systems, reusable parts of the programs can be stored in a program library to support rapid prototyping. In addition, runtime performance data on different computing platforms is collected in a database. A selection process determines dynamically the software and the hardware platform to be used to solve the problem in minimal wall-clock time. The environment is currently being tested on a Grand Challenge problem, the NASA four-dimensional data assimilation system.

Evaluating the Implementation of International Computing Curricular in African Universities: A Design-Reality Gap Approach

ERIC Educational Resources Information Center

Dasuki, Salihu Ibrahim; Ogedebe, Peter; Kanya, Rislana Abdulazeez; Ndume, Hauwa; Makinde, Julius

2015-01-01

Efforts are been made by Universities in developing countries to ensure that it's graduate are not left behind in the competitive global information society; thus have adopted international computing curricular for their computing degree programs. However, adopting these international curricula seem to be very challenging for developing countries…

Cane Toad or Computer Mouse? Real and Computer-Simulated Laboratory Exercises in Physiology Classes

ERIC Educational Resources Information Center

West, Jan; Veenstra, Anneke

2012-01-01

Traditional practical classes in many countries are being rationalised to reduce costs. The challenge for university educators is to provide students with the opportunity to reinforce theoretical concepts by running something other than a traditional practical program. One alternative is to replace wet labs with comparable computer simulations.…

Abstractions for DNA circuit design.

PubMed

Lakin, Matthew R; Youssef, Simon; Cardelli, Luca; Phillips, Andrew

2012-03-07

DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations.

Report on the FY17 Development of Computer Program for ASME Section III, Division 5, Subsection HB, Subpart B Rules

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

Swindeman, M. J.; Jetter, R. I.; Sham, T. -L.

One of the objectives of the high temperature design methodology activities is to develop and validate both improvements and the basic features of ASME Boiler and Pressure Vessel Code, Section III, Rules for Construction of Nuclear Facility Components, Division 5, High Temperature Reactors, Subsection HB, Subpart B (HBB). The overall scope of this task is to develop a computer program to aid assessment procedures of components under specified loading conditions in accordance with the elevated temperature design requirements for Division 5 Class A components. There are many features and alternative paths of varying complexity in HBB. The initial focus ofmore » this computer program is a basic path through the various options for a single reference material, 316H stainless steel. However, the computer program is being structured for eventual incorporation all of the features and permitted materials of HBB. This report will first provide a description of the overall computer program, particular challenges in developing numerical procedures for the assessment, and an overall approach to computer program development. This is followed by a more comprehensive appendix, which is the draft computer program manual for the program development. The strain limits rules have been implemented in the computer program. The evaluation of creep-fatigue damage will be implemented in future work scope.« less

An Integrative and Collaborative Approach to Creating a Diverse and Computationally Competent Geoscience Workforce

NASA Astrophysics Data System (ADS)

Moore, S. L.; Kar, A.; Gomez, R.

2015-12-01

A partnership between Fort Valley State University (FVSU), the Jackson School of Geosciences at The University of Texas (UT) at Austin, and the Texas Advanced Computing Center (TACC) is engaging computational geoscience faculty and researchers with academically talented underrepresented minority (URM) students, training them to solve grand challenges . These next generation computational geoscientists are being trained to solve some of the world's most challenging geoscience grand challenges requiring data intensive large scale modeling and simulation on high performance computers . UT Austin's geoscience outreach program GeoFORCE, recently awarded the Presidential Award in Excellence in Science, Mathematics and Engineering Mentoring, contributes to the collaborative best practices in engaging researchers with URM students. Collaborative efforts over the past decade are providing data demonstrating that integrative pipeline programs with mentoring and paid internship opportunities, multi-year scholarships, computational training, and communication skills development are having an impact on URMs developing middle skills for geoscience careers. Since 1997, the Cooperative Developmental Energy Program at FVSU and its collaborating universities have graduated 87 engineers, 33 geoscientists, and eight health physicists. Recruited as early as high school, students enroll for three years at FVSU majoring in mathematics, chemistry or biology, and then transfer to UT Austin or other partner institutions to complete a second STEM degree, including geosciences. A partnership with the Integrative Computational Education and Research Traineeship (ICERT), a National Science Foundation (NSF) Research Experience for Undergraduates (REU) Site at TACC provides students with a 10-week summer research experience at UT Austin. Mentored by TACC researchers, students with no previous background in computational science learn to use some of the world's most powerful high performance computing resources to address a grand geosciences problem. Students increase their ability to understand and explain the societal impact of their research and communicate the research to multidisciplinary and lay audiences via near-peer mentoring, poster presentations, and publication opportunities.

Arithmetic 400. A Computer Educational Program.

ERIC Educational Resources Information Center

Firestein, Laurie

"ARITHMETIC 400" is the first of the next generation of educational programs designed to encourage thinking about arithmetic problems. Presented in video game format, performance is a measure of correctness, speed, accuracy, and fortune as well. Play presents a challenge to individuals at various skill levels. The program, run on an Apple…

Notional Machines and Introductory Programming Education

ERIC Educational Resources Information Center

Sorva, Juha

2013-01-01

This article brings together, summarizes, and comments on several threads of research that have contributed to our understanding of the challenges that novice programmers face when learning about the runtime dynamics of programs and the role of the computer in program execution. More specifically, the review covers the literature on programming…

STREAM: A First Programming Process

ERIC Educational Resources Information Center

Caspersen, Michael E.; Kolling, Michael

2009-01-01

Programming is recognized as one of seven grand challenges in computing education. Decades of research have shown that the major problems novices experience are composition-based---they may know what the individual programming language constructs are, but they do not know how to put them together. Despite this fact, textbooks, educational…

Data systems and computer science space data systems: Onboard networking and testbeds

NASA Technical Reports Server (NTRS)

Dalton, Dan

1991-01-01

The technical objectives are to develop high-performance, space-qualifiable, onboard computing, storage, and networking technologies. The topics are presented in viewgraph form and include the following: justification; technology challenges; program description; and state-of-the-art assessment.

The Challenge '88 Project: Interfacing of Chemical Instruments to Computers.

ERIC Educational Resources Information Center

Lyons, Jim; Verghese, Manoj

The main part of this project involved using a computer, either an Apple or an IBM, as a chart recorder for the infrared (IR) and nuclear magnetic resonance (NMR) spectrophotometers. The computer "reads" these machines and displays spectra on its monitor. The graphs can then be stored for future reference and manipulation. The program to…

Meeting the Challenge.

ERIC Educational Resources Information Center

Palestis, Ernest

1997-01-01

Describes the award-winning technology endeavors and parent involvement programs developed in the Mine Hill School District (New Jersey). Topics include the multiyear plan, community and board of education support, funding, measuring student learning outcomes, and evening computer education programs for parents and children. (LRW)

Denuded Data! Grounded Theory Using the NUDIST Computer Analysis Program: In Researching the Challenge to Teacher Self-Efficacy Posed by Students with Learning Disabilities in Australian Education.

ERIC Educational Resources Information Center

Burroughs-Lange, Sue G.; Lange, John

This paper evaluates the effects of using the NUDIST (Non-numerical, Unstructured Data Indexing, Searching and Theorising) computer program to organize coded, qualitative data. The use of the software is discussed within the context of the study for which it was used: an Australian study that aimed to develop a theoretical understanding of the…

What Works: The Results of Evaluations on Two Interactive Multimedia Programs.

ERIC Educational Resources Information Center

Schmidt, Kathy J.

The American Institute for Learning (AIL) has developed two interactive multimedia drug-awareness programs for secondary students who have used substances experimentally or are being challenged by others to experiment with drugs. The first, "Addiction and Its Processes," is an awareness program with video and computer capabilities and an…

The Impact of Different Teaching Approaches and Languages on Student Learning of Introductory Programming Concepts

ERIC Educational Resources Information Center

Kunkle, Wanda M.

2010-01-01

Many students experience difficulties learning to program. They find learning to program in the object-oriented paradigm particularly challenging. As a result, computing educators have tried a variety of instructional methods to assist beginning programmers. These include developing approaches geared specifically toward novices and experimenting…

A Computer-Assisted Instruction Unit on Diffusion and Osmosis with a Conceptual Change Design.

ERIC Educational Resources Information Center

Jensen, Murray S.; And Others

1996-01-01

Describes the development, use, and evaluation of the "Osmosis Program" as a teaching tool to elicit and challenge college students' understanding about diffusion and osmosis. Results showed students using the program performed better on a diffusion and osmosis assessment test than students not using the program. (Author/MKR)

R and D Productivity: New Challenges for the US Space Program

NASA Technical Reports Server (NTRS)

Baskin, O. W. (Editor); Sullivan, L. J. (Editor)

1985-01-01

Various topics related to research and development activities applicable to their U.S. space program are discussed. Project management, automatic control technology, human resources, management information systems, computer aided design, systems engineering, and personnel management were among the topics covered.

International Symposium on 21st Century Challenges in Computational Engineering and Science

DTIC Science & Technology

2010-02-26

REPORT DOCUMENTATION PAGE Form Approved OMB No. 0704-0188 The public reporting burden for this collection of information is estimated to average 1 ...it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ORGANIZATION. 1 . REPORT DATE (DD-MM-YYYY) 26...CHALLENGES IN COMPUTATIONAL ENGINEERING AND SCIENCE 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-09- 1 -0648 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S

Integrating numerical computation into the undergraduate education physics curriculum using spreadsheet excel

NASA Astrophysics Data System (ADS)

Fauzi, Ahmad

2017-11-01

Numerical computation has many pedagogical advantages: it develops analytical skills and problem-solving skills, helps to learn through visualization, and enhances physics education. Unfortunately, numerical computation is not taught to undergraduate education physics students in Indonesia. Incorporate numerical computation into the undergraduate education physics curriculum presents many challenges. The main challenges are the dense curriculum that makes difficult to put new numerical computation course and most students have no programming experience. In this research, we used case study to review how to integrate numerical computation into undergraduate education physics curriculum. The participants of this research were 54 students of the fourth semester of physics education department. As a result, we concluded that numerical computation could be integrated into undergraduate education physics curriculum using spreadsheet excel combined with another course. The results of this research become complements of the study on how to integrate numerical computation in learning physics using spreadsheet excel.

Identification of Program Signatures from Cloud Computing System Telemetry Data

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

Nichols, Nicole M.; Greaves, Mark T.; Smith, William P.

Malicious cloud computing activity can take many forms, including running unauthorized programs in a virtual environment. Detection of these malicious activities while preserving the privacy of the user is an important research challenge. Prior work has shown the potential viability of using cloud service billing metrics as a mechanism for proxy identification of malicious programs. Previously this novel detection method has been evaluated in a synthetic and isolated computational environment. In this paper we demonstrate the ability of billing metrics to identify programs, in an active cloud computing environment, including multiple virtual machines running on the same hypervisor. The openmore » source cloud computing platform OpenStack, is used for private cloud management at Pacific Northwest National Laboratory. OpenStack provides a billing tool (Ceilometer) to collect system telemetry measurements. We identify four different programs running on four virtual machines under the same cloud user account. Programs were identified with up to 95% accuracy. This accuracy is dependent on the distinctiveness of telemetry measurements for the specific programs we tested. Future work will examine the scalability of this approach for a larger selection of programs to better understand the uniqueness needed to identify a program. Additionally, future work should address the separation of signatures when multiple programs are running on the same virtual machine.« less

Capturing, Codifying and Scoring Complex Data for Innovative, Computer-Based Items.

ERIC Educational Resources Information Center

Luecht, Richard M.

The Microsoft Certification Program (MCP) includes many new computer-based item types, based on complex cases involving the Windows 2000 (registered) operating system. This Innovative Item Technology (IIT) has presented challenges beyond traditional psychometric considerations such as capturing and storing the relevant response data from…

Aeroelasticity Benchmark Assessment: Subsonic Fixed Wing Program

NASA Technical Reports Server (NTRS)

Florance, Jennifer P.; Chwalowski, Pawel; Wieseman, Carol D.

2010-01-01

The fundamental technical challenge in computational aeroelasticity is the accurate prediction of unsteady aerodynamic phenomena and the effect on the aeroelastic response of a vehicle. Currently, a benchmarking standard for use in validating the accuracy of computational aeroelasticity codes does not exist. Many aeroelastic data sets have been obtained in wind-tunnel and flight testing throughout the world; however, none have been globally presented or accepted as an ideal data set. There are numerous reasons for this. One reason is that often, such aeroelastic data sets focus on the aeroelastic phenomena alone (flutter, for example) and do not contain associated information such as unsteady pressures and time-correlated structural dynamic deflections. Other available data sets focus solely on the unsteady pressures and do not address the aeroelastic phenomena. Other discrepancies can include omission of relevant data, such as flutter frequency and / or the acquisition of only qualitative deflection data. In addition to these content deficiencies, all of the available data sets present both experimental and computational technical challenges. Experimental issues include facility influences, nonlinearities beyond those being modeled, and data processing. From the computational perspective, technical challenges include modeling geometric complexities, coupling between the flow and the structure, grid issues, and boundary conditions. The Aeroelasticity Benchmark Assessment task seeks to examine the existing potential experimental data sets and ultimately choose the one that is viewed as the most suitable for computational benchmarking. An initial computational evaluation of that configuration will then be performed using the Langley-developed computational fluid dynamics (CFD) software FUN3D1 as part of its code validation process. In addition to the benchmarking activity, this task also includes an examination of future research directions. Researchers within the Aeroelasticity Branch will examine other experimental efforts within the Subsonic Fixed Wing (SFW) program (such as testing of the NASA Common Research Model (CRM)) and other NASA programs and assess aeroelasticity issues and research topics.

Makerspaces across Settings: Didactic Design for Programming in Formal and Informal Teacher Education in the Nordic Countries

ERIC Educational Resources Information Center

Kjällander, Susanne; Åkerfeldt, Anna; Mannila, Linda; Parnes, Peter

2018-01-01

For education to provide knowledge reflecting our current and future society, many countries are revising their curricula, including a vivid discussion on digital competence, programming and computational thinking. This article builds an understanding of the maker movement in relation to education in programming, by demonstrating challenges and…

Final Report from The University of Texas at Austin for DEGAS: Dynamic Global Address Space programming environments

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

Erez, Mattan; Yelick, Katherine; Sarkar, Vivek

The Dynamic, Exascale Global Address Space programming environment (DEGAS) project will develop the next generation of programming models and runtime systems to meet the challenges of Exascale computing. Our approach is to provide an efficient and scalable programming model that can be adapted to application needs through the use of dynamic runtime features and domain-specific languages for computational kernels. We address the following technical challenges: Programmability: Rich set of programming constructs based on a Hierarchical Partitioned Global Address Space (HPGAS) model, demonstrated in UPC++. Scalability: Hierarchical locality control, lightweight communication (extended GASNet), and ef- ficient synchronization mechanisms (Phasers). Performance Portability:more » Just-in-time specialization (SEJITS) for generating hardware-specific code and scheduling libraries for domain-specific adaptive runtimes (Habanero). Energy Efficiency: Communication-optimal code generation to optimize energy efficiency by re- ducing data movement. Resilience: Containment Domains for flexible, domain-specific resilience, using state capture mechanisms and lightweight, asynchronous recovery mechanisms. Interoperability: Runtime and language interoperability with MPI and OpenMP to encourage broad adoption.« less

Some key considerations in evolving a computer system and software engineering support environment for the space station program

NASA Technical Reports Server (NTRS)

Mckay, C. W.; Bown, R. L.

1985-01-01

The space station data management system involves networks of computing resources that must work cooperatively and reliably over an indefinite life span. This program requires a long schedule of modular growth and an even longer period of maintenance and operation. The development and operation of space station computing resources will involve a spectrum of systems and software life cycle activities distributed across a variety of hosts, an integration, verification, and validation host with test bed, and distributed targets. The requirement for the early establishment and use of an apporopriate Computer Systems and Software Engineering Support Environment is identified. This environment will support the Research and Development Productivity challenges presented by the space station computing system.

Multicore Programming Challenges

NASA Astrophysics Data System (ADS)

Perrone, Michael

The computer industry is facing fundamental challenges that are driving a major change in the design of computer processors. Due to restrictions imposed by quantum physics, one historical path to higher computer processor performance - by increased clock frequency - has come to an end. Increasing clock frequency now leads to power consumption costs that are too high to justify. As a result, we have seen in recent years that the processor frequencies have peaked and are receding from their high point. At the same time, competitive market conditions are giving business advantage to those companies that can field new streaming applications, handle larger data sets, and update their models to market conditions faster. The desire for newer, faster and larger is driving continued demand for higher computer performance.

Manycore Performance-Portability: Kokkos Multidimensional Array Library

DOE PAGES

Edwards, H. Carter; Sunderland, Daniel; Porter, Vicki; ...

2012-01-01

Large, complex scientific and engineering application code have a significant investment in computational kernels to implement their mathematical models. Porting these computational kernels to the collection of modern manycore accelerator devices is a major challenge in that these devices have diverse programming models, application programming interfaces (APIs), and performance requirements. The Kokkos Array programming model provides library-based approach to implement computational kernels that are performance-portable to CPU-multicore and GPGPU accelerator devices. This programming model is based upon three fundamental concepts: (1) manycore compute devices each with its own memory space, (2) data parallel kernels and (3) multidimensional arrays. Kernel executionmore » performance is, especially for NVIDIA® devices, extremely dependent on data access patterns. Optimal data access pattern can be different for different manycore devices – potentially leading to different implementations of computational kernels specialized for different devices. The Kokkos Array programming model supports performance-portable kernels by (1) separating data access patterns from computational kernels through a multidimensional array API and (2) introduce device-specific data access mappings when a kernel is compiled. An implementation of Kokkos Array is available through Trilinos [Trilinos website, http://trilinos.sandia.gov/, August 2011].« less

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.

Virtual School, Real Experience: Simulations Replicate the World of Practice for Aspiring Principals

ERIC Educational Resources Information Center

Mann, Dale; Shakeshaft, Charol

2013-01-01

A web-enabled computer simulation program presents real-world opportunities, problems, and challenges for aspiring principals. The simulation challenges areas that are not always covered in lectures, textbooks, or workshops. For example, using the simulation requires dealing--on-screen and in real time--with demanding parents, observing…

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).…

Computer-Based Signing Accommodations: Comparing a Recorded Human with an Avatar

ERIC Educational Resources Information Center

Russell, Michael; Kavanaugh, Maureen; Masters, Jessica; Higgins, Jennifer; Hoffmann, Thomas

2009-01-01

Many students who are deaf or hard-of-hearing are eligible for a signing accommodation for state and other standardized tests. The signing accommodation, however, presents several challenges for testing programs that attempt to administer tests under standardized conditions. One potential solution for many of these challenges is the use of…

Data systems and computer science space data systems: Onboard memory and storage

NASA Technical Reports Server (NTRS)

Shull, Tom

1991-01-01

The topics are presented in viewgraph form and include the following: technical objectives; technology challenges; state-of-the-art assessment; mass storage comparison; SODR drive and system concepts; program description; vertical Bloch line (VBL) device concept; relationship to external programs; and backup charts for memory and storage.

Towards a Virtual Teaching Assistant to Answer Questions Asked by Students in Introductory Computer Science

ERIC Educational Resources Information Center

Heiner, Cecily

2009-01-01

Students in introductory programming classes often articulate their questions and information needs incompletely. Consequently, the automatic classification of student questions to provide automated tutorial responses is a challenging problem. This dissertation analyzes 411 questions from an introductory Java programming course by reducing the…

The Impact of a Computerized Dietary Assessment on Nutrition Knowledge

ERIC Educational Resources Information Center

Hensleigh, Katherine Elizabeth; Eddy, James M.; Wang, Min Qi; Dennison, Darwin; Chaney, J. Don

2004-01-01

In recent years, many health educators have integrated computer applications into their health education program interventions. The assessment of the impact of these interventions is limited. This study assessed the impact of the Pyramid Challenge nutrition software program on nutrition knowledge levels of students enrolled in traditional personal…

Algebraic Functions, Computer Programming, and the Challenge of Transfer

ERIC Educational Resources Information Center

Schanzer, Emmanuel Tanenbaum

2015-01-01

Students' struggles with algebra are well documented. Prior to the introduction of functions, mathematics is typically focused on applying a set of arithmetic operations to compute an answer. The introduction of functions, however, marks the point at which mathematics begins to focus on building up abstractions as a way to solve complex problems.…

Computing Robust, Bootstrap-Adjusted Fit Indices for Use with Nonnormal Data

ERIC Educational Resources Information Center

Walker, David A.; Smith, Thomas J.

2017-01-01

Nonnormality of data presents unique challenges for researchers who wish to carry out structural equation modeling. The subsequent SPSS syntax program computes bootstrap-adjusted fit indices (comparative fit index, Tucker-Lewis index, incremental fit index, and root mean square error of approximation) that adjust for nonnormality, along with the…

Health Informatics Program Design and Outcomes: Learning from an Early Offering at a Mid-Level University

ERIC Educational Resources Information Center

Parker, Kevin R.; Srinivasan, Sankara Subramanian; Houghton, Robert F.; Kordzadeh, Nima; Bozan, Karoly; Ottaway, Thomas; Davey, Bill

2017-01-01

Curriculum development is particularly challenging in computing-related disciplines as the computing industry changes more quickly than most. As information technology degrees have become relatively pervasive, some institutions that offer information systems degrees have recognized a need to develop specialist studies in information systems. This…

Multimodal Learning Analytics and Education Data Mining: Using Computational Technologies to Measure Complex Learning Tasks

ERIC Educational Resources Information Center

Blikstein, Paulo; Worsley, Marcelo

2016-01-01

New high-frequency multimodal data collection technologies and machine learning analysis techniques could offer new insights into learning, especially when students have the opportunity to generate unique, personalized artifacts, such as computer programs, robots, and solutions engineering challenges. To date most of the work on learning analytics…

Adapting Extension Food Safety Programming for Vegetable Growers to Accommodate Differences in Ethnicity, Farming Scale, and Other Individual Factors

ERIC Educational Resources Information Center

Kline, Terence R.; Kneen, Harold; Barrett, Eric; Kleinschmidt, Andy; Doohan, Doug

2012-01-01

Differences in vegetable production methods utilized by American growers create distinct challenges for Extension personnel providing food safety training to producer groups. A program employing computers and projectors will not be accepted by an Amish group that does not accept modern technology. We have developed an outreach program that covers…

A Blended Learning Approach for Teaching Computer Programming: Design for Large Classes in Sub-Saharan Africa

ERIC Educational Resources Information Center

Bati, Tesfaye Bayu; Gelderblom, Helene; van Biljon, Judy

2014-01-01

The challenge of teaching programming in higher education is complicated by problems associated with large class teaching, a prevalent situation in many developing countries. This paper reports on an investigation into the use of a blended learning approach to teaching and learning of programming in a class of more than 200 students. A course and…

A Computational Approach for Probabilistic Analysis of Water Impact Simulations

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Mason, Brian H.; Lyle, Karen H.

2009-01-01

NASA's development of new concepts for the Crew Exploration Vehicle Orion presents many similar challenges to those worked in the sixties during the Apollo program. However, with improved modeling capabilities, new challenges arise. For example, the use of the commercial code LS-DYNA, although widely used and accepted in the technical community, often involves high-dimensional, time consuming, and computationally intensive simulations. The challenge is to capture what is learned from a limited number of LS-DYNA simulations to develop models that allow users to conduct interpolation of solutions at a fraction of the computational time. This paper presents a description of the LS-DYNA model, a brief summary of the response surface techniques, the analysis of variance approach used in the sensitivity studies, equations used to estimate impact parameters, results showing conditions that might cause injuries, and concluding remarks.

Fundamental Aeronautics Program: Overview of Propulsion Work in the Supersonic Cruise Efficiency Technical Challenge

NASA Technical Reports Server (NTRS)

Castner, Ray

2012-01-01

The Supersonics Project, part of NASA's Fundamental Aeronautics Program, contains a number of technical challenge areas which include sonic boom community response, airport noise, high altitude emissions, cruise efficiency, light weight durable engines/airframes, and integrated multi-discipline system design. This presentation provides an overview of the current (2012) activities in the supersonic cruise efficiency technical challenge, and is focused specifically on propulsion technologies. The intent is to develop and validate high-performance supersonic inlet and nozzle technologies. Additional work is planned for design and analysis tools for highly-integrated low-noise, low-boom applications. If successful, the payoffs include improved technologies and tools for optimized propulsion systems, propulsion technologies for a minimized sonic boom signature, and a balanced approach to meeting efficiency and community noise goals. In this propulsion area, the work is divided into advanced supersonic inlet concepts, advanced supersonic nozzle concepts, low fidelity computational tool development, high fidelity computational tools, and improved sensors and measurement capability. The current work in each area is summarized.

XPRESS: eXascale PRogramming Environment and System Software

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

Brightwell, Ron; Sterling, Thomas; Koniges, Alice

The XPRESS Project is one of four major projects of the DOE Office of Science Advanced Scientific Computing Research X-stack Program initiated in September, 2012. The purpose of XPRESS is to devise an innovative system software stack to enable practical and useful exascale computing around the end of the decade with near-term contributions to efficient and scalable operation of trans-Petaflops performance systems in the next two to three years; both for DOE mission-critical applications. To this end, XPRESS directly addresses critical challenges in computing of efficiency, scalability, and programmability through introspective methods of dynamic adaptive resource management and task scheduling.

Reflections on Teaching App Inventor for Non-Beginner Programmers: Issues, Challenges and Opportunities

ERIC Educational Resources Information Center

Soares, Andrey

2014-01-01

App Inventor has been used successfully to teach introduction to programming course for CS/IS/IT and Non-CS majors. Now, researchers are looking on how to include the tool in the curriculum of more advanced computing courses. This paper presents some Issues, Challenges and Opportunities observed while teaching courses on Mobile Application…

Big Data: Next-Generation Machines for Big Science

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

Hack, James J.; Papka, Michael E.

Addressing the scientific grand challenges identified by the US Department of Energy’s (DOE’s) Office of Science’s programs alone demands a total leadership-class computing capability of 150 to 400 Pflops by the end of this decade. The successors to three of the DOE’s most powerful leadership-class machines are set to arrive in 2017 and 2018—the products of the Collaboration Oak Ridge Argonne Livermore (CORAL) initiative, a national laboratory–industry design/build approach to engineering nextgeneration petascale computers for grand challenge science. These mission-critical machines will enable discoveries in key scientific fields such as energy, biotechnology, nanotechnology, materials science, and high-performance computing, and servemore » as a milestone on the path to deploying exascale computing capabilities.« less

Achievements and Challenges: Implementing a 1:1 Program in a Secondary School

ERIC Educational Resources Information Center

Keane, Therese; Keane, William

2017-01-01

This longitudinal study explores one secondary school's approach towards implementing a one computer to one student (1:1) program, which commenced in 2011. Prior to 2011, the school was not very technologically advanced, mainly due to financial constraints which impacted on infrastructure, procurement of hardware and software, the availability of…

2007 Mississippi Curriculum Framework: Secondary Computer Graphics. (Program CIP: 50.0402 - Commercial and Advertising Art)

ERIC Educational Resources Information Center

Creel, Jo Anne; Denson, Cornelius; New, Ray

2007-01-01

Secondary vocational-technical education programs in Mississippi are faced with many challenges resulting from sweeping educational reforms at the national and state levels. Schools and teachers are increasingly being held accountable for providing true learning activities to every student in the classroom. This accountability is measured through…

Investigating the Role of Computer-Supported Annotation in Problem-Solving-Based Teaching: An Empirical Study of a Scratch Programming Pedagogy

ERIC Educational Resources Information Center

Su, Addison Y. S.; Yang, Stephen J. H.; Hwang, Wu-Yuin; Huang, Chester S. J.; Tern, Ming-Yu

2014-01-01

For more than 2 years, Scratch programming has been taught in Taiwanese elementary schools. However, past studies have shown that it is difficult to find appropriate learning methods or tools to boost students' Scratch programming performance. This inability to readily identify tutoring tools has become one of the primary challenges addressed in…

Software engineering as an engineering discipline

NASA Technical Reports Server (NTRS)

Freedman, Glenn B.

1988-01-01

The purpose of this panel is to explore the emerging field of software engineering from a variety of perspectives: university programs; industry training and definition; government development; and technology transfer. In doing this, the panel will address the issues of distinctions among software engineering, computer science, and computer hardware engineering as they relate to the challenges of large, complex systems.

Using Visual Technologies in the Introductory Programming Courses for Computer Science Majors

ERIC Educational Resources Information Center

Price, Kellie W.

2013-01-01

Decreasing enrollments, lower rates of student retention and changes in the learning styles of today's students are all issues that the Computer Science (CS) academic community is currently facing. As a result, CS educators are being challenged to find the right blend of technology and pedagogy for their curriculum in order to help students…

Finally, a Good Way to Teach City Government! A Review of the Computer Simulation Game "SimCity."

ERIC Educational Resources Information Center

Pahl, Ronald H.

1991-01-01

Offers an evaluation of the computer simulation game "SimCity." Suggests possible uses for the game at different age and experience levels. Recommends the program as challenging, humorous, and an excellent aid in teaching about the problems and solutions facing city government. Explains that students serve as public officials. (DK)

Designing Programs for Multiple Configurations: "You Mean Everyone Doesn't Have a Pentium or Better!"

ERIC Educational Resources Information Center

Conkright, Thomas D.; Joliat, Judy

1996-01-01

Discusses the challenges, solutions, and compromises involved in creating computer-delivered training courseware for Apollo Travel Services, a company whose 50,000 agents must access a mainframe from many different computing configurations. Initial difficulties came in trying to manage random access memory and quicken response time, but the future…

Introduction to Computational Methods for Stability and Control (COMSAC)

NASA Technical Reports Server (NTRS)

Hall, Robert M.; Fremaux, C. Michael; Chambers, Joseph R.

2004-01-01

This Symposium is intended to bring together the often distinct cultures of the Stability and Control (S&C) community and the Computational Fluid Dynamics (CFD) community. The COMSAC program is itself a new effort by NASA Langley to accelerate the application of high end CFD methodologies to the demanding job of predicting stability and control characteristics of aircraft. This talk is intended to set the stage for needing a program like COMSAC. It is not intended to give details of the program itself. The topics include: 1) S&C Challenges; 2) Aero prediction methodology; 3) CFD applications; 4) NASA COMSAC planning; 5) Objectives of symposium; and 6) Closing remarks.

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide.

PubMed

Anupama, Jigisha; Francescatto, Margherita; Rahman, Farzana; Fatima, Nazeefa; DeBlasio, Dan; Shanmugam, Avinash Kumar; Satagopam, Venkata; Santos, Alberto; Kolekar, Pandurang; Michaut, Magali; Guney, Emre

2018-01-01

Education and training are two essential ingredients for a successful career. On one hand, universities provide students a curriculum for specializing in one's field of study, and on the other, internships complement coursework and provide invaluable training experience for a fruitful career. Consequently, undergraduates and graduates are encouraged to undertake an internship during the course of their degree. The opportunity to explore one's research interests in the early stages of their education is important for students because it improves their skill set and gives their career a boost. In the long term, this helps to close the gap between skills and employability among students across the globe and balance the research capacity in the field of computational biology. However, training opportunities are often scarce for computational biology students, particularly for those who reside in less-privileged regions. Aimed at helping students develop research and academic skills in computational biology and alleviating the divide across countries, the Student Council of the International Society for Computational Biology introduced its Internship Program in 2009. The Internship Program is committed to providing access to computational biology training, especially for students from developing regions, and improving competencies in the field. Here, we present how the Internship Program works and the impact of the internship opportunities so far, along with the challenges associated with this program.

Statis Program Analysis for Reliable, Trusted Apps

DTIC Science & Technology

2017-02-01

flexibility to system design. However, it is challenging for a static analysis to compute or verify properties about a system that uses implicit control...sources might affect the variable’s value. The type qualifier @Sink indicates where (information computed from) the value might be output. These...upper bound on the set of sensitive sources that were actually used to compute the value. If the type of x is qualified by @Source({INTERNET, LOCATION

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.

Computing, information, and communications: Technologies for the 21. Century

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

NONE

1998-11-01

To meet the challenges of a radically new and technologically demanding century, the Federal Computing, Information, and Communications (CIC) programs are investing in long-term research and development (R and D) to advance computing, information, and communications in the United States. CIC R and D programs help Federal departments and agencies to fulfill their evolving missions, assure the long-term national security, better understand and manage the physical environment, improve health care, help improve the teaching of children, provide tools for lifelong training and distance learning to the workforce, and sustain critical US economic competitiveness. One of the nine committees of themore » National Science and Technology Council (NSTC), the Committee on Computing, Information, and Communications (CCIC)--through its CIC R and D Subcommittee--coordinates R and D programs conducted by twelve Federal departments and agencies in cooperation with US academia and industry. These R and D programs are organized into five Program Component Areas: (1) HECC--High End Computing and Computation; (2) LSN--Large Scale Networking, including the Next Generation Internet Initiative; (3) HCS--High Confidence Systems; (4) HuCS--Human Centered Systems; and (5) ETHR--Education, Training, and Human Resources. A brief synopsis of FY 1997 accomplishments and FY 1998 goals by PCA is presented. This report, which supplements the President`s Fiscal Year 1998 Budget, describes the interagency CIC programs.« less

Persistence of elementary programming skills

NASA Astrophysics Data System (ADS)

Bennedsen, Jens; Caspersen, Michael E.

2012-06-01

Programming is recognised as one of seven grand challenges in computing education and attracts much attention in computing education research. Most research in the area concerns teaching methods, educational technology and student understanding/misconceptions. Typically, evaluation of learning outcome takes place during or immediately following the educational activity. In this research, we conduct a qualitative investigation of sustainability of programming competence by studying the effect of recalling programming competence long time after the educational activity has taken place. Our population consists of 10 students who have taken an introductory object-oriented programming course 3, 15 or 27 months prior to our study. None of the students have been exposed to programming in the intervening period. As expected, our research shows that syntactical issues in general hinder immediate programming productivity, but more interestingly it also indicate that a tiny retraining activity and simple guidelines is enough to recall programming competence and overcome syntactical issues.

Final Report: Correctness Tools for Petascale Computing

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

Mellor-Crummey, John

2014-10-27

In the course of developing parallel programs for leadership computing systems, subtle programming errors often arise that are extremely difficult to diagnose without tools. To meet this challenge, University of Maryland, the University of Wisconsin—Madison, and Rice University worked to develop lightweight tools to help code developers pinpoint a variety of program correctness errors that plague parallel scientific codes. The aim of this project was to develop software tools that help diagnose program errors including memory leaks, memory access errors, round-off errors, and data races. Research at Rice University focused on developing algorithms and data structures to support efficient monitoringmore » of multithreaded programs for memory access errors and data races. This is a final report about research and development work at Rice University as part of this project.« less

NASA Aerosciences Activities to Support Human Space Flight

NASA Technical Reports Server (NTRS)

LeBeau, Gerald J.

2011-01-01

The Lyndon B. Johnson Space Center (JSC) has been a critical element of the United State's human space flight program for over 50 years. It is the home to NASA s Mission Control Center, the astronaut corps, and many major programs and projects including the Space Shuttle Program, International Space Station Program, and the Orion Project. As part of JSC's Engineering Directorate, the Applied Aeroscience and Computational Fluid Dynamics Branch is charted to provide aerosciences support to all human spacecraft designs and missions for all phases of flight, including ascent, exo-atmospheric, and entry. The presentation will review past and current aeroscience applications and how NASA works to apply a balanced philosophy that leverages ground testing, computational modeling and simulation, and flight testing, to develop and validate related products. The speaker will address associated aspects of aerodynamics, aerothermodynamics, rarefied gas dynamics, and decelerator systems, involving both spacecraft vehicle design and analysis, and operational mission support. From these examples some of NASA leading aerosciences challenges will be identified. These challenges will be used to provide foundational motivation for the development of specific advanced modeling and simulation capabilities, and will also be used to highlight how development activities are increasing becoming more aligned with flight projects. NASA s efforts to apply principles of innovation and inclusion towards improving its ability to support the myriad of vehicle design and operational challenges will also be briefly reviewed.

Efficient Memory Access with NumPy Global Arrays using Local Memory Access

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

Daily, Jeffrey A.; Berghofer, Dan C.

This paper discusses the work completed working with Global Arrays of data on distributed multi-computer systems and improving their performance. The tasks completed were done at Pacific Northwest National Laboratory in the Science Undergrad Laboratory Internship program in the summer of 2013 for the Data Intensive Computing Group in the Fundamental and Computational Sciences DIrectorate. This work was done on the Global Arrays Toolkit developed by this group. This toolkit is an interface for programmers to more easily create arrays of data on networks of computers. This is useful because scientific computation is often done on large amounts of datamore » sometimes so large that individual computers cannot hold all of it. This data is held in array form and can best be processed on supercomputers which often consist of a network of individual computers doing their computation in parallel. One major challenge for this sort of programming is that operations on arrays on multiple computers is very complex and an interface is needed so that these arrays seem like they are on a single computer. This is what global arrays does. The work done here is to use more efficient operations on that data that requires less copying of data to be completed. This saves a lot of time because copying data on many different computers is time intensive. The way this challenge was solved is when data to be operated on with binary operations are on the same computer, they are not copied when they are accessed. When they are on separate computers, only one set is copied when accessed. This saves time because of less copying done although more data access operations were done.« less

Stochastic Dynamic Mixed-Integer Programming (SD-MIP)

DTIC Science & Technology

2015-05-05

stochastic linear programming ( SLP ) problems. By using a combination of ideas from cutting plane theory of deterministic MIP (especially disjunctive...developed to date. b) As part of this project, we have also developed tools for very large scale Stochastic Linear Programming ( SLP ). There are...several reasons for this. First, SLP models continue to challenge many of the fastest computers to date, and many applications within the DoD (e.g

Increasing Student Performance through the Use of Web Services in Introductory Programming Classrooms: Results from a Series of Quasi-Experiments

ERIC Educational Resources Information Center

Hosack, Bryan; Lim, Billy; Vogt, W. Paul

2012-01-01

An introduction to programming course can be a challenge for both students and instructors. This paper describes a study that introduced Web services (WS) and Service-Oriented Architecture in Information Systems 1 (IS 1) and Computer Science 1 (CS 1) programming courses over a two-year period. WS were used as an instruction tool based on their…

Rapid Development and Distribution of Mobile Media-Rich Clinical Practice Guidelines Nationwide in Colombia.

PubMed

Flórez-Arango, José F; Sriram Iyengar, M; Caicedo, Indira T; Escobar, German

2017-01-01

Development and electronic distribution of Clinical Practice Guidelines production is costly and challenging. This poster presents a rapid method to represent existing guidelines in auditable, computer executable multimedia format. We used a technology that enables a small number of clinicians to, in a short period of time, develop a substantial amount of computer executable guidelines without programming.

Selecting Software for Students with Learning and Other Disabilities

ERIC Educational Resources Information Center

Marino, Matthew T.; Tsurusaki, Blakely K.; Basham, James D.

2011-01-01

Have you ever bought a computer program that you thought would be great for your struggling students, only to find that it did not work on your school computers, or that your students found it difficult to use? Selecting science software for students with learning and other disabilities can be a challenge. This Idea Bank provides a list of…

CFD in design - A government perspective

NASA Technical Reports Server (NTRS)

Kutler, Paul; Gross, Anthony R.

1989-01-01

Some of the research programs involving the use of CFD in the aerodynamic design process at government laboratories around the United States are presented. Technology transfer issues and future directions in the discipline or CFD are addressed. The major challengers in the aerosciences as well as other disciplines that will require high-performance computing resources such as massively parallel computers are examined.

Meeting the Challenge: Computers and Higher Order Thinking. A Research Agenda. Program Report 86-15. Report of a Research Conference Held at the National Academy of Sciences (Washington, DC, October 31-November 1, 1985).

ERIC Educational Resources Information Center

Patterson, Janice H.; Smith, Marshall S.

This report presents a national agenda for research on the learning of thinking skills via computer technology which was developed at a National Academy of Sciences conference on educational, methodological, and practical issues involved in the use of computers to promote complex thought in grades K-12. The discussion of research topics agreed…

2015 Final Reports from the Los Alamos National Laboratory Computational Physics Student Summer Workshop

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

Runnels, Scott Robert; Caldwell, Wendy; Brown, Barton Jed

The two primary purposes of LANL’s Computational Physics Student Summer Workshop are (1) To educate graduate and exceptional undergraduate students in the challenges and applications of computational physics of interest to LANL, and (2) Entice their interest toward those challenges. Computational physics is emerging as a discipline in its own right, combining expertise in mathematics, physics, and computer science. The mathematical aspects focus on numerical methods for solving equations on the computer as well as developing test problems with analytical solutions. The physics aspects are very broad, ranging from low-temperature material modeling to extremely high temperature plasma physics, radiation transportmore » and neutron transport. The computer science issues are concerned with matching numerical algorithms to emerging architectures and maintaining the quality of extremely large codes built to perform multi-physics calculations. Although graduate programs associated with computational physics are emerging, it is apparent that the pool of U.S. citizens in this multi-disciplinary field is relatively small and is typically not focused on the aspects that are of primary interest to LANL. Furthermore, more structured foundations for LANL interaction with universities in computational physics is needed; historically interactions rely heavily on individuals’ personalities and personal contacts. Thus a tertiary purpose of the Summer Workshop is to build an educational network of LANL researchers, university professors, and emerging students to advance the field and LANL’s involvement in it. This report includes both the background for the program and the reports from the students.« less

Leadership Under Challenge: Information Technology R&D in a Competitive World. An Assessment of the Federal Networking and Information Technology R&D Program

DTIC Science & Technology

2007-08-01

challenges. The challengers are not only established competitors in Asia and Western Europe but also newcomers such as India and China. Their methods...or regions. Today’s Major Competitors Presently, the three strongest country and regional competitors to the United States are Japan, East Asia ...photography, and their strong position in computer components and office machinery. Education is another advantage. Japan’s universities are the best in Asia

Applications of genetic programming in cancer research.

PubMed

Worzel, William P; Yu, Jianjun; Almal, Arpit A; Chinnaiyan, Arul M

2009-02-01

The theory of Darwinian evolution is the fundamental keystones of modern biology. Late in the last century, computer scientists began adapting its principles, in particular natural selection, to complex computational challenges, leading to the emergence of evolutionary algorithms. The conceptual model of selective pressure and recombination in evolutionary algorithms allow scientists to efficiently search high dimensional space for solutions to complex problems. In the last decade, genetic programming has been developed and extensively applied for analysis of molecular data to classify cancer subtypes and characterize the mechanisms of cancer pathogenesis and development. This article reviews current successes using genetic programming and discusses its potential impact in cancer research and treatment in the near future.

Comparing the OpenMP, MPI, and Hybrid Programming Paradigm on an SMP Cluster

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Jin, Haoqiang; anMey, Dieter; Hatay, Ferhat F.

2003-01-01

With the advent of parallel hardware and software technologies users are faced with the challenge to choose a programming paradigm best suited for the underlying computer architecture. With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors (SMP), parallel programming techniques have evolved to support parallelism beyond a single level. Which programming paradigm is the best will depend on the nature of the given problem, the hardware architecture, and the available software. In this study we will compare different programming paradigms for the parallelization of a selected benchmark application on a cluster of SMP nodes. We compare the timings of different implementations of the same CFD benchmark application employing the same numerical algorithm on a cluster of Sun Fire SMP nodes. The rest of the paper is structured as follows: In section 2 we briefly discuss the programming models under consideration. We describe our compute platform in section 3. The different implementations of our benchmark code are described in section 4 and the performance results are presented in section 5. We conclude our study in section 6.

From Operating-System Correctness to Pervasively Verified Applications

NASA Astrophysics Data System (ADS)

Daum, Matthias; Schirmer, Norbert W.; Schmidt, Mareike

Though program verification is known and has been used for decades, the verification of a complete computer system still remains a grand challenge. Part of this challenge is the interaction of application programs with the operating system, which is usually entrusted with retrieving input data from and transferring output data to peripheral devices. In this scenario, the correct operation of the applications inherently relies on operating-system correctness. Based on the formal correctness of our real-time operating system Olos, this paper describes an approach to pervasively verify applications running on top of the operating system.

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide

PubMed Central

Anupama, Jigisha; Shanmugam, Avinash Kumar; Santos, Alberto; Michaut, Magali

2018-01-01

Education and training are two essential ingredients for a successful career. On one hand, universities provide students a curriculum for specializing in one’s field of study, and on the other, internships complement coursework and provide invaluable training experience for a fruitful career. Consequently, undergraduates and graduates are encouraged to undertake an internship during the course of their degree. The opportunity to explore one’s research interests in the early stages of their education is important for students because it improves their skill set and gives their career a boost. In the long term, this helps to close the gap between skills and employability among students across the globe and balance the research capacity in the field of computational biology. However, training opportunities are often scarce for computational biology students, particularly for those who reside in less-privileged regions. Aimed at helping students develop research and academic skills in computational biology and alleviating the divide across countries, the Student Council of the International Society for Computational Biology introduced its Internship Program in 2009. The Internship Program is committed to providing access to computational biology training, especially for students from developing regions, and improving competencies in the field. Here, we present how the Internship Program works and the impact of the internship opportunities so far, along with the challenges associated with this program. PMID:29346365

Multicore Challenges and Benefits for High Performance Scientific Computing

DOE PAGES

Nielsen, Ida M. B.; Janssen, Curtis L.

2008-01-01

Until recently, performance gains in processors were achieved largely by improvements in clock speeds and instruction level parallelism. Thus, applications could obtain performance increases with relatively minor changes by upgrading to the latest generation of computing hardware. Currently, however, processor performance improvements are realized by using multicore technology and hardware support for multiple threads within each core, and taking full advantage of this technology to improve the performance of applications requires exposure of extreme levels of software parallelism. We will here discuss the architecture of parallel computers constructed from many multicore chips as well as techniques for managing the complexitymore » of programming such computers, including the hybrid message-passing/multi-threading programming model. We will illustrate these ideas with a hybrid distributed memory matrix multiply and a quantum chemistry algorithm for energy computation using Møller–Plesset perturbation theory.« less

The grand challenge of managing the petascale facility.

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

Aiken, R. J.; Mathematics and Computer Science

2007-02-28

This report is the result of a study of networks and how they may need to evolve to support petascale leadership computing and science. As Dr. Ray Orbach, director of the Department of Energy's Office of Science, says in the spring 2006 issue of SciDAC Review, 'One remarkable example of growth in unexpected directions has been in high-end computation'. In the same article Dr. Michael Strayer states, 'Moore's law suggests that before the end of the next cycle of SciDAC, we shall see petaflop computers'. Given the Office of Science's strong leadership and support for petascale computing and facilities, wemore » should expect to see petaflop computers in operation in support of science before the end of the decade, and DOE/SC Advanced Scientific Computing Research programs are focused on making this a reality. This study took its lead from this strong focus on petascale computing and the networks required to support such facilities, but it grew to include almost all aspects of the DOE/SC petascale computational and experimental science facilities, all of which will face daunting challenges in managing and analyzing the voluminous amounts of data expected. In addition, trends indicate the increased coupling of unique experimental facilities with computational facilities, along with the integration of multidisciplinary datasets and high-end computing with data-intensive computing; and we can expect these trends to continue at the petascale level and beyond. Coupled with recent technology trends, they clearly indicate the need for including capability petascale storage, networks, and experiments, as well as collaboration tools and programming environments, as integral components of the Office of Science's petascale capability metafacility. The objective of this report is to recommend a new cross-cutting program to support the management of petascale science and infrastructure. The appendices of the report document current and projected DOE computation facilities, science trends, and technology trends, whose combined impact can affect the manageability and stewardship of DOE's petascale facilities. This report is not meant to be all-inclusive. Rather, the facilities, science projects, and research topics presented are to be considered examples to clarify a point.« less

Case Study of a Discontinued Start-Up Engineering Program: Critical Challenges and Lessons Learned

ERIC Educational Resources Information Center

Friess, Wilhelm A.

2017-01-01

The explanatory case study presented here analyzes the factors that have contributed to the failure of a start-up engineering program launched at an off-campus site, and aimed at imparting the first two years of the BSc Mechanical, Electrical, Computer and Civil Engineering utilizing an integrated curriculum. Findings indicate the root cause for…

CESDIS

NASA Technical Reports Server (NTRS)

1994-01-01

CESDIS, the Center of Excellence in Space Data and Information Sciences was developed jointly by NASA, Universities Space Research Association (USRA), and the University of Maryland in 1988 to focus on the design of advanced computing techniques and data systems to support NASA Earth and space science research programs. CESDIS is operated by USRA under contract to NASA. The Director, Associate Director, Staff Scientists, and administrative staff are located on-site at NASA's Goddard Space Flight Center in Greenbelt, Maryland. The primary CESDIS mission is to increase the connection between computer science and engineering research programs at colleges and universities and NASA groups working with computer applications in Earth and space science. The 1993-94 CESDIS year included a broad range of computer science research applied to NASA problems. This report provides an overview of these research projects and programs as well as a summary of the various other activities of CESDIS in support of NASA and the university research community, We have had an exciting and challenging year.

Security and Cloud Outsourcing Framework for Economic Dispatch

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

Sarker, Mushfiqur R.; Wang, Jianhui; Li, Zuyi

The computational complexity and problem sizes of power grid applications have increased significantly with the advent of renewable resources and smart grid technologies. The current paradigm of solving these issues consist of inhouse high performance computing infrastructures, which have drawbacks of high capital expenditures, maintenance, and limited scalability. Cloud computing is an ideal alternative due to its powerful computational capacity, rapid scalability, and high cost-effectiveness. A major challenge, however, remains in that the highly confidential grid data is susceptible for potential cyberattacks when outsourced to the cloud. In this work, a security and cloud outsourcing framework is developed for themore » Economic Dispatch (ED) linear programming application. As a result, the security framework transforms the ED linear program into a confidentiality-preserving linear program, that masks both the data and problem structure, thus enabling secure outsourcing to the cloud. Results show that for large grid test cases the performance gain and costs outperforms the in-house infrastructure.« less

Security and Cloud Outsourcing Framework for Economic Dispatch

DOE PAGES

Sarker, Mushfiqur R.; Wang, Jianhui; Li, Zuyi; ...

2017-04-24

The computational complexity and problem sizes of power grid applications have increased significantly with the advent of renewable resources and smart grid technologies. The current paradigm of solving these issues consist of inhouse high performance computing infrastructures, which have drawbacks of high capital expenditures, maintenance, and limited scalability. Cloud computing is an ideal alternative due to its powerful computational capacity, rapid scalability, and high cost-effectiveness. A major challenge, however, remains in that the highly confidential grid data is susceptible for potential cyberattacks when outsourced to the cloud. In this work, a security and cloud outsourcing framework is developed for themore » Economic Dispatch (ED) linear programming application. As a result, the security framework transforms the ED linear program into a confidentiality-preserving linear program, that masks both the data and problem structure, thus enabling secure outsourcing to the cloud. Results show that for large grid test cases the performance gain and costs outperforms the in-house infrastructure.« less

Exploring Asynchronous Many-Task Runtime Systems toward Extreme Scales

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

Knight, Samuel; Baker, Gavin Matthew; Gamell, Marc

2015-10-01

Major exascale computing reports indicate a number of software challenges to meet the dramatic change of system architectures in near future. While several-orders-of-magnitude increase in parallelism is the most commonly cited of those, hurdles also include performance heterogeneity of compute nodes across the system, increased imbalance between computational capacity and I/O capabilities, frequent system interrupts, and complex hardware architectures. Asynchronous task-parallel programming models show a great promise in addressing these issues, but are not yet fully understood nor developed su ciently for computational science and engineering application codes. We address these knowledge gaps through quantitative and qualitative exploration of leadingmore » candidate solutions in the context of engineering applications at Sandia. In this poster, we evaluate MiniAero code ported to three leading candidate programming models (Charm++, Legion and UINTAH) to examine the feasibility of these models that permits insertion of new programming model elements into an existing code base.« less

Parallel Rendering of Large Time-Varying Volume Data

NASA Technical Reports Server (NTRS)

Garbutt, Alexander E.

2005-01-01

Interactive visualization of large time-varying 3D volume datasets has been and still is a great challenge to the modem computational world. It stretches the limits of the memory capacity, the disk space, the network bandwidth and the CPU speed of a conventional computer. In this SURF project, we propose to develop a parallel volume rendering program on SGI's Prism, a cluster computer equipped with state-of-the-art graphic hardware. The proposed program combines both parallel computing and hardware rendering in order to achieve an interactive rendering rate. We use 3D texture mapping and a hardware shader to implement 3D volume rendering on each workstation. We use SGI's VisServer to enable remote rendering using Prism's graphic hardware. And last, we will integrate this new program with ParVox, a parallel distributed visualization system developed at JPL. At the end of the project, we Will demonstrate remote interactive visualization using this new hardware volume renderer on JPL's Prism System using a time-varying dataset from selected JPL applications.

Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends

PubMed Central

2014-01-01

The emergence of massive datasets in a clinical setting presents both challenges and opportunities in data storage and analysis. This so called “big data” challenges traditional analytic tools and will increasingly require novel solutions adapted from other fields. Advances in information and communication technology present the most viable solutions to big data analysis in terms of efficiency and scalability. It is vital those big data solutions are multithreaded and that data access approaches be precisely tailored to large volumes of semi-structured/unstructured data. The MapReduce programming framework uses two tasks common in functional programming: Map and Reduce. MapReduce is a new parallel processing framework and Hadoop is its open-source implementation on a single computing node or on clusters. Compared with existing parallel processing paradigms (e.g. grid computing and graphical processing unit (GPU)), MapReduce and Hadoop have two advantages: 1) fault-tolerant storage resulting in reliable data processing by replicating the computing tasks, and cloning the data chunks on different computing nodes across the computing cluster; 2) high-throughput data processing via a batch processing framework and the Hadoop distributed file system (HDFS). Data are stored in the HDFS and made available to the slave nodes for computation. In this paper, we review the existing applications of the MapReduce programming framework and its implementation platform Hadoop in clinical big data and related medical health informatics fields. The usage of MapReduce and Hadoop on a distributed system represents a significant advance in clinical big data processing and utilization, and opens up new opportunities in the emerging era of big data analytics. The objective of this paper is to summarize the state-of-the-art efforts in clinical big data analytics and highlight what might be needed to enhance the outcomes of clinical big data analytics tools. This paper is concluded by summarizing the potential usage of the MapReduce programming framework and Hadoop platform to process huge volumes of clinical data in medical health informatics related fields. PMID:25383096

Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends.

PubMed

Mohammed, Emad A; Far, Behrouz H; Naugler, Christopher

2014-01-01

The emergence of massive datasets in a clinical setting presents both challenges and opportunities in data storage and analysis. This so called "big data" challenges traditional analytic tools and will increasingly require novel solutions adapted from other fields. Advances in information and communication technology present the most viable solutions to big data analysis in terms of efficiency and scalability. It is vital those big data solutions are multithreaded and that data access approaches be precisely tailored to large volumes of semi-structured/unstructured data. THE MAPREDUCE PROGRAMMING FRAMEWORK USES TWO TASKS COMMON IN FUNCTIONAL PROGRAMMING: Map and Reduce. MapReduce is a new parallel processing framework and Hadoop is its open-source implementation on a single computing node or on clusters. Compared with existing parallel processing paradigms (e.g. grid computing and graphical processing unit (GPU)), MapReduce and Hadoop have two advantages: 1) fault-tolerant storage resulting in reliable data processing by replicating the computing tasks, and cloning the data chunks on different computing nodes across the computing cluster; 2) high-throughput data processing via a batch processing framework and the Hadoop distributed file system (HDFS). Data are stored in the HDFS and made available to the slave nodes for computation. In this paper, we review the existing applications of the MapReduce programming framework and its implementation platform Hadoop in clinical big data and related medical health informatics fields. The usage of MapReduce and Hadoop on a distributed system represents a significant advance in clinical big data processing and utilization, and opens up new opportunities in the emerging era of big data analytics. The objective of this paper is to summarize the state-of-the-art efforts in clinical big data analytics and highlight what might be needed to enhance the outcomes of clinical big data analytics tools. This paper is concluded by summarizing the potential usage of the MapReduce programming framework and Hadoop platform to process huge volumes of clinical data in medical health informatics related fields.

Designing, programming, and optimizing a (small) quantum computer

NASA Astrophysics Data System (ADS)

Svore, Krysta

In 1982, Richard Feynman proposed to use a computer founded on the laws of quantum physics to simulate physical systems. In the more than thirty years since, quantum computers have shown promise to solve problems in number theory, chemistry, and materials science that would otherwise take longer than the lifetime of the universe to solve on an exascale classical machine. The practical realization of a quantum computer requires understanding and manipulating subtle quantum states while experimentally controlling quantum interference. It also requires an end-to-end software architecture for programming, optimizing, and implementing a quantum algorithm on the quantum device hardware. In this talk, we will introduce recent advances in connecting abstract theory to present-day real-world applications through software. We will highlight recent advancement of quantum algorithms and the challenges in ultimately performing a scalable solution on a quantum device.

The Challenge of Technology: Action Strategies for the School Library Media Specialist. School Library Media Programs: Focus on Trends and Issues; No. 13.

ERIC Educational Resources Information Center

Wright, Kieth

This book describes some of the challenges facing school library media specialists as they work with teachers and administrators in making appropriate use of computers in schools. Five chapters address the following topics: (1) the school in the context of the emerging information society; (2) the roles of school library media specialists in the…

Using Ada: The deeper challenges

NASA Technical Reports Server (NTRS)

Feinberg, David A.

1986-01-01

The Ada programming language and the associated Ada Programming Support Environment (APSE) and Ada Run Time Environment (ARTE) provide the potential for significant life-cycle cost reductions in computer software development and maintenance activities. The Ada programming language itself is standardized, trademarked, and controlled via formal validation procedures. Though compilers are not yet production-ready as most would desire, the technology for constructing them is sufficiently well known and understood that time and money should suffice to correct current deficiencies. The APSE and ARTE are, on the other hand, significantly newer issues within most software development and maintenance efforts. Currently, APSE and ARTE are highly dependent on differing implementer concepts, strategies, and market objectives. Complex and sophisticated mission-critical computing systems require the use of a complete Ada-based capability, not just the programming language itself; yet the range of APSE and ARTE features which must actually be utilized can vary significantly from one system to another. As a consequence, the need to understand, objectively evaluate, and select differing APSE and ARTE capabilities and features is critical to the effective use of Ada and the life-cycle efficiencies it is intended to promote. It is the selection, collection, and understanding of APSE and ARTE which provide the deeper challenges of using Ada for real-life mission-critical computing systems. Some of the current issues which must be clarified, often on a case-by-case basis, in order to successfully realize the full capabilities of Ada are discussed.

Building professional identity as computer science teachers: Supporting high school computer science teachers through reflection and community building

NASA Astrophysics Data System (ADS)

Ni, Lijun

Computing education requires qualified computing teachers. The reality is that too few high schools in the U.S. have computing/computer science teachers with formal computer science (CS) training, and many schools do not have CS teacher at all. Moreover, teacher retention rate is often low. Beginning teacher attrition rate is particularly high in secondary education. Therefore, in addition to the need for preparing new CS teachers, we also need to support those teachers we have recruited and trained to become better teachers and continue to teach CS. Teacher education literature, especially teacher identity theory, suggests that a strong sense of teacher identity is a major indicator or feature of committed, qualified teachers. However, under the current educational system in the U.S., it could be challenging to establish teacher identity for high school (HS) CS teachers, e.g., due to a lack of teacher certification for CS. This thesis work centers upon understanding the sense of identity HS CS teachers hold and exploring ways of supporting their identity development through a professional development program: the Disciplinary Commons for Computing Educators (DCCE). DCCE has a major focus on promoting reflection on teaching practice and community building. With scaffolded activities such as course portfolio creation, peer review and peer observation among a group of HS CS teachers, it offers opportunities for CS teachers to explicitly reflect on and narrate their teaching, which is a central process of identity building through their participation within the community. In this thesis research, I explore the development of CS teacher identity through professional development programs. I first conducted an interview study with local HS CS teachers to understand their sense of identity and factors influencing their identity formation. I designed and enacted the professional program (DCCE) and conducted case studies with DCCE participants to understand how their participation in DCCE supported their identity development as a CS teacher. Overall, I found that these CS teachers held different teacher identities with varied features related to their motivation and commitment in teaching CS. I identified four concrete factors that contributed to these teachers' sense of professional identity as a CS teacher. I addressed some of these issues for CS teachers' identity development (especially the issue of lacking community) through offering professional development opportunities with a major focus on teacher reflection and community building. Results from this work indicate a potential model of supporting CS identity development, mapping the characteristics of the professional development program with particular facets of CS teacher identity. This work offers further understanding of the unique challenges that current CS teachers are facing in their CS teaching, as well as the challenges of preparing and supporting CS teachers. My findings also suggest guidelines for teacher education and professional development program design and implementation for building committed, qualified CS teachers in ways that promote the development of CS teacher identity.

Metacomputing on Commodity Computers

DTIC Science & Technology

1999-05-01

on NOWs, and this has contributed to the popularity of systems such as PVM [59], MPI [67], Linda [33], and TreadMarks [2]. 26 Challenges Given that...presents the performance of Calypso and Persistent Linda (PLinda) [77] programs and compares how they can tolerate failures. A biological pattern...adds fault tolerance to Linda programs by using light-weight transac- tions, whereas Calypso uses the combination of eager scheduling and two-phase

Just for Fun: Using Programming Games in Software Programming Training and Education--A Field Study of IBM Robocode Community

ERIC Educational Resources Information Center

Long, Ju

2007-01-01

Improving learning effectiveness has always been a constant challenge in software education and training. One of the primary tasks educators face is to motivate learners to perform to their best abilities. Using computer games is one means to encourage learners to learn (Klawe, 1994). When games are used in general education, they could enhance…

Object-oriented Tools for Distributed Computing

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1993-01-01

Distributed computing systems are proliferating, owing to the availability of powerful, affordable microcomputers and inexpensive communication networks. A critical problem in developing such systems is getting application programs to interact with one another across a computer network. Remote interprogram connectivity is particularly challenging across heterogeneous environments, where applications run on different kinds of computers and operating systems. NetWorks! (trademark) is an innovative software product that provides an object-oriented messaging solution to these problems. This paper describes the design and functionality of NetWorks! and illustrates how it is being used to build complex distributed applications for NASA and in the commercial sector.

Quantum machine learning.

PubMed

Biamonte, Jacob; Wittek, Peter; Pancotti, Nicola; Rebentrost, Patrick; Wiebe, Nathan; Lloyd, Seth

2017-09-13

Fuelled by increasing computer power and algorithmic advances, machine learning techniques have become powerful tools for finding patterns in data. Quantum systems produce atypical patterns that classical systems are thought not to produce efficiently, so it is reasonable to postulate that quantum computers may outperform classical computers on machine learning tasks. The field of quantum machine learning explores how to devise and implement quantum software that could enable machine learning that is faster than that of classical computers. Recent work has produced quantum algorithms that could act as the building blocks of machine learning programs, but the hardware and software challenges are still considerable.

Quantum machine learning

NASA Astrophysics Data System (ADS)

Biamonte, Jacob; Wittek, Peter; Pancotti, Nicola; Rebentrost, Patrick; Wiebe, Nathan; Lloyd, Seth

2017-09-01

Fuelled by increasing computer power and algorithmic advances, machine learning techniques have become powerful tools for finding patterns in data. Quantum systems produce atypical patterns that classical systems are thought not to produce efficiently, so it is reasonable to postulate that quantum computers may outperform classical computers on machine learning tasks. The field of quantum machine learning explores how to devise and implement quantum software that could enable machine learning that is faster than that of classical computers. Recent work has produced quantum algorithms that could act as the building blocks of machine learning programs, but the hardware and software challenges are still considerable.

BraX-Ray: an X-ray of the Brazilian computer science graduate programs.

PubMed

Digiampietri, Luciano A; Mena-Chalco, Jesús P; Vaz de Melo, Pedro O S; Malheiro, Ana P R; Meira, Dânia N O; Franco, Laryssa F; Oliveira, Leonardo B

2014-01-01

Research productivity assessment is increasingly relevant for allocation of research funds. On one hand, this assessment is challenging because it involves both qualitative and quantitative analysis of several characteristics, most of them subjective in nature. On the other hand, current tools and academic social networks make bibliometric data web-available to everyone for free. Those tools, especially when combined with other data, are able to create a rich environment from which information on research productivity can be extracted. In this context, our work aims at characterizing the Brazilian Computer Science graduate programs and the relationship among themselves. We (i) present views of the programs from different perspectives, (ii) rank the programs according to each perspective and a combination of them, (iii) show correlation between assessment metrics, (iv) discuss how programs relate to another, and (v) infer aspects that boost programs' research productivity. The results indicate that programs with a higher insertion in the coauthorship network topology also possess a higher research productivity between 2004 and 2009.

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.

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

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

Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. Tomore » alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.« less

RIACS/USRA

NASA Technical Reports Server (NTRS)

Oliger, Joseph

1993-01-01

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on 6 June 1983. RIACS is privately operated by USRA, a consortium of universities with research programs in the aerospace sciences, under contract with NASA. The primary mission of RIACS is to provide research and expertise in computer science and scientific computing to support the scientific missions of NASA ARC. The research carried out at RIACS must change its emphasis from year to year in response to NASA ARC's changing needs and technological opportunities. A flexible scientific staff is provided through a university faculty visitor program, a post doctoral program, and a student visitor program. Not only does this provide appropriate expertise but it also introduces scientists outside of NASA to NASA problems. A small group of core RIACS staff provides continuity and interacts with an ARC technical monitor and scientific advisory group to determine the RIACS mission. RIACS activities are reviewed and monitored by a USRA advisory council and ARC technical monitor. Research at RIACS is currently being done in the following areas: Parallel Computing, Advanced Methods for Scientific Computing, High Performance Networks and Technology, and Learning Systems. Parallel compiler techniques, adaptive numerical methods for flows in complicated geometries, and optimization were identified as important problems to investigate for ARC's involvement in the Computational Grand Challenges of the next decade.

Mobile game development: improving student engagement and motivation in introductory computing courses

NASA Astrophysics Data System (ADS)

Kurkovsky, Stan

2013-06-01

Computer games have been accepted as an engaging and motivating tool in the computer science (CS) curriculum. However, designing and implementing a playable game is challenging, and is best done in advanced courses. Games for mobile devices, on the other hand, offer the advantage of being simpler and, thus, easier to program for lower level students. Learning context of mobile game development can be used to reinforce many core programming topics, such as loops, classes, and arrays. Furthermore, it can also be used to expose students in introductory computing courses to a wide range of advanced topics in order to illustrate that CS can be much more than coding. This paper describes the author's experience with using mobile game development projects in CS I and II, how these projects were integrated into existing courses at several universities, and the lessons learned from this experience.

Speeding up parallel processing

NASA Technical Reports Server (NTRS)

Denning, Peter J.

1988-01-01

In 1967 Amdahl expressed doubts about the ultimate utility of multiprocessors. The formulation, now called Amdahl's law, became part of the computing folklore and has inspired much skepticism about the ability of the current generation of massively parallel processors to efficiently deliver all their computing power to programs. The widely publicized recent results of a group at Sandia National Laboratory, which showed speedup on a 1024 node hypercube of over 500 for three fixed size problems and over 1000 for three scalable problems, have convincingly challenged this bit of folklore and have given new impetus to parallel scientific computing.

Advances in mixed-integer programming methods for chemical production scheduling.

PubMed

Velez, Sara; Maravelias, Christos T

2014-01-01

The goal of this paper is to critically review advances in the area of chemical production scheduling over the past three decades and then present two recently proposed solution methods that have led to dramatic computational enhancements. First, we present a general framework and problem classification and discuss modeling and solution methods with an emphasis on mixed-integer programming (MIP) techniques. Second, we present two solution methods: (a) a constraint propagation algorithm that allows us to compute parameters that are then used to tighten MIP scheduling models and (b) a reformulation that introduces new variables, thus leading to effective branching. We also present computational results and an example illustrating how these methods are implemented, as well as the resulting enhancements. We close with a discussion of open research challenges and future research directions.

Manyscale Computing for Sensor Processing in Support of Space Situational Awareness

NASA Astrophysics Data System (ADS)

Schmalz, M.; Chapman, W.; Hayden, E.; Sahni, S.; Ranka, S.

2014-09-01

Increasing image and signal data burden associated with sensor data processing in support of space situational awareness implies continuing computational throughput growth beyond the petascale regime. In addition to growing applications data burden and diversity, the breadth, diversity and scalability of high performance computing architectures and their various organizations challenge the development of a single, unifying, practicable model of parallel computation. Therefore, models for scalable parallel processing have exploited architectural and structural idiosyncrasies, yielding potential misapplications when legacy programs are ported among such architectures. In response to this challenge, we have developed a concise, efficient computational paradigm and software called Manyscale Computing to facilitate efficient mapping of annotated application codes to heterogeneous parallel architectures. Our theory, algorithms, software, and experimental results support partitioning and scheduling of application codes for envisioned parallel architectures, in terms of work atoms that are mapped (for example) to threads or thread blocks on computational hardware. Because of the rigor, completeness, conciseness, and layered design of our manyscale approach, application-to-architecture mapping is feasible and scalable for architectures at petascales, exascales, and above. Further, our methodology is simple, relying primarily on a small set of primitive mapping operations and support routines that are readily implemented on modern parallel processors such as graphics processing units (GPUs) and hybrid multi-processors (HMPs). In this paper, we overview the opportunities and challenges of manyscale computing for image and signal processing in support of space situational awareness applications. We discuss applications in terms of a layered hardware architecture (laboratory > supercomputer > rack > processor > component hierarchy). Demonstration applications include performance analysis and results in terms of execution time as well as storage, power, and energy consumption for bus-connected and/or networked architectures. The feasibility of the manyscale paradigm is demonstrated by addressing four principal challenges: (1) architectural/structural diversity, parallelism, and locality, (2) masking of I/O and memory latencies, (3) scalability of design as well as implementation, and (4) efficient representation/expression of parallel applications. Examples will demonstrate how manyscale computing helps solve these challenges efficiently on real-world computing systems.

Early Education Success Is Good Business.

ERIC Educational Resources Information Center

Odell, Mary

1992-01-01

Examines the Riordan Foundation's successful strategy in establishing computer-assisted reading labs in public and private elementary schools nationwide. The foundation provides challenge grants to applicant schools to purchase equipment for the "Writing to Read" program and assists them in raising additional funds from local businesses.…

Fundamental Aeronautics Program: Overview of Project Work in Supersonic Cruise Efficiency

NASA Technical Reports Server (NTRS)

Castner, Raymond

2011-01-01

The Supersonics Project, part of NASA?s Fundamental Aeronautics Program, contains a number of technical challenge areas which include sonic boom community response, airport noise, high altitude emissions, cruise efficiency, light weight durable engines/airframes, and integrated multi-discipline system design. This presentation provides an overview of the current (2011) activities in the supersonic cruise efficiency technical challenge, and is focused specifically on propulsion technologies. The intent is to develop and validate high-performance supersonic inlet and nozzle technologies. Additional work is planned for design and analysis tools for highly-integrated low-noise, low-boom applications. If successful, the payoffs include improved technologies and tools for optimized propulsion systems, propulsion technologies for a minimized sonic boom signature, and a balanced approach to meeting efficiency and community noise goals. In this propulsion area, the work is divided into advanced supersonic inlet concepts, advanced supersonic nozzle concepts, low fidelity computational tool development, high fidelity computational tools, and improved sensors and measurement capability. The current work in each area is summarized.

Designing and Implementing a Computational Methods Course for Upper-level Undergraduates and Postgraduates in Atmospheric and Oceanic Sciences

NASA Astrophysics Data System (ADS)

Nelson, E.; L'Ecuyer, T. S.; Douglas, A.; Hansen, Z.

2017-12-01

In the modern computing age, scientists must utilize a wide variety of skills to carry out scientific research. Programming, including a focus on collaborative development, has become more prevalent in both academic and professional career paths. Faculty in the Department of Atmospheric and Oceanic Sciences at the University of Wisconsin—Madison recognized this need and recently approved a new course offering for undergraduates and postgraduates in computational methods that was first held in Spring 2017. Three programming languages were covered in the inaugural course semester and development themes such as modularization, data wrangling, and conceptual code models were woven into all of the sections. In this presentation, we will share successes and challenges in developing a research project-focused computational course that leverages hands-on computer laboratory learning and open-sourced course content. Improvements and changes in future iterations of the course based on the first offering will also be discussed.

Breaking the hype cycle: using the computer effectively with learners with intellectual disabilities.

PubMed

Lloyd, Jan; Moni, Karen B; Jobling, Anne

2006-06-01

There has been huge growth in the use of information technology (IT) in classrooms for learners of all ages. It has been suggested that computers in the classroom encourage independent and self-paced learning, provide immediate feedback and improve self-motivation and self-confidence. Concurrently there is increasing interest related to the role of technology in educational programs for individuals with intellectual disabilities. However, although many claims are made about the benefits of computers and software packages there is limited evidence based information to support these claims. Researchers are now starting to look at the specific instructional design features that are hypothesised to facilitate education outcomes rather than the over-emphasis on graphics and sounds. Research undertaken as part of a post-school program (Latch-On: Literacy and Technology - Hands On) at the University of Queensland investigated the use of computers by young adults with intellectual disabilities. The aims of the research reported in this paper were to address the challenges identified in the 'hype' surrounding different pieces of educational software and to develop a means of systematically analysing software for use in teaching programs.

Models@Home: distributed computing in bioinformatics using a screensaver based approach.

PubMed

Krieger, Elmar; Vriend, Gert

2002-02-01

Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world's largest distributed computing project. We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster. We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.

Neuromorphic Computing, Architectures, Models, and Applications. A Beyond-CMOS Approach to Future Computing, June 29-July 1, 2016, Oak Ridge, TN

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

Potok, Thomas; Schuman, Catherine; Patton, Robert

The White House and Department of Energy have been instrumental in driving the development of a neuromorphic computing program to help the United States continue its lead in basic research into (1) Beyond Exascale—high performance computing beyond Moore’s Law and von Neumann architectures, (2) Scientific Discovery—new paradigms for understanding increasingly large and complex scientific data, and (3) Emerging Architectures—assessing the potential of neuromorphic and quantum architectures. Neuromorphic computing spans a broad range of scientific disciplines from materials science to devices, to computer science, to neuroscience, all of which are required to solve the neuromorphic computing grand challenge. In our workshopmore » we focus on the computer science aspects, specifically from a neuromorphic device through an application. Neuromorphic devices present a very different paradigm to the computer science community from traditional von Neumann architectures, which raises six major questions about building a neuromorphic application from the device level. We used these fundamental questions to organize the workshop program and to direct the workshop panels and discussions. From the white papers, presentations, panels, and discussions, there emerged several recommendations on how to proceed.« less

The impact of computer usage on the perceptions of hospital secretaries.

PubMed

Foner, C; Nour, M; Luo, X; Kim, J

1991-09-01

This study explored the perceptions of hospital unit secretaries regarding computer usage. Specifically, six attitudinal variables: performance, resistance, interpersonal relations, satisfaction, challenge, and work overload were examined. The study had two major findings: (1) hospital unit secretaries have positive perceptions of job performance, satisfaction, and challenge as a result of using the PHAMIS computer system and (2) hospital unit secretaries do not feel resistant to the system, overloaded with work, or inclined to increase their interpersonal interaction with coworkers. These two findings might appear contradictory on the surface, but in fact are consistent with overall positive perceptions about the PHAMIS system. The study also considered the impact of two independent variables--age and number of years at work--on the responses of subjects. The analysis indicated that together these two variables explained some variations in the values of at least two of the dependent variables--resistance and challenge. The authors therefore concluded that the installation of the hospital computer system has established a favorable working environment for those whose work is affected by it. The dramatic expansion of computer systems in nonprofit institutions as well as in profit-oriented institutions has made people more familiar with computer technology. This trend can account for the overall positive perception of the unit secretaries toward the new computer system. Moreover, training programs and the support of top management for the system may also have enhanced the positive attitude of the users.

Information technology developments within the national biological information infrastructure

USGS Publications Warehouse

Cotter, G.; Frame, M.T.

2000-01-01

Looking out an office window or exploring a community park, one can easily see the tremendous challenges that biological information presents the computer science community. Biological information varies in format and content depending whether or not it is information pertaining to a particular species (i.e. Brown Tree Snake), or a specific ecosystem, which often includes multiple species, land use characteristics, and geospatially referenced information. The complexity and uniqueness of each individual species or ecosystem do not easily lend themselves to today's computer science tools and applications. To address the challenges that the biological enterprise presents the National Biological Information Infrastructure (NBII) (http://www.nbii.gov) was established in 1993. The NBII is designed to address these issues on a National scale within the United States, and through international partnerships abroad. This paper discusses current computer science efforts within the National Biological Information Infrastructure Program and future computer science research endeavors that are needed to address the ever-growing issues related to our Nation's biological concerns.

Automated Discovery of Functional Generality of Human Gene Expression Programs

PubMed Central

Gerber, Georg K; Dowell, Robin D; Jaakkola, Tommi S; Gifford, David K

2007-01-01

An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional breadth of these programs. The use of human expression data compendia for discovery of such programs presents several challenges including cellular inhomogeneity within samples, genetic and environmental variation across samples, uncertainty in the numbers of programs and sample populations, and temporal behavior. We developed GeneProgram, a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings. Using synthetic and real gene expression data, we showed that GeneProgram outperformed several popular expression analysis methods. We applied GeneProgram to a compendium of 62 short time-series gene expression datasets exploring the responses of human cells to infectious agents and immune-modulating molecules. GeneProgram produced a map of 104 expression programs, a substantial number of which were significantly enriched for genes involved in key signaling pathways and/or bound by NF-κB transcription factors in genome-wide experiments. Further, GeneProgram discovered expression programs that appear to implicate surprising signaling pathways or receptor types in the response to infection, including Wnt signaling and neurotransmitter receptors. We believe the discovered map of expression programs involved in the response to infection will be useful for guiding future biological experiments; genes from programs with low generality scores might serve as new drug targets that exhibit minimal “cross-talk,” and genes from high generality programs may maintain common physiological responses that go awry in disease states. Further, our method is multipurpose, and can be applied readily to novel compendia of biological data. PMID:17696603

Discovery of Novel MDR-Mycobacterium tuberculosis Inhibitor by New FRIGATE Computational Screen

PubMed Central

Vértessy, Beáta; Pütter, Vera; Grolmusz, Vince; Schade, Markus

2011-01-01

With 1.6 million casualties annually and 2 billion people being infected, tuberculosis is still one of the most pressing healthcare challenges. Here we report on the new computational docking algorithm FRIGATE which unites continuous local optimization techniques (conjugate gradient method) with an inherently discrete computational approach in forcefield computation, resulting in equal or better scoring accuracies than several benchmark docking programs. By utilizing FRIGATE for a virtual screen of the ZINC library against the Mycobacterium tuberculosis (Mtb) enzyme antigen 85C, we identified novel small molecule inhibitors of multiple drug-resistant Mtb, which bind in vitro to the catalytic site of antigen 85C. PMID:22164290

A Programming Framework for Scientific Applications on CPU-GPU Systems

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

Owens, John

2013-03-24

At a high level, my research interests center around designing, programming, and evaluating computer systems that use new approaches to solve interesting problems. The rapid change of technology allows a variety of different architectural approaches to computationally difficult problems, and a constantly shifting set of constraints and trends makes the solutions to these problems both challenging and interesting. One of the most important recent trends in computing has been a move to commodity parallel architectures. This sea change is motivated by the industry’s inability to continue to profitably increase performance on a single processor and instead to move to multiplemore » parallel processors. In the period of review, my most significant work has been leading a research group looking at the use of the graphics processing unit (GPU) as a general-purpose processor. GPUs can potentially deliver superior performance on a broad range of problems than their CPU counterparts, but effectively mapping complex applications to a parallel programming model with an emerging programming environment is a significant and important research problem.« less

Data Structures for Extreme Scale Computing

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

Kahan, Simon

As computing problems of national importance grow, the government meets the increased demand by funding the development of ever larger systems. The overarching goal of the work supported in part by this grant is to increase efficiency of programming and performing computations on these large computing systems. In past work, we have demonstrated that some of these computations once thought to require expensive hardware designs and/or complex, special-purpose programming may be executed efficiently on low-cost commodity cluster computing systems using a general-purpose “latency-tolerant” programming framework. One important developed application of the ideas underlying this framework is graph database technology supportingmore » social network pattern matching used by US intelligence agencies to more quickly identify potential terrorist threats. This database application has been spun out by the Pacific Northwest National Laboratory, a Department of Energy Laboratory, into a commercial start-up, Trovares Inc. We explore an alternative application of the same underlying ideas to a well-studied challenge arising in engineering: solving unstructured sparse linear equations. Solving these equations is key to predicting the behavior of large electronic circuits before they are fabricated. Predicting that behavior ahead of fabrication means that designs can optimized and errors corrected ahead of the expense of manufacture.« less

Acceleration of fluoro-CT reconstruction for a mobile C-Arm on GPU and FPGA hardware: a simulation study

NASA Astrophysics Data System (ADS)

Xue, Xinwei; Cheryauka, Arvi; Tubbs, David

2006-03-01

CT imaging in interventional and minimally-invasive surgery requires high-performance computing solutions that meet operational room demands, healthcare business requirements, and the constraints of a mobile C-arm system. The computational requirements of clinical procedures using CT-like data are increasing rapidly, mainly due to the need for rapid access to medical imagery during critical surgical procedures. The highly parallel nature of Radon transform and CT algorithms enables embedded computing solutions utilizing a parallel processing architecture to realize a significant gain of computational intensity with comparable hardware and program coding/testing expenses. In this paper, using a sample 2D and 3D CT problem, we explore the programming challenges and the potential benefits of embedded computing using commodity hardware components. The accuracy and performance results obtained on three computational platforms: a single CPU, a single GPU, and a solution based on FPGA technology have been analyzed. We have shown that hardware-accelerated CT image reconstruction can be achieved with similar levels of noise and clarity of feature when compared to program execution on a CPU, but gaining a performance increase at one or more orders of magnitude faster. 3D cone-beam or helical CT reconstruction and a variety of volumetric image processing applications will benefit from similar accelerations.

Biocellion: accelerating computer simulation of multicellular biological system models

PubMed Central

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-01-01

Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

Programming languages and compiler design for realistic quantum hardware.

PubMed

Chong, Frederic T; Franklin, Diana; Martonosi, Margaret

2017-09-13

Quantum computing sits at an important inflection point. For years, high-level algorithms for quantum computers have shown considerable promise, and recent advances in quantum device fabrication offer hope of utility. A gap still exists, however, between the hardware size and reliability requirements of quantum computing algorithms and the physical machines foreseen within the next ten years. To bridge this gap, quantum computers require appropriate software to translate and optimize applications (toolflows) and abstraction layers. Given the stringent resource constraints in quantum computing, information passed between layers of software and implementations will differ markedly from in classical computing. Quantum toolflows must expose more physical details between layers, so the challenge is to find abstractions that expose key details while hiding enough complexity.

Programming languages and compiler design for realistic quantum hardware

NASA Astrophysics Data System (ADS)

Chong, Frederic T.; Franklin, Diana; Martonosi, Margaret

2017-09-01

Quantum computing sits at an important inflection point. For years, high-level algorithms for quantum computers have shown considerable promise, and recent advances in quantum device fabrication offer hope of utility. A gap still exists, however, between the hardware size and reliability requirements of quantum computing algorithms and the physical machines foreseen within the next ten years. To bridge this gap, quantum computers require appropriate software to translate and optimize applications (toolflows) and abstraction layers. Given the stringent resource constraints in quantum computing, information passed between layers of software and implementations will differ markedly from in classical computing. Quantum toolflows must expose more physical details between layers, so the challenge is to find abstractions that expose key details while hiding enough complexity.

Autonomy for Constellation

NASA Technical Reports Server (NTRS)

Truszkowski, Walt; Szczur, Martha R. (Technical Monitor)

2000-01-01

The newer types of space systems, which are planned for the future, are placing challenging demands for newer autonomy concepts and techniques. Motivating these challenges are resource constraints. Even though onboard computing power will surely increase in the coming years, the resource constraints associated with space-based processes will continue to be a major factor that needs to be considered when dealing with, for example, agent-based spacecraft autonomy. To realize "economical intelligence", i.e., constrained computational intelligence that can reside within a process under severe resource constraints (time, power, space, etc.), is a major goal for such space systems as the Nanosat constellations. To begin to address the new challenges, we are developing approaches to constellation autonomy with constraints in mind. Within the Agent Concepts Testbed (ACT) at the Goddard Space Flight Center we are currently developing a Nanosat-related prototype for the first of the two-step program.

International Deaf Education Teacher-Training Projects.

ERIC Educational Resources Information Center

Moulton, Robert; Chinn, Kathleen

2002-01-01

This article discusses the need and challenges of developing nations regarding audiological and educational services for children who are deaf or hard-of-hearing. Stellar international programs are described. Availability and use of current computer technology is discussed and suggestions are made for international projects in audiology and deaf…

The Use of Monte Carlo Techniques to Teach Probability.

ERIC Educational Resources Information Center

Newell, G. J.; MacFarlane, J. D.

1985-01-01

Presents sports-oriented examples (cricket and football) in which Monte Carlo methods are used on microcomputers to teach probability concepts. Both examples include computer programs (with listings) which utilize the microcomputer's random number generator. Instructional strategies, with further challenges to help students understand the role of…

A pervasive parallel framework for visualization: final report for FWP 10-014707

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

Moreland, Kenneth D.

2014-01-01

We are on the threshold of a transformative change in the basic architecture of highperformance computing. The use of accelerator processors, characterized by large core counts, shared but asymmetrical memory, and heavy thread loading, is quickly becoming the norm in high performance computing. These accelerators represent significant challenges in updating our existing base of software. An intrinsic problem with this transition is a fundamental programming shift from message passing processes to much more fine thread scheduling with memory sharing. Another problem is the lack of stability in accelerator implementation; processor and compiler technology is currently changing rapidly. This report documentsmore » the results of our three-year ASCR project to address these challenges. Our project includes the development of the Dax toolkit, which contains the beginnings of new algorithms for a new generation of computers and the underlying infrastructure to rapidly prototype and build further algorithms as necessary.« less

A uniform approach for programming distributed heterogeneous computing systems

PubMed Central

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-01-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater’s performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations. PMID:25844015

Optimizing a mobile robot control system using GPU acceleration

NASA Astrophysics Data System (ADS)

Tuck, Nat; McGuinness, Michael; Martin, Fred

2012-01-01

This paper describes our attempt to optimize a robot control program for the Intelligent Ground Vehicle Competition (IGVC) by running computationally intensive portions of the system on a commodity graphics processing unit (GPU). The IGVC Autonomous Challenge requires a control program that performs a number of different computationally intensive tasks ranging from computer vision to path planning. For the 2011 competition our Robot Operating System (ROS) based control system would not run comfortably on the multicore CPU on our custom robot platform. The process of profiling the ROS control program and selecting appropriate modules for porting to run on a GPU is described. A GPU-targeting compiler, Bacon, is used to speed up development and help optimize the ported modules. The impact of the ported modules on overall performance is discussed. We conclude that GPU optimization can free a significant amount of CPU resources with minimal effort for expensive user-written code, but that replacing heavily-optimized library functions is more difficult, and a much less efficient use of time.

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

Koenka, Israel Joel; Sáiz, Jorge; Hauser, Peter C

2015-01-01

Scientists often need to build dedicated computer-controlled experimental systems. For this purpose, it is becoming common to employ open-source microcontroller platforms, such as the Arduino. These boards and associated integrated software development environments provide affordable yet powerful solutions for the implementation of hardware control of transducers and acquisition of signals from detectors and sensors. It is, however, a challenge to write programs that allow interactive use of such arrangements from a personal computer. This task is particularly complex if some of the included hardware components are connected directly to the computer and not via the microcontroller. A graphical user interface framework, Instrumentino, was therefore developed to allow the creation of control programs for complex systems with minimal programming effort. By writing a single code file, a powerful custom user interface is generated, which enables the automatic running of elaborate operation sequences and observation of acquired experimental data in real time. The framework, which is written in Python, allows extension by users, and is made available as an open source project.

Translating an effective group-based HIV prevention program to a program delivered primarily by a computer: methods and outcomes.

PubMed

Card, Josefina J; Kuhn, Tamara; Solomon, Julie; Benner, Tabitha A; Wingood, Gina M; DiClemente, Ralph J

2011-04-01

We describe development of SAHARA (SISTAS Accessing HIV/AIDS Resources At-a-click), an innovative HIV prevention program that uses a computer to deliver an updated version of SiSTA, a widely used, effective group-level HIV prevention intervention for African American women ages 18-29. Fidelity to SiSTA's core components was achieved using: (1) video clips featuring group discussions and modeling of appropriate sexual- and contraceptive-related behavior; and (2) interactive Flash modules facilitating cognitive rehearsal, providing learning experiences through games and quizzes, and providing opportunities for simulated role-play. A preliminary outcome study of SAHARA conducted at Planned Parenthood, Atlanta, found that SAHARA, when followed by a brief 20-minute wrap-up group session facilitated by a health educator, was effective in promoting consistent condom use for vaginal sex. We discuss the potential advantages and challenges of an intervention like SAHARA delivered by computer to an individual, versus one like SiSTA delivered by a health educator to a small group.

A uniform approach for programming distributed heterogeneous computing systems.

PubMed

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-12-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater's performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations.

NASA high performance computing and communications program

NASA Technical Reports Server (NTRS)

Holcomb, Lee; Smith, Paul; Hunter, Paul

1993-01-01

The National Aeronautics and Space Administration's HPCC program is part of a new Presidential initiative aimed at producing a 1000-fold increase in supercomputing speed and a 100-fold improvement in available communications capability by 1997. As more advanced technologies are developed under the HPCC program, they will be used to solve NASA's 'Grand Challenge' problems, which include improving the design and simulation of advanced aerospace vehicles, allowing people at remote locations to communicate more effectively and share information, increasing scientist's abilities to model the Earth's climate and forecast global environmental trends, and improving the development of advanced spacecraft. NASA's HPCC program is organized into three projects which are unique to the agency's mission: the Computational Aerosciences (CAS) project, the Earth and Space Sciences (ESS) project, and the Remote Exploration and Experimentation (REE) project. An additional project, the Basic Research and Human Resources (BRHR) project exists to promote long term research in computer science and engineering and to increase the pool of trained personnel in a variety of scientific disciplines. This document presents an overview of the objectives and organization of these projects as well as summaries of individual research and development programs within each project.

CaseLog: semantic network interface to a student computer-based patient record system.

PubMed Central

Cimino, C.; Goldman, E. K.; Curtis, J. A.; Reichgott, M. J.

1993-01-01

We have developed a computer program called CaseLog, which serves as an exemplary, computer-based patient record (CPR) system. The program allows for the introduction of the students to issues unique to patient record systems. These include record security, unique patient identifiers, and the use of controlled vocabularies. A particularly challenging aspect of the development of this program was allowing for student entry of controlled vocabulary terms. There were four goals we wished to achieve: students should be able to find the terms they are looking for; once a term has been found, it should be easy to find contextually related terms; it should be easy to determine that a sought-for term is not in the vocabulary; and the structure of the vocabulary should be dynamically altered by contextual information to allow its use for a variety of purposes. We chose a semantic network for our vocabulary structure. Within the processing power of the equipment we were working with, we achieved our goals. This paper will describe the development of the vocabulary, the design of the CaseLog program, and the feedback from student users of the program. PMID:8130581

Legacy model integration for enhancing hydrologic interdisciplinary research

NASA Astrophysics Data System (ADS)

Dozier, A.; Arabi, M.; David, O.

2013-12-01

Many challenges are introduced to interdisciplinary research in and around the hydrologic science community due to advances in computing technology and modeling capabilities in different programming languages, across different platforms and frameworks by researchers in a variety of fields with a variety of experience in computer programming. Many new hydrologic models as well as optimization, parameter estimation, and uncertainty characterization techniques are developed in scripting languages such as Matlab, R, Python, or in newer languages such as Java and the .Net languages, whereas many legacy models have been written in FORTRAN and C, which complicates inter-model communication for two-way feedbacks. However, most hydrologic researchers and industry personnel have little knowledge of the computing technologies that are available to address the model integration process. Therefore, the goal of this study is to address these new challenges by utilizing a novel approach based on a publish-subscribe-type system to enhance modeling capabilities of legacy socio-economic, hydrologic, and ecologic software. Enhancements include massive parallelization of executions and access to legacy model variables at any point during the simulation process by another program without having to compile all the models together into an inseparable 'super-model'. Thus, this study provides two-way feedback mechanisms between multiple different process models that can be written in various programming languages and can run on different machines and operating systems. Additionally, a level of abstraction is given to the model integration process that allows researchers and other technical personnel to perform more detailed and interactive modeling, visualization, optimization, calibration, and uncertainty analysis without requiring deep understanding of inter-process communication. To be compatible, a program must be written in a programming language with bindings to a common implementation of the message passing interface (MPI), which includes FORTRAN, C, Java, the .NET languages, Python, R, Matlab, and many others. The system is tested on a longstanding legacy hydrologic model, the Soil and Water Assessment Tool (SWAT), to observe and enhance speed-up capabilities for various optimization, parameter estimation, and model uncertainty characterization techniques, which is particularly important for computationally intensive hydrologic simulations. Initial results indicate that the legacy extension system significantly decreases developer time, computation time, and the cost of purchasing commercial parallel processing licenses, while enhancing interdisciplinary research by providing detailed two-way feedback mechanisms between various process models with minimal changes to legacy code.

Distributed Drug Discovery: Advancing Chemical Education through Contextualized Combinatorial Solid-Phase Organic Laboratories

ERIC Educational Resources Information Center

Scott, William L.; Denton, Ryan E.; Marrs, Kathleen A.; Durrant, Jacob D.; Samaritoni, J. Geno; Abraham, Milata M.; Brown, Stephen P.; Carnahan, Jon M.; Fischer, Lindsey G.; Glos, Courtney E.; Sempsrott, Peter J.; O'Donnell, Martin J.

2015-01-01

The Distributed Drug Discovery (D3) program trains students in three drug discovery disciplines (synthesis, computational analysis, and biological screening) while addressing the important challenge of discovering drug leads for neglected diseases. This article focuses on implementation of the synthesis component in the second-semester…

Challenge '89: Interfacing of Chemical Instruments to Computers.

ERIC Educational Resources Information Center

Lyons, Jim; Lamarre, Colin

This project involved interfacing of microcomputers with three chemical instruments--Nuclear Magnetic Resonance (NMR), Infrared Spectroscopy (IR), and the spectrophotometer. A Pascal program called "Spectrum" allows data from the NMR to be read and graphed, a specific area of the graph zoomed, ratios of specified areas of the graph…

Identifying Challenges to the Integration of Computer-Based Surveillance Information Systems in a Large City Health Department: A Case Study.

PubMed

Jennings, Jacky M; Stover, Jeffrey A; Bair-Merritt, Megan H; Fichtenberg, Caroline; Munoz, Mary Grace; Maziad, Rafiq; Ketemepi, Sherry Johnson; Zenilman, Jonathan

2009-01-01

Integrated infectious disease surveillance information systems have the potential to provide important new surveillance capacities and business efficiencies for local health departments. We conducted a case study at a large city health department of the primary computer-based infectious disease surveillance information systems during a 10-year period to identify the major challenges for information integration across the systems. The assessment included key informant interviews and evaluations of the computer-based surveillance information systems used for acute communicable diseases, human immunodeficiency virus/acquired immunodeficiency syndrome, sexually transmitted diseases, and tuberculosis. Assessments were conducted in 1998 with a follow-up in 2008. Assessments specifically identified and described the primary computer-based surveillance information system, any duplicative information systems, and selected variables collected. Persistent challenges to information integration across the information systems included the existence of duplicative data systems, differences in the variables used to collect similar information, and differences in basic architecture. The assessments identified a number of challenges for information integration across the infectious disease surveillance information systems at this city health department. The results suggest that local disease control programs use computer-based surveillance information systems that were not designed for data integration. To the extent that integration provides important new surveillance capacities and business efficiencies, we recommend that patient-centric information systems be designed that provide all the epidemiologic, clinical, and research needs in one system. In addition, the systems should include a standard system of elements and fields across similar surveillance systems.

High Performance Processors for Space Environments: A Subproject of the NASA Exploration Missions Systems Directorate "Radiation Hardened Electronics for Space Environments" Technology Development Program

NASA Technical Reports Server (NTRS)

Johnson, M.; Label, K.; McCabe, J.; Powell, W.; Bolotin, G.; Kolawa, E.; Ng, T.; Hyde, D.

2007-01-01

Implementation of challenging Exploration Systems Missions Directorate objectives and strategies can be constrained by onboard computing capabilities and power efficiencies. The Radiation Hardened Electronics for Space Environments (RHESE) High Performance Processors for Space Environments project will address this challenge by significantly advancing the sustained throughput and processing efficiency of high-per$ormance radiation-hardened processors, targeting delivery of products by the end of FY12.

Critical analysis of a computer-assisted tutorial on ECG interpretation and its ability to determine competency.

PubMed

Burke, J F; Gnall, E; Umrudden, Z; Kyaw, M; Schick, P K

2008-01-01

We developed a computer-based tutorial and a posttest on ECG interpretation for training residents and determining competency. Forty residents, 6 cardiology fellows, and 4 experienced physicians participated. The tutorial emphasized recognition and understanding of abnormal ECG features. Active learning was promoted by asking questions prior to the discussion of ECGs. Interactivity was facilitated by providing rapid and in-depth rationale for correct answers. Responses to questions were recorded and extensively analyzed to determine the quality of questions, baseline knowledge at different levels of training and improvement of grades in posttest. Posttest grades were used to assess improvement and to determine competency. The questions were found to be challenging, fair, appropriate and discriminative. This was important since the quality of Socratic questions is critical for the success of interactive programs. The information on strengths and weakness in baseline knowledge at different levels of training were used to adapt our training program to the needs of residents. The posttest revealed that the tutorial contributed to marked improvement in feature recognition. Competency testing distinguished between residents with outstanding grades and those who needed remediation. The strategy for critical evaluation of our computer program could be applied to any computer-based educational program, regardless of topic.

Modeling sustainability in renewable energy supply chain systems

NASA Astrophysics Data System (ADS)

Xie, Fei

This dissertation aims at modeling sustainability of renewable fuel supply chain systems against emerging challenges. In particular, the dissertation focuses on the biofuel supply chain system design, and manages to develop advanced modeling framework and corresponding solution methods in tackling challenges in sustaining biofuel supply chain systems. These challenges include: (1) to integrate "environmental thinking" into the long-term biofuel supply chain planning; (2) to adopt multimodal transportation to mitigate seasonality in biofuel supply chain operations; (3) to provide strategies in hedging against uncertainty from conversion technology; and (4) to develop methodologies in long-term sequential planning of the biofuel supply chain under uncertainties. All models are mixed integer programs, which also involves multi-objective programming method and two-stage/multistage stochastic programming methods. In particular for the long-term sequential planning under uncertainties, to reduce the computational challenges due to the exponential expansion of the scenario tree, I also developed efficient ND-Max method which is more efficient than CPLEX and Nested Decomposition method. Through result analysis of four independent studies, it is found that the proposed modeling frameworks can effectively improve the economic performance, enhance environmental benefits and reduce risks due to systems uncertainties for the biofuel supply chain systems.

Advanced Technology System Scheduling Governance Model

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

Ang, Jim; Carnes, Brian; Hoang, Thuc

In the fall of 2005, the Advanced Simulation and Computing (ASC) Program appointed a team to formulate a governance model for allocating resources and scheduling the stockpile stewardship workload on ASC capability systems. This update to the original document takes into account the new technical challenges and roles for advanced technology (AT) systems and the new ASC Program workload categories that must be supported. The goal of this updated model is to effectively allocate and schedule AT computing resources among all three National Nuclear Security Administration (NNSA) laboratories for weapons deliverables that merit priority on this class of resource. Themore » process outlined below describes how proposed work can be evaluated and approved for resource allocations while preserving high effective utilization of the systems. This approach will provide the broadest possible benefit to the Stockpile Stewardship Program (SSP).« less

Strengthening LLNL Missions through Laboratory Directed Research and Development in High Performance Computing

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

Willis, D. K.

2016-12-01

High performance computing (HPC) has been a defining strength of Lawrence Livermore National Laboratory (LLNL) since its founding. Livermore scientists have designed and used some of the world’s most powerful computers to drive breakthroughs in nearly every mission area. Today, the Laboratory is recognized as a world leader in the application of HPC to complex science, technology, and engineering challenges. Most importantly, HPC has been integral to the National Nuclear Security Administration’s (NNSA’s) Stockpile Stewardship Program—designed to ensure the safety, security, and reliability of our nuclear deterrent without nuclear testing. A critical factor behind Lawrence Livermore’s preeminence in HPC ismore » the ongoing investments made by the Laboratory Directed Research and Development (LDRD) Program in cutting-edge concepts to enable efficient utilization of these powerful machines. Congress established the LDRD Program in 1991 to maintain the technical vitality of the Department of Energy (DOE) national laboratories. Since then, LDRD has been, and continues to be, an essential tool for exploring anticipated needs that lie beyond the planning horizon of our programs and for attracting the next generation of talented visionaries. Through LDRD, Livermore researchers can examine future challenges, propose and explore innovative solutions, and deliver creative approaches to support our missions. The present scientific and technical strengths of the Laboratory are, in large part, a product of past LDRD investments in HPC. Here, we provide seven examples of LDRD projects from the past decade that have played a critical role in building LLNL’s HPC, computer science, mathematics, and data science research capabilities, and describe how they have impacted LLNL’s mission.« less

A Computational Approach for Probabilistic Analysis of LS-DYNA Water Impact Simulations

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Mason, Brian H.; Lyle, Karen H.

2010-01-01

NASA s development of new concepts for the Crew Exploration Vehicle Orion presents many similar challenges to those worked in the sixties during the Apollo program. However, with improved modeling capabilities, new challenges arise. For example, the use of the commercial code LS-DYNA, although widely used and accepted in the technical community, often involves high-dimensional, time consuming, and computationally intensive simulations. Because of the computational cost, these tools are often used to evaluate specific conditions and rarely used for statistical analysis. The challenge is to capture what is learned from a limited number of LS-DYNA simulations to develop models that allow users to conduct interpolation of solutions at a fraction of the computational time. For this problem, response surface models are used to predict the system time responses to a water landing as a function of capsule speed, direction, attitude, water speed, and water direction. Furthermore, these models can also be used to ascertain the adequacy of the design in terms of probability measures. This paper presents a description of the LS-DYNA model, a brief summary of the response surface techniques, the analysis of variance approach used in the sensitivity studies, equations used to estimate impact parameters, results showing conditions that might cause injuries, and concluding remarks.

It takes a village: supporting inquiry- and equity-oriented computer science pedagogy through a professional learning community

NASA Astrophysics Data System (ADS)

Ryoo, Jean; Goode, Joanna; Margolis, Jane

2015-10-01

This article describes the importance that high school computer science teachers place on a teachers' professional learning community designed around an inquiry- and equity-oriented approach for broadening participation in computing. Using grounded theory to analyze four years of teacher surveys and interviews from the Exploring Computer Science (ECS) program in the Los Angeles Unified School District, this article describes how participating in professional development activities purposefully aimed at fostering a teachers' professional learning community helps ECS teachers make the transition to an inquiry-based classroom culture and break professional isolation. This professional learning community also provides experiences that challenge prevalent deficit notions and stereotypes about which students can or cannot excel in computer science.

The National Shipbuilding Research Program. 1989 Ship Production Symposium. Paper No. 13: NIDDESC: Meeting the Data Exchange Challenge Through a Cooperative Effort

DTIC Science & Technology

1989-09-01

RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT unclassified c . THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18... Computer Aided Design (CAD) and Manufacturing (CAM) techniques in the marine industry has increased significantly in recent years, With more...somewhat from ship to ship. All of the activities and companies involved have improved this process by utilizing computer tools. For example, many

Computational Materials: Modeling and Simulation of Nanostructured Materials and Systems

NASA Technical Reports Server (NTRS)

Gates, Thomas S.; Hinkley, Jeffrey A.

2003-01-01

The paper provides details on the structure and implementation of the Computational Materials program at the NASA Langley Research Center. Examples are given that illustrate the suggested approaches to predicting the behavior and influencing the design of nanostructured materials such as high-performance polymers, composites, and nanotube-reinforced polymers. Primary simulation and measurement methods applicable to multi-scale modeling are outlined. Key challenges including verification and validation of models are highlighted and discussed within the context of NASA's broad mission objectives.

Curriculum-Based Handwriting Programs: A Systematic Review With Effect Sizes

PubMed Central

Engel, Courtney; Lillie, Kristin; Zurawski, Sarah; Travers, Brittany G.

2018-01-01

Challenges with handwriting can have a negative impact on academic performance, and these challenges are commonly addressed by occupational therapy practitioners in school settings. This systematic review examined the efficacy of curriculum-based interventions to address children’s handwriting difficulties in the classroom (preschool to second grade). We reviewed and computed effect sizes for 13 studies (11 Level II, 2 Level III) identified through a comprehensive database search. The evidence shows that curriculum-based handwriting interventions resulted in small- to medium-sized improvements in legibility, a commonly reported challenge in this age group. The evidence for whether these interventions improved speed is mixed, and the evidence for whether they improved fluency is insufficient. No clear support was found for one handwriting program over another. These results suggest that curriculum-based interventions can lead to improvements in handwriting legibility, but Level I research is needed to validate the efficacy of these curricula. PMID:29689170

CPMIP: measurements of real computational performance of Earth system models in CMIP6

NASA Astrophysics Data System (ADS)

Balaji, Venkatramani; Maisonnave, Eric; Zadeh, Niki; Lawrence, Bryan N.; Biercamp, Joachim; Fladrich, Uwe; Aloisio, Giovanni; Benson, Rusty; Caubel, Arnaud; Durachta, Jeffrey; Foujols, Marie-Alice; Lister, Grenville; Mocavero, Silvia; Underwood, Seth; Wright, Garrett

2017-01-01

A climate model represents a multitude of processes on a variety of timescales and space scales: a canonical example of multi-physics multi-scale modeling. The underlying climate system is physically characterized by sensitive dependence on initial conditions, and natural stochastic variability, so very long integrations are needed to extract signals of climate change. Algorithms generally possess weak scaling and can be I/O and/or memory-bound. Such weak-scaling, I/O, and memory-bound multi-physics codes present particular challenges to computational performance. Traditional metrics of computational efficiency such as performance counters and scaling curves do not tell us enough about real sustained performance from climate models on different machines. They also do not provide a satisfactory basis for comparative information across models. codes present particular challenges to computational performance. We introduce a set of metrics that can be used for the study of computational performance of climate (and Earth system) models. These measures do not require specialized software or specific hardware counters, and should be accessible to anyone. They are independent of platform and underlying parallel programming models. We show how these metrics can be used to measure actually attained performance of Earth system models on different machines, and identify the most fruitful areas of research and development for performance engineering. codes present particular challenges to computational performance. We present results for these measures for a diverse suite of models from several modeling centers, and propose to use these measures as a basis for a CPMIP, a computational performance model intercomparison project (MIP).

Conceptual Memory: A Theory and Computer Program for Processing the Meaning Content of Natural Language Utterances

DTIC Science & Technology

1974-07-01

iiWU -immmemmmmm This document was generated by the Stanford Artificial Intelligence Laboratory’s document compiler, "PUB" and reproducec’ on a...for more sophisticated artificial (programming) languages. The new issues became those of how to represent a grammar as precise syntactic structures...challenge lies in discovering - either by synthesis of an artificial system, or by analysis of a natural one - the underlying logical (a. opposed to

IBM PC enhances the world's future

NASA Technical Reports Server (NTRS)

Cox, Jozelle

1988-01-01

Although the purpose of this research is to illustrate the importance of computers to the public, particularly the IBM PC, present examinations will include computers developed before the IBM PC was brought into use. IBM, as well as other computing facilities, began serving the public years ago, and is continuing to find ways to enhance the existence of man. With new developments in supercomputers like the Cray-2, and the recent advances in artificial intelligence programming, the human race is gaining knowledge at a rapid pace. All have benefited from the development of computers in the world; not only have they brought new assets to life, but have made life more and more of a challenge everyday.

Biocellion: accelerating computer simulation of multicellular biological system models.

PubMed

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Student Use of Physics to Make Sense of Incomplete but Functional VPython Programs in a Lab Setting

NASA Astrophysics Data System (ADS)

Weatherford, Shawn A.

2011-12-01

Computational activities in Matter & Interactions, an introductory calculus-based physics course, have the instructional goal of providing students with the experience of applying the same set of a small number of fundamental principles to model a wide range of physical systems. However there are significant instructional challenges for students to build computer programs under limited time constraints, especially for students who are unfamiliar with programming languages and concepts. Prior attempts at designing effective computational activities were successful at having students ultimately build working VPython programs under the tutelage of experienced teaching assistants in a studio lab setting. A pilot study revealed that students who completed these computational activities had significant difficultly repeating the exact same tasks and further, had difficulty predicting the animation that would be produced by the example program after interpreting the program code. This study explores the interpretation and prediction tasks as part of an instructional sequence where students are asked to read and comprehend a functional, but incomplete program. Rather than asking students to begin their computational tasks with modifying program code, we explicitly ask students to interpret an existing program that is missing key lines of code. The missing lines of code correspond to the algebraic form of fundamental physics principles or the calculation of forces which would exist between analogous physical objects in the natural world. Students are then asked to draw a prediction of what they would see in the simulation produced by the VPython program and ultimately run the program to evaluate the students' prediction. This study specifically looks at how the participants use physics while interpreting the program code and creating a whiteboard prediction. This study also examines how students evaluate their understanding of the program and modification goals at the beginning of the modification task. While working in groups over the course of a semester, study participants were recorded while they completed three activities using these incomplete programs. Analysis of the video data showed that study participants had little difficulty interpreting physics quantities, generating a prediction, or determining how to modify the incomplete program. Participants did not base their prediction solely from the information from the incomplete program. When participants tried to predict the motion of the objects in the simulation, many turned to their knowledge of how the system would evolve if it represented an analogous real-world physical system. For example, participants attributed the real-world behavior of springs to helix objects even though the program did not include calculations for the spring to exert a force when stretched. Participants rarely interpreted lines of code in the computational loop during the first computational activity, but this changed during latter computational activities with most participants using their physics knowledge to interpret the computational loop. Computational activities in the Matter & Interactions curriculum were revised in light of these findings to include an instructional sequence of tasks to build a comprehension of the example program. The modified activities also ask students to create an additional whiteboard prediction for the time-evolution of the real-world phenomena which the example program will eventually model. This thesis shows how comprehension tasks identified by Palinscar and Brown (1984) as effective in improving reading comprehension are also effective in helping students apply their physics knowledge to interpret a computer program which attempts to model a real-world phenomena and identify errors in their understanding of the use, or omission, of fundamental physics principles in a computational model.

Constructing linkage maps in the genomics era with MapDisto 2.0.

PubMed

Heffelfinger, Christopher; Fragoso, Christopher A; Lorieux, Mathias

2017-07-15

Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. The program is available free of charge at mapdisto.free.fr. mapdisto@gmail.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Women's decision to major in STEM fields

NASA Astrophysics Data System (ADS)

Conklin, Stephanie

This paper explores the lived experiences of high school female students who choose to enter into STEM fields, and describes the influencing factors which steered these women towards majors in computer science, engineering and biology. Utilizing phenomenological methodology, this study seeks to understand the essence of women's decisions to enter into STEM fields and further describe how the decision-making process varies for women in high female enrollment fields, like biology, as compared with low enrollment fields like, computer science and engineering. Using Bloom's 3-Stage Theory, this study analyzes how relationships, experiences and barriers influenced women towards, and possibly away, from STEM fields. An analysis of women's experiences highlight that support of family, sustained experience in a STEM program during high school as well as the presence of an influential teacher were all salient factors in steering women towards STEM fields. Participants explained that influential teacher worked individually with them, modified and extended assignments and also steered participants towards coursework and experiences. This study also identifies factors, like guidance counselors as well as personal challenges, which inhibited participant's path to STEM fields. Further, through analyzing all six participants' experiences, it is clear that a linear model, like Bloom's 3-Stage Model, with limited ability to include potential barriers inhibited the ability to capture the essence of each participant's decision-making process. Therefore, a revised model with no linear progression which allows for emerging factors, like personal challenges, has been proposed; this model focuses on how interest in STEM fields begins to develop and is honed and then mastered. This study also sought to identify key differences in the paths of female students pursuing different majors. The findings of this study suggest that the path to computer science and engineering is limited. Computer science majors faced few, if any, challenges, hoped to use computers as a tool to innovate and also participated in the same computer science program. For female engineering students, the essence of their experience focused on interaction at a young age with an expert in an engineering-related field as well as a strong desire to help solve world problems using engineering. These participants were able to articulate clearly future careers. In contrast, biology majors, faced more challenges and were undecided about their future career goals. These results suggest that a longitudinal study focused on women pursuing engineering and computer science fields is warranted; this will hopefully allow these findings to be substantiated and also for refinement of the revised theoretical model.

Integrating computers in physics teaching: An Indian perspective

NASA Astrophysics Data System (ADS)

Jolly, Pratibha

1997-03-01

The University of Delhi has around twenty affiliated undergraduate colleges that offer a three-year physics major program to nearly five hundred students. All follow a common curriculum and submit to a centralized examination. This structure of tertiary education makes it relatively difficult to implement radical or rapid changes in the formal curriculum. The technology onslaught has, at last, irrevocably altered this; computers are carving new windows in old citadels and defining the agenda in teaching-learning environments the world over. In 1992, we formally introduced Computational Physics as a core paper in the second year of the Bachelor's program. As yet, the emphasis is on imparting familiarity with computers, a programming language and rudiments of numerical algorithms. In a parallel development, we also introduced a strong component of instrumentation with modern day electronic devices, including microprocessors. Many of us, however, would like to see not just computer presence in our curriculum but a totally new curriculum and teaching strategy that exploits, befittingly, the new technology. The current challenge is to realize in practice the full potential of the computer as the proverbial versatile tool: interfacing laboratory experiments for real-time acquisition and control of data; enabling rigorous analysis and data modeling; simulating micro-worlds and real life phenomena; establishing new cognitive linkages between theory and empirical observation; and between abstract constructs and visual representations.

Turbulence modeling of free shear layers for high-performance aircraft

NASA Technical Reports Server (NTRS)

Sondak, Douglas L.

1993-01-01

The High Performance Aircraft (HPA) Grand Challenge of the High Performance Computing and Communications (HPCC) program involves the computation of the flow over a high performance aircraft. A variety of free shear layers, including mixing layers over cavities, impinging jets, blown flaps, and exhaust plumes, may be encountered in such flowfields. Since these free shear layers are usually turbulent, appropriate turbulence models must be utilized in computations in order to accurately simulate these flow features. The HPCC program is relying heavily on parallel computers. A Navier-Stokes solver (POVERFLOW) utilizing the Baldwin-Lomax algebraic turbulence model was developed and tested on a 128-node Intel iPSC/860. Algebraic turbulence models run very fast, and give good results for many flowfields. For complex flowfields such as those mentioned above, however, they are often inadequate. It was therefore deemed that a two-equation turbulence model will be required for the HPA computations. The k-epsilon two-equation turbulence model was implemented on the Intel iPSC/860. Both the Chien low-Reynolds-number model and a generalized wall-function formulation were included.

A knowledge-based approach to automated flow-field zoning for computational fluid dynamics

NASA Technical Reports Server (NTRS)

Vogel, Alison Andrews

1989-01-01

An automated three-dimensional zonal grid generation capability for computational fluid dynamics is shown through the development of a demonstration computer program capable of automatically zoning the flow field of representative two-dimensional (2-D) aerodynamic configurations. The applicability of a knowledge-based programming approach to the domain of flow-field zoning is examined. Several aspects of flow-field zoning make the application of knowledge-based techniques challenging: the need for perceptual information, the role of individual bias in the design and evaluation of zonings, and the fact that the zoning process is modeled as a constructive, design-type task (for which there are relatively few examples of successful knowledge-based systems in any domain). Engineering solutions to the problems arising from these aspects are developed, and a demonstration system is implemented which can design, generate, and output flow-field zonings for representative 2-D aerodynamic configurations.

Computational approaches to protein inference in shotgun proteomics

PubMed Central

2012-01-01

Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughput nature, shotgun proteomics faces challenges with respect to the analysis and interpretation of experimental data. Among such challenges, the identification of proteins present in a sample has been recognized as an important computational task. This task generally consists of (1) assigning experimental tandem mass spectra to peptides derived from a protein database, and (2) mapping assigned peptides to proteins and quantifying the confidence of identified proteins. Protein identification is fundamentally a statistical inference problem with a number of methods proposed to address its challenges. In this review we categorize current approaches into rule-based, combinatorial optimization and probabilistic inference techniques, and present them using integer programing and Bayesian inference frameworks. We also discuss the main challenges of protein identification and propose potential solutions with the goal of spurring innovative research in this area. PMID:23176300

Characteristics of Learning Computer-Controlled Mechanisms by Teachers and Students in a Common Laboratory Environment

ERIC Educational Resources Information Center

Korchnoy, Evgeny; Verner, Igor M.

2010-01-01

Growing popularity of robotics education motivates developing its didactics and studying it in teacher training programs. This paper presents a study conducted in the Department of Education in Technology and Science, Technion, in which university students and school pupils cope with robotics challenges of designing, building and operating…

Teaching and Learning Recursive Programming: A Review of the Research Literature

ERIC Educational Resources Information Center

McCauley, Renée; Grissom, Scott; Fitzgerald, Sue; Murphy, Laurie

2015-01-01

Hundreds of articles have been published on the topics of teaching and learning recursion, yet fewer than 50 of them have published research results. This article surveys the computing education research literature and presents findings on challenges students encounter in learning recursion, mental models students develop as they learn recursion,…

IT Field Provides Some Stability for Workers Changing Careers

ERIC Educational Resources Information Center

Allen, Peg

2011-01-01

When it comes to curriculum, certifying and training, no industry is more challenged to keep current than the information technology field (IT). IT industry professionals experience constant changes in computer software and hardware. As one of the top fields listed nationally, IT training programs are thriving at the Warren County Career Center…

Using Broadcast Journalism To Motivate Hypermedia Exploration.

ERIC Educational Resources Information Center

Kass, Alex; And Others

An effective learning environment must ensure that students are motivated to access whatever information is available, that they have an authentic context in which to situate that knowledge, and that they face challenges that allow them to put that knowledge to use. In an attempt to address these issues, a computer program was developed, called…

Teaching Software Engineering by Means of Computer-Game Development: Challenges and Opportunities

ERIC Educational Resources Information Center

Cagiltay, Nergiz Ercil

2007-01-01

Software-engineering education programs are intended to prepare students for a field that involves rapidly changing conditions and expectations. Thus, there is always a danger that the skills and the knowledge provided may soon become obsolete. This paper describes results and draws on experiences from the implementation of a computer…

ECommerce: Meeting the Needs of Local Business with Cross-Departmental Education.

ERIC Educational Resources Information Center

Sagi, John P.

This document offers a brief introduction to electronic commerce (known as eCommerce) and explains the challenges and frustrations of developing a course around the topic. ECommerce blends elements of computer science (HTML and JavaScript programming, for example) with traditional business functions, such as marketing, salesmanship, finance and…

Security Metrics: A Solution in Search of a Problem

ERIC Educational Resources Information Center

Rosenblatt, Joel

2008-01-01

Computer security is one of the most complicated and challenging fields in technology today. A security metrics program provides a major benefit: looking at the metrics on a regular basis offers early clues to changes in attack patterns or environmental factors that may require changes in security strategy. The term "security metrics"…

Challenging Elementary Learners with Programmable Robots during Free Play and Direct Instruction

ERIC Educational Resources Information Center

McCoy-Parker, Kimberly S.; Paull, Lindsey N.; Rule, Audrey C.; Montgomery, Sarah E.

2017-01-01

Computer programming skills are important to many current careers; teaching robot coding to elementary students can start a positive foundation for technological careers, develop problem-solving skills, and growth mindsets. This study, through a repeated measures design involving students in two classrooms at two widely-separated grade levels…

Advancing Diagnostic Skills for Technology and Engineering Undergraduates: A Summary of the Validation Data

ERIC Educational Resources Information Center

Foster, W. Tad; Shahhosseini, A. Mehran; Maughan, George

2016-01-01

Facilitating student growth and development in diagnosing and solving technical problems remains a challenge for technology and engineering educators. With funding from the National Science Foundation, this team of researchers developed a self-guided, computer-based instructional program to experiment with conceptual mapping as a treatment to…

Faculty experiences with providing online courses. Thorns among the roses.

PubMed

Cravener, P A

1999-01-01

This article presents a review of the literature summarizing faculty reports of their experiences with computer-mediated distance education compared with their traditional face-to-face teaching experiences. Both challenges and benefits of distance learning programs contrasted with classroom-based teaching are revealed. Specific difficulties and advantages identified by online faculty were categorized into four broad areas of impact on the teaching/learning experience: (a) faculty workload, (b) access to education, (c) adapting to technology, and (d) instructional quality. Challenges appear to be related predominantly to faculty workloads, new technologies, and online course management. Benefits identified by online educators indicate that computer-mediated distance education has high potential for expanding student access to educational resources, for providing individualized instruction, and for promoting active learning among geographically separated members of learning groups.

Virtual Screening with AutoDock: Theory and Practice

PubMed Central

Cosconati, Sandro; Forli, Stefano; Perryman, Alex L.; Harris, Rodney; Goodsell, David S.; Olson, Arthur J.

2011-01-01

Importance to the field Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. Areas covered in this review We describe virtual screening methods that are available in the AutoDock suite of programs, and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. What the reader will gain A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. Take home message Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening. PMID:21532931

Biomedical wellness challenges and opportunities

NASA Astrophysics Data System (ADS)

Tangney, John F.

2012-06-01

The mission of ONR's Human and Bioengineered Systems Division is to direct, plan, foster, and encourage Science and Technology in cognitive science, computational neuroscience, bioscience and bio-mimetic technology, social/organizational science, training, human factors, and decision making as related to future Naval needs. This paper highlights current programs that contribute to future biomedical wellness needs in context of humanitarian assistance and disaster relief. ONR supports fundamental research and related technology demonstrations in several related areas, including biometrics and human activity recognition; cognitive sciences; computational neurosciences and bio-robotics; human factors, organizational design and decision research; social, cultural and behavioral modeling; and training, education and human performance. In context of a possible future with automated casualty evacuation, elements of current science and technology programs are illustrated.

The Design and Evaluation of "CAPTools"--A Computer Aided Parallelization Toolkit

NASA Technical Reports Server (NTRS)

Yan, Jerry; Frumkin, Michael; Hribar, Michelle; Jin, Haoqiang; Waheed, Abdul; Johnson, Steve; Cross, Jark; Evans, Emyr; Ierotheou, Constantinos; Leggett, Pete;

NASA High Performance Computing and Communications program

NASA Technical Reports Server (NTRS)

Holcomb, Lee; Smith, Paul; Hunter, Paul

1994-01-01

The National Aeronautics and Space Administration's HPCC program is part of a new Presidential initiative aimed at producing a 1000-fold increase in supercomputing speed and a 1(X)-fold improvement in available communications capability by 1997. As more advanced technologies are developed under the HPCC program, they will be used to solve NASA's 'Grand Challenge' problems, which include improving the design and simulation of advanced aerospace vehicles, allowing people at remote locations to communicate more effectively and share information, increasing scientists' abilities to model the Earth's climate and forecast global environmental trends, and improving the development of advanced spacecraft. NASA's HPCC program is organized into three projects which are unique to the agency's mission: the Computational Aerosciences (CAS) project, the Earth and Space Sciences (ESS) project, and the Remote Exploration and Experimentation (REE) project. An additional project, the Basic Research and Human Resources (BRHR) project, exists to promote long term research in computer science and engineering and to increase the pool of trained personnel in a variety of scientific disciplines. This document presents an overview of the objectives and organization of these projects, as well as summaries of early accomplishments and the significance, status, and plans for individual research and development programs within each project. Areas of emphasis include benchmarking, testbeds, software and simulation methods.

CERN openlab: Engaging industry for innovation in the LHC Run 3-4 R&D programme

NASA Astrophysics Data System (ADS)

Girone, M.; Purcell, A.; Di Meglio, A.; Rademakers, F.; Gunne, K.; Pachou, M.; Pavlou, S.

2017-10-01

LHC Run3 and Run4 represent an unprecedented challenge for HEP computing in terms of both data volume and complexity. New approaches are needed for how data is collected and filtered, processed, moved, stored and analysed if these challenges are to be met with a realistic budget. To develop innovative techniques we are fostering relationships with industry leaders. CERN openlab is a unique resource for public-private partnership between CERN and leading Information Communication and Technology (ICT) companies. Its mission is to accelerate the development of cutting-edge solutions to be used by the worldwide HEP community. In 2015, CERN openlab started its phase V with a strong focus on tackling the upcoming LHC challenges. Several R&D programs are ongoing in the areas of data acquisition, networks and connectivity, data storage architectures, computing provisioning, computing platforms and code optimisation and data analytics. This paper gives an overview of the various innovative technologies that are currently being explored by CERN openlab V and discusses the long-term strategies that are pursued by the LHC communities with the help of industry in closing the technological gap in processing and storage needs expected in Run3 and Run4.

CLOCS (Computer with Low Context-Switching Time) Architecture Reference Documents

DTIC Science & Technology

1988-05-06

Peculiarities The only state inside the central processing unit(CPU) is a program status word. All data operations are memory to memory. One result of this... to the challenge "if I whore to design RISC, this is how I would do it." The architecture was designed by Mark Davis and Bill Gallmeister. 1.2...are memory to memory. Any special devices added should be memory mapped. The program counter is even memory mapped. 1.3.1 Working storage There is no

Playing Tic-Tac-Toe with a Sugar-Based Molecular Computer.

PubMed

Elstner, M; Schiller, A

2015-08-24

Today, molecules can perform Boolean operations and circuits at a level of higher complexity. However, concatenation of logic gates and inhomogeneous inputs and outputs are still challenging tasks. Novel approaches for logic gate integration are possible when chemical programming and software programming are combined. Here it is shown that a molecular finite automaton based on the concatenated implication function (IMP) of a fluorescent two-component sugar probe via a wiring algorithm is able to play tic-tac-toe.

Advantages and disadvantages in usage of bioinformatic programs in promoter region analysis

NASA Astrophysics Data System (ADS)

Pawełkowicz, Magdalena E.; Skarzyńska, Agnieszka; Posyniak, Kacper; ZiÄ bska, Karolina; PlÄ der, Wojciech; Przybecki, Zbigniew

2015-09-01

An important computational challenge is finding the regulatory elements across the promotor region. In this work we present the advantages and disadvantages from the application of different bioinformatics programs for localization of transcription factor binding sites in the upstream region of genes connected with sex determination in cucumber. We use PlantCARE, PlantPAN and SignalScan to find motifs in the promotor regions. The results have been compared and possible function of chosen motifs has been described.

Automation of multi-agent control for complex dynamic systems in heterogeneous computational network

NASA Astrophysics Data System (ADS)

Oparin, Gennady; Feoktistov, Alexander; Bogdanova, Vera; Sidorov, Ivan

2017-01-01

The rapid progress of high-performance computing entails new challenges related to solving large scientific problems for various subject domains in a heterogeneous distributed computing environment (e.g., a network, Grid system, or Cloud infrastructure). The specialists in the field of parallel and distributed computing give the special attention to a scalability of applications for problem solving. An effective management of the scalable application in the heterogeneous distributed computing environment is still a non-trivial issue. Control systems that operate in networks, especially relate to this issue. We propose a new approach to the multi-agent management for the scalable applications in the heterogeneous computational network. The fundamentals of our approach are the integrated use of conceptual programming, simulation modeling, network monitoring, multi-agent management, and service-oriented programming. We developed a special framework for an automation of the problem solving. Advantages of the proposed approach are demonstrated on the parametric synthesis example of the static linear regulator for complex dynamic systems. Benefits of the scalable application for solving this problem include automation of the multi-agent control for the systems in a parallel mode with various degrees of its detailed elaboration.

Citizens unite for computational immunology!

PubMed

Belden, Orrin S; Baker, Sarah Catherine; Baker, Brian M

2015-07-01

Recruiting volunteers who can provide computational time, programming expertise, or puzzle-solving talent has emerged as a powerful tool for biomedical research. Recent projects demonstrate the potential for such 'crowdsourcing' efforts in immunology. Tools for developing applications, new funding opportunities, and an eager public make crowdsourcing a serious option for creative solutions for computationally-challenging problems. Expanded uses of crowdsourcing in immunology will allow for more efficient large-scale data collection and analysis. It will also involve, inspire, educate, and engage the public in a variety of meaningful ways. The benefits are real - it is time to jump in! Copyright © 2015 Elsevier Ltd. All rights reserved.

Code IN Exhibits - Supercomputing 2000

NASA Technical Reports Server (NTRS)

Yarrow, Maurice; McCann, Karen M.; Biswas, Rupak; VanderWijngaart, Rob F.; Kwak, Dochan (Technical Monitor)

2000-01-01

The creation of parameter study suites has recently become a more challenging problem as the parameter studies have become multi-tiered and the computational environment has become a supercomputer grid. The parameter spaces are vast, the individual problem sizes are getting larger, and researchers are seeking to combine several successive stages of parameterization and computation. Simultaneously, grid-based computing offers immense resource opportunities but at the expense of great difficulty of use. We present ILab, an advanced graphical user interface approach to this problem. Our novel strategy stresses intuitive visual design tools for parameter study creation and complex process specification, and also offers programming-free access to grid-based supercomputer resources and process automation.

Algorithms and software for nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Belytschko, Ted; Gilbertsen, Noreen D.; Neal, Mark O.

1989-01-01

The objective of this research is to develop efficient methods for explicit time integration in nonlinear structural dynamics for computers which utilize both concurrency and vectorization. As a framework for these studies, the program WHAMS, which is described in Explicit Algorithms for the Nonlinear Dynamics of Shells (T. Belytschko, J. I. Lin, and C.-S. Tsay, Computer Methods in Applied Mechanics and Engineering, Vol. 42, 1984, pp 225 to 251), is used. There are two factors which make the development of efficient concurrent explicit time integration programs a challenge in a structural dynamics program: (1) the need for a variety of element types, which complicates the scheduling-allocation problem; and (2) the need for different time steps in different parts of the mesh, which is here called mixed delta t integration, so that a few stiff elements do not reduce the time steps throughout the mesh.

The AcCell series 2000 as a support system for training and evaluation in educational and clinical settings.

PubMed

Greening, S E; Grohs, D H; Guidos, B J

1997-01-01

Providing effective training, retraining and evaluation programs, including proficiency testing programs, for cytoprofessionals is a challenge shared by many academic and clinical educators internationally. In cytopathology the quality of training has immediately transferable and critically important impacts on satisfactory performance in the clinical setting. Well-designed interactive computer-assisted instruction and testing programs have been shown to enhance initial learning and to reinforce factual and conceptual knowledge. Computer systems designed not only to promote diagnostic accuracy but to integrate and streamline work flow in clinical service settings are candidates for educational adaptation. The AcCell 2000 system, designed as a diagnostic screening support system, offers technology that is adaptable to educational needs during basic and in-service training as well as testing of screening proficiency in both locator and identification skills. We describe the considerations, approaches and applications of the AcCell 2000 system in education programs for both training and evaluation of gynecologic diagnostic screening proficiency.

Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells.

PubMed

Chen, Feng; Bai, Min; Cao, Ke; Zhao, Yue; Cao, Xiaowen; Wei, Jing; Wu, Na; Li, Jiang; Wang, Lihua; Fan, Chunhai; Zhao, Yongxi

2017-12-26

Molecular nanodevices are computational assemblers that switch defined states upon external stimulation. However, interfacing artificial nanodevices with natural molecular machineries in living cells remains a great challenge. Here, we delineate a generic method for programming assembly of enzyme-initiated DNAzyme nanodevices (DzNanos). Two programs including split assembly of two partzymes and toehold exchange displacement assembly of one intact DNAzyme initiated by telomerase are computed. The intact one obtains higher assembly yield and catalytic performance ascribed to proper conformation folding and active misplaced assembly. By employing MnO 2 nanosheets as both DNA carriers and source of Mn 2+ as DNAzyme cofactor, we find that this DzNano is well assembled via a series of conformational states in living cells and operates autonomously with sustained cleavage activity. Other enzymes can also induce corresponding DzNano assembly with defined programming modules. These DzNanos not only can monitor enzyme catalysis in situ but also will enable the implementation of cellular stages, behaviors, and pathways for basic science, diagnostic, and therapeutic applications as genetic circuits.

Double degree master program: Optical Design

NASA Astrophysics Data System (ADS)

Bakholdin, Alexey; Kujawinska, Malgorzata; Livshits, Irina; Styk, Adam; Voznesenskaya, Anna; Ezhova, Kseniia; Ermolayeva, Elena; Ivanova, Tatiana; Romanova, Galina; Tolstoba, Nadezhda

2015-10-01

Modern tendencies of higher education require development of master programs providing achievement of learning outcomes corresponding to quickly variable job market needs. ITMO University represented by Applied and Computer Optics Department and Optical Design and Testing Laboratory jointly with Warsaw University of Technology represented by the Institute of Micromechanics and Photonics at The Faculty of Mechatronics have developed a novel international master double-degree program "Optical Design" accumulating the expertise of both universities including experienced teaching staff, educational technologies, and experimental resources. The program presents studies targeting research and professional activities in high-tech fields connected with optical and optoelectronics devices, optical engineering, numerical methods and computer technologies. This master program deals with the design of optical systems of various types, assemblies and layouts using computer modeling means; investigation of light distribution phenomena; image modeling and formation; development of optical methods for image analysis and optical metrology including optical testing, materials characterization, NDT and industrial control and monitoring. The goal of this program is training a graduate capable to solve a wide range of research and engineering tasks in optical design and metrology leading to modern manufacturing and innovation. Variability of the program structure provides its flexibility and adoption according to current job market demands and personal learning paths for each student. In addition considerable proportion of internship and research expands practical skills. Some special features of the "Optical Design" program which implements the best practices of both Universities, the challenges and lessons learnt during its realization are presented in the paper.

Computational Materials Program for Alloy Design

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo

2005-01-01

The research program sponsored by this grant, "Computational Materials Program for Alloy Design", covers a period of time of enormous change in the emerging field of computational materials science. The computational materials program started with the development of the BFS method for alloys, a quantum approximate method for atomistic analysis of alloys specifically tailored to effectively deal with the current challenges in the area of atomistic modeling and to support modern experimental programs. During the grant period, the program benefited from steady growth which, as detailed below, far exceeds its original set of goals and objectives. Not surprisingly, by the end of this grant, the methodology and the computational materials program became an established force in the materials communitiy, with substantial impact in several areas. Major achievements during the duration of the grant include the completion of a Level 1 Milestone for the HITEMP program at NASA Glenn, consisting of the planning, development and organization of an international conference held at the Ohio Aerospace Institute in August of 2002, finalizing a period of rapid insertion of the methodology in the research community worlwide. The conference, attended by citizens of 17 countries representing various fields of the research community, resulted in a special issue of the leading journal in the area of applied surface science. Another element of the Level 1 Milestone was the presentation of the first version of the Alloy Design Workbench software package, currently known as "adwTools". This software package constitutes the first PC-based piece of software for atomistic simulations for both solid alloys and surfaces in the market.Dissemination of results and insertion in the materials community worldwide was a primary focus during this period. As a result, the P.I. was responsible for presenting 37 contributed talks, 19 invited talks, and publishing 71 articles in peer-reviewed journals, as detailed later in this Report.

Final Report. Institute for Ultralscale Visualization

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

Ma, Kwan-Liu; Galli, Giulia; Gygi, Francois

The SciDAC Institute for Ultrascale Visualization brought together leading experts from visualization, high-performance computing, and science application areas to make advanced visualization solutions for SciDAC scientists and the broader community. Over the five-year project, the Institute introduced many new enabling visualization techniques, which have significantly enhanced scientists’ ability to validate their simulations, interpret their data, and communicate with others about their work and findings. This Institute project involved a large number of junior and student researchers, who received the opportunities to work on some of the most challenging science applications and gain access to the most powerful high-performance computing facilitiesmore » in the world. They were readily trained and prepared for facing the greater challenges presented by extreme-scale computing. The Institute’s outreach efforts, through publications, workshops and tutorials, successfully disseminated the new knowledge and technologies to the SciDAC and the broader scientific communities. The scientific findings and experience of the Institute team helped plan the SciDAC3 program.« less

Using Alice 2.0 to Design Games for People with Stroke.

PubMed

Proffitt, Rachel; Kelleher, Caitlin; Baum, M Carolyn; Engsberg, Jack

2012-08-01

Computer and videogames are gaining in popularity as rehabilitation tools. Unfortunately, most systems still require extensive programming/engineering knowledge to create, something that therapists, as novice programmers, do not possess. There is software designed to allow novice programmers to create storyboard and games through simple drag-and-drop formats; however, the applications for therapeutic game development have not been studied. The purpose of this study was to have an occupational therapy (OT) student with no prior computer programming experience learn how to create computer games for persons with stroke using Alice 2.0, a drag-and-drop editor, designed by Carnegie Mellon University (Pittsburgh, PA). The OT student learned how to use Alice 2.0 through a textbook, tutorials, and assistance from computer science students. She kept a journal of her process, detailing her successes and challenges. The OT student created three games for people with stroke using Alice 2.0. She found that although there were many supports in Alice for creating stories, it lacked critical pieces necessary for game design. Her recommendations for a future programming environment for therapists were that it (1) be efficient, (2) include basic game design pieces so therapists do not have to create them, (3) provide technical support, and (4) be simple. With the incorporation of these recommendations, a future programming environment for therapists will be an effective tool for therapeutic game development.

Is thinking computable?

NASA Technical Reports Server (NTRS)

Denning, Peter J.

1990-01-01

Strong artificial intelligence claims that conscious thought can arise in computers containing the right algorithms even though none of the programs or components of those computers understand which is going on. As proof, it asserts that brains are finite webs of neurons, each with a definite function governed by the laws of physics; this web has a set of equations that can be solved (or simulated) by a sufficiently powerful computer. Strong AI claims the Turing test as a criterion of success. A recent debate in Scientific American concludes that the Turing test is not sufficient, but leaves intact the underlying premise that thought is a computable process. The recent book by Roger Penrose, however, offers a sharp challenge, arguing that the laws of quantum physics may govern mental processes and that these laws may not be computable. In every area of mathematics and physics, Penrose finds evidence of nonalgorithmic human activity and concludes that mental processes are inherently more powerful than computational processes.

Accelerated Application Development: The ORNL Titan Experience

DOE PAGES

Joubert, Wayne; Archibald, Richard K.; Berrill, Mark A.; ...

2015-05-09

The use of computational accelerators such as NVIDIA GPUs and Intel Xeon Phi processors is now widespread in the high performance computing community, with many applications delivering impressive performance gains. However, programming these systems for high performance, performance portability and software maintainability has been a challenge. In this paper we discuss experiences porting applications to the Titan system. Titan, which began planning in 2009 and was deployed for general use in 2013, was the first multi-petaflop system based on accelerator hardware. To ready applications for accelerated computing, a preparedness effort was undertaken prior to delivery of Titan. In this papermore » we report experiences and lessons learned from this process and describe how users are currently making use of computational accelerators on Titan.« less

Accelerated application development: The ORNL Titan experience

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

Joubert, Wayne; Archibald, Rick; Berrill, Mark

2015-08-01

The use of computational accelerators such as NVIDIA GPUs and Intel Xeon Phi processors is now widespread in the high performance computing community, with many applications delivering impressive performance gains. However, programming these systems for high performance, performance portability and software maintainability has been a challenge. In this paper we discuss experiences porting applications to the Titan system. Titan, which began planning in 2009 and was deployed for general use in 2013, was the first multi-petaflop system based on accelerator hardware. To ready applications for accelerated computing, a preparedness effort was undertaken prior to delivery of Titan. In this papermore » we report experiences and lessons learned from this process and describe how users are currently making use of computational accelerators on Titan.« less

Technology in Education. The Progress of Education Reform, 2006. Volume 6, Number 6

ERIC Educational Resources Information Center

Weiss, Suzanne

2006-01-01

For policymakers, educators and others interested in learning more about the one-to-one computing movement, this issue of "The Progress of Education Reform" spotlights three particularly useful resources: (1) a detailed review of the challenges faced by states and districts implementing laptop programs, and of lessons learned to date in…

Observations on Student Misconceptions--A Case Study of the Build-Heap Algorithm

ERIC Educational Resources Information Center

Seppala, Otto; Malmi, Lauri; Korhonen, Ari

2006-01-01

Data structures and algorithms are core issues in computer programming. However, learning them is challenging for most students and many of them have various types of misconceptions on how algorithms work. In this study, we discuss the problem of identifying misconceptions on the principles of how algorithms work. Our context is algorithm…

Deception Detection in a Computer-Mediated Environment: Gender, Trust, and Training Issues

DTIC Science & Technology

2003-03-01

to the understanding of deception detection from both a practical and academic point of view. The lessons learned from the limitations of this...has truly been a learning experience and a great capstone to a challenging Master’s program. I also owe great appreciation to individuals that...83 Academic Implications and Suggestions

The Paradigm Recursion: Is It More Accessible When Introduced in Middle School?

ERIC Educational Resources Information Center

Gunion, Katherine; Milford, Todd; Stege, Ulrike

2009-01-01

Recursion is a programming paradigm as well as a problem solving strategy thought to be very challenging to grasp for university students. This article outlines a pilot study, which expands the age range of students exposed to the concept of recursion in computer science through instruction in a series of interesting and engaging activities. In…

A Pilot Study of Short Computing Video Tutorials in a Graduate Public Health Biostatistics Course

ERIC Educational Resources Information Center

Hund, Lauren; Getrich, Christina

2015-01-01

Traditional lecture-centered classrooms are being challenged by active learning hybrid curricula. In small graduate programs with limited resources and primarily non-traditional students, exploring how to use online technology to optimize the role of the professor in the classroom is imperative. However, very little research exists in this area.…

An Innovative Plant Genomics and Gene Annotation Program for High School, Community College, and University Faculty

ERIC Educational Resources Information Center

Hacisalihoglu, Gokhan; Hilgert, Uwe; Nash, E. Bruce; Micklos, David A.

2008-01-01

Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day…

Parallel Flux Tensor Analysis for Efficient Moving Object Detection

DTIC Science & Technology

2011-07-01

computing as well as parallelization to enable real time performance in analyzing complex video [3, 4 ]. There are a number of challenging computer vision... 4 . TITLE AND SUBTITLE Parallel Flux Tensor Analysis for Efficient Moving Object Detection 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...We use the trace of the flux tensor matrix, referred to as Tr JF , that is defined below, Tr JF = ∫ Ω W (x− y)(I2xt(y) + I2yt(y) + I2tt(y))dy ( 4 ) as

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.

PubMed

Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

2017-08-01

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs. The software is implemented in Matlab, and is provided as supplementary information . hyunseob.song@pnnl.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

Advancing Capabilities for Understanding the Earth System Through Intelligent Systems, the NSF Perspective

NASA Astrophysics Data System (ADS)

Gil, Y.; Zanzerkia, E. E.; Munoz-Avila, H.

2015-12-01

The National Science Foundation (NSF) Directorate for Geosciences (GEO) and Directorate for Computer and Information Science (CISE) acknowledge the significant scientific challenges required to understand the fundamental processes of the Earth system, within the atmospheric and geospace, Earth, ocean and polar sciences, and across those boundaries. A broad view of the opportunities and directions for GEO are described in the report "Dynamic Earth: GEO imperative and Frontiers 2015-2020." Many of the aspects of geosciences research, highlighted both in this document and other community grand challenges, pose novel problems for researchers in intelligent systems. Geosciences research will require solutions for data-intensive science, advanced computational capabilities, and transformative concepts for visualizing, using, analyzing and understanding geo phenomena and data. Opportunities for the scientific community to engage in addressing these challenges are available and being developed through NSF's portfolio of investments and activities. The NSF-wide initiative, Cyberinfrastructure Framework for 21st Century Science and Engineering (CIF21), looks to accelerate research and education through new capabilities in data, computation, software and other aspects of cyberinfrastructure. EarthCube, a joint program between GEO and the Advanced Cyberinfrastructure Division, aims to create a well-connected and facile environment to share data and knowledge in an open, transparent, and inclusive manner, thus accelerating our ability to understand and predict the Earth system. EarthCube's mission opens an opportunity for collaborative research on novel information systems enhancing and supporting geosciences research efforts. NSF encourages true, collaborative partnerships between scientists in computer sciences and the geosciences to meet these challenges.

Information revolution in nursing and health care: educating for tomorrow's challenge.

PubMed

Kooker, B M; Richardson, S S

1994-06-01

Current emphasis on the national electronic highway and a national health database for comparative health care reporting demonstrates society's increasing reliance on information technology. The efficient electronic processing and managing of data, information, and knowledge are critical for survival in tomorrow's health care organization. To take a leadership role in this information revolution, informatics nurse specialists must possess competencies that incorporate information science, computer science, and nursing science for successful information system development. In selecting an appropriate informatics educational program or to hire an individual capable of meeting this challenge, nurse administrators must look for the following technical knowledge and skill set: information management principles, system development life cycle, programming languages, file design and access, hardware and network architecture, project management skills, and leadership abilities.

2016 Final Reports from the Los Alamos National Laboratory Computational Physics Student Summer Workshop

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

Runnels, Scott Robert; Bachrach, Harrison Ian; Carlson, Nils

The two primary purposes of LANL’s Computational Physics Student Summer Workshop are (1) To educate graduate and exceptional undergraduate students in the challenges and applications of computational physics of interest to LANL, and (2) Entice their interest toward those challenges. Computational physics is emerging as a discipline in its own right, combining expertise in mathematics, physics, and computer science. The mathematical aspects focus on numerical methods for solving equations on the computer as well as developing test problems with analytical solutions. The physics aspects are very broad, ranging from low-temperature material modeling to extremely high temperature plasma physics, radiation transportmore » and neutron transport. The computer science issues are concerned with matching numerical algorithms to emerging architectures and maintaining the quality of extremely large codes built to perform multi-physics calculations. Although graduate programs associated with computational physics are emerging, it is apparent that the pool of U.S. citizens in this multi-disciplinary field is relatively small and is typically not focused on the aspects that are of primary interest to LANL. Furthermore, more structured foundations for LANL interaction with universities in computational physics is needed; historically interactions rely heavily on individuals’ personalities and personal contacts. Thus a tertiary purpose of the Summer Workshop is to build an educational network of LANL researchers, university professors, and emerging students to advance the field and LANL’s involvement in it.« less

2009 ALCF annual report.

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

Beckman, P.; Martin, D.; Drugan, C.

2010-11-23

This year the Argonne Leadership Computing Facility (ALCF) delivered nearly 900 million core hours of science. The research conducted at their leadership class facility touched our lives in both minute and massive ways - whether it was studying the catalytic properties of gold nanoparticles, predicting protein structures, or unearthing the secrets of exploding stars. The authors remained true to their vision to act as the forefront computational center in extending science frontiers by solving pressing problems for our nation. Our success in this endeavor was due mainly to the Department of Energy's (DOE) INCITE (Innovative and Novel Computational Impact onmore » Theory and Experiment) program. The program awards significant amounts of computing time to computationally intensive, unclassified research projects that can make high-impact scientific advances. This year, DOE allocated 400 million hours of time to 28 research projects at the ALCF. Scientists from around the world conducted the research, representing such esteemed institutions as the Princeton Plasma Physics Laboratory, National Institute of Standards and Technology, and European Center for Research and Advanced Training in Scientific Computation. Argonne also provided Director's Discretionary allocations for research challenges, addressing such issues as reducing aerodynamic noise, critical for next-generation 'green' energy systems. Intrepid - the ALCF's 557-teraflops IBM Blue/Gene P supercomputer - enabled astounding scientific solutions and discoveries. Intrepid went into full production five months ahead of schedule. As a result, the ALCF nearly doubled the days of production computing available to the DOE Office of Science, INCITE awardees, and Argonne projects. One of the fastest supercomputers in the world for open science, the energy-efficient system uses about one-third as much electricity as a machine of comparable size built with more conventional parts. In October 2009, President Barack Obama recognized the excellence of the entire Blue Gene series by awarding it to the National Medal of Technology and Innovation. Other noteworthy achievements included the ALCF's collaboration with the National Energy Research Scientific Computing Center (NERSC) to examine cloud computing as a potential new computing paradigm for scientists. Named Magellan, the DOE-funded initiative will explore which science application programming models work well within the cloud, as well as evaluate the challenges that come with this new paradigm. The ALCF obtained approval for its next-generation machine, a 10-petaflops system to be delivered in 2012. This system will allow us to resolve ever more pressing problems, even more expeditiously through breakthrough science in the years to come.« less

Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

NASA Astrophysics Data System (ADS)

Tang, Jingyin; Matyas, Corene J.

2018-02-01

Big Data in geospatial technology is a grand challenge for processing capacity. The ability to use a GIS for geospatial analysis on Cloud Computing and High Performance Computing (HPC) clusters has emerged as a new approach to provide feasible solutions. However, users lack the ability to migrate existing research tools to a Cloud Computing or HPC-based environment because of the incompatibility of the market-dominating ArcGIS software stack and Linux operating system. This manuscript details a cross-platform geospatial library "arc4nix" to bridge this gap. Arc4nix provides an application programming interface compatible with ArcGIS and its Python library "arcpy". Arc4nix uses a decoupled client-server architecture that permits geospatial analytical functions to run on the remote server and other functions to run on the native Python environment. It uses functional programming and meta-programming language to dynamically construct Python codes containing actual geospatial calculations, send them to a server and retrieve results. Arc4nix allows users to employ their arcpy-based script in a Cloud Computing and HPC environment with minimal or no modification. It also supports parallelizing tasks using multiple CPU cores and nodes for large-scale analyses. A case study of geospatial processing of a numerical weather model's output shows that arcpy scales linearly in a distributed environment. Arc4nix is open-source software.

Preface: SciDAC 2008

NASA Astrophysics Data System (ADS)

Stevens, Rick

2008-07-01

The fourth annual Scientific Discovery through Advanced Computing (SciDAC) Conference was held June 13-18, 2008, in Seattle, Washington. The SciDAC conference series is the premier communitywide venue for presentation of results from the DOE Office of Science's interdisciplinary computational science program. Started in 2001 and renewed in 2006, the DOE SciDAC program is the country's - and arguably the world's - most significant interdisciplinary research program supporting the development of advanced scientific computing methods and their application to fundamental and applied areas of science. SciDAC supports computational science across many disciplines, including astrophysics, biology, chemistry, fusion sciences, and nuclear physics. Moreover, the program actively encourages the creation of long-term partnerships among scientists focused on challenging problems and computer scientists and applied mathematicians developing the technology and tools needed to address those problems. The SciDAC program has played an increasingly important role in scientific research by allowing scientists to create more accurate models of complex processes, simulate problems once thought to be impossible, and analyze the growing amount of data generated by experiments. To help further the research community's ability to tap into the capabilities of current and future supercomputers, Under Secretary for Science, Raymond Orbach, launched the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program in 2003. The INCITE program was conceived specifically to seek out computationally intensive, large-scale research projects with the potential to significantly advance key areas in science and engineering. The program encourages proposals from universities, other research institutions, and industry. During the first two years of the INCITE program, 10 percent of the resources at NERSC were allocated to INCITE awardees. However, demand for supercomputing resources far exceeded available systems; and in 2003, the Office of Science identified increasing computing capability by a factor of 100 as the second priority on its Facilities of the Future list. The goal was to establish leadership-class computing resources to support open science. As a result of a peer reviewed competition, the first leadership computing facility was established at Oak Ridge National Laboratory in 2004. A second leadership computing facility was established at Argonne National Laboratory in 2006. This expansion of computational resources led to a corresponding expansion of the INCITE program. In 2008, Argonne, Lawrence Berkeley, Oak Ridge, and Pacific Northwest national laboratories all provided resources for INCITE. By awarding large blocks of computer time on the DOE leadership computing facilities, the INCITE program enables the largest-scale computations to be pursued. In 2009, INCITE will award over half a billion node-hours of time. The SciDAC conference celebrates progress in advancing science through large-scale modeling and simulation. Over 350 participants attended this year's talks, poster sessions, and tutorials, spanning the disciplines supported by DOE. While the principal focus was on SciDAC accomplishments, this year's conference also included invited presentations and posters from DOE INCITE awardees. Another new feature in the SciDAC conference series was an electronic theater and video poster session, which provided an opportunity for the community to see over 50 scientific visualizations in a venue equipped with many high-resolution large-format displays. To highlight the growing international interest in petascale computing, this year's SciDAC conference included a keynote presentation by Herman Lederer from the Max Planck Institut, one of the leaders of DEISA (Distributed European Infrastructure for Supercomputing Applications) project and a member of the PRACE consortium, Europe's main petascale project. We also heard excellent talks from several European groups, including Laurent Gicquel of CERFACS, who spoke on `Large-Eddy Simulations of Turbulent Reacting Flows of Real Burners: Status and Challenges', and Jean-Francois Hamelin from EDF, who presented a talk on `Getting Ready for Petaflop Capacities and Beyond: A Utility Perspective'. Two other compelling addresses gave attendees a glimpse into the future. Tomas Diaz de la Rubia of Lawrence Livermore National Laboratory spoke on a vision for a fusion/fission hybrid reactor known as the `LIFE Engine' and discussed some of the materials and modeling challenges that need to be overcome to realize the vision for a 1000-year greenhouse-gas-free power source. Dan Reed from Microsoft gave a capstone talk on the convergence of technology, architecture, and infrastructure for cloud computing, data-intensive computing, and exascale computing (1018 flops/sec). High-performance computing is making rapid strides. The SciDAC community's computational resources are expanding dramatically. In the summer of 2008 the first general purpose petascale system (IBM Cell-based RoadRunner at Los Alamos National Laboratory) was recognized in the top 500 list of fastest machines heralding in the dawning of the petascale era. The DOE's leadership computing facility at Argonne reached number three on the Top 500 and is at the moment the most capable open science machine based on an IBM BG/P system with a peak performance of over 550 teraflops/sec. Later this year Oak Ridge is expected to deploy a 1 petaflops/sec Cray XT system. And even before the scientific community has had an opportunity to make significant use of petascale systems, the computer science research community is forging ahead with ideas and strategies for development of systems that may by the end of the next decade sustain exascale performance. Several talks addressed barriers to, and strategies for, achieving exascale capabilities. The last day of the conference was devoted to tutorials hosted by Microsoft Research at a new conference facility in Redmond, Washington. Over 90 people attended the tutorials, which covered topics ranging from an introduction to BG/P programming to advanced numerical libraries. The SciDAC and INCITE programs and the DOE Office of Advanced Scientific Computing Research core program investments in applied mathematics, computer science, and computational and networking facilities provide a nearly optimum framework for advancing computational science for DOE's Office of Science. At a broader level this framework also is benefiting the entire American scientific enterprise. As we look forward, it is clear that computational approaches will play an increasingly significant role in addressing challenging problems in basic science, energy, and environmental research. It takes many people to organize and support the SciDAC conference, and I would like to thank as many of them as possible. The backbone of the conference is the technical program; and the task of selecting, vetting, and recruiting speakers is the job of the organizing committee. I thank the members of this committee for all the hard work and the many tens of conference calls that enabled a wonderful program to be assembled. This year the following people served on the organizing committee: Jim Ahrens, LANL; David Bader, LLNL; Bryan Barnett, Microsoft; Peter Beckman, ANL; Vincent Chan, GA; Jackie Chen, SNL; Lori Diachin, LLNL; Dan Fay, Microsoft; Ian Foster, ANL; Mark Gordon, Ames; Mohammad Khaleel, PNNL; David Keyes, Columbia University; Bob Lucas, University of Southern California; Tony Mezzacappa, ORNL; Jeff Nichols, ORNL; David Nowak, ANL; Michael Papka, ANL; Thomas Schultess, ORNL; Horst Simon, LBNL; David Skinner, LBNL; Panagiotis Spentzouris, Fermilab; Bob Sugar, UCSB; and Kathy Yelick, LBNL. I owe a special thanks to Mike Papka and Jim Ahrens for handling the electronic theater. I also thank all those who submitted videos. It was a highly successful experiment. Behind the scenes an enormous amount of work is required to make a large conference go smoothly. First I thank Cheryl Zidel for her tireless efforts as organizing committee liaison and posters chair and, in general, handling all of my end of the program and keeping me calm. I also thank Gail Pieper for her work in editing the proceedings, Beth Cerny Patino for her work on the Organizing Committee website and electronic theater, and Ken Raffenetti for his work in keeping that website working. Jon Bashor and John Hules did an excellent job in handling conference communications. I thank Caitlin Youngquist for the striking graphic design; Dan Fay for tutorials arrangements; and Lynn Dory, Suzanne Stevenson, Sarah Pebelske and Sarah Zidel for on-site registration and conference support. We all owe Yeen Mankin an extra-special thanks for choosing the hotel, handling contracts, arranging menus, securing venues, and reassuring the chair that everything was under control. We are pleased to have obtained corporate sponsorship from Cray, IBM, Intel, HP, and SiCortex. I thank all the speakers and panel presenters. I also thank the former conference chairs Tony Metzzacappa, Bill Tang, and David Keyes, who were never far away for advice and encouragement. Finally, I offer my thanks to Michael Strayer, without whose leadership, vision, and persistence the SciDAC program would not have come into being and flourished. I am honored to be part of his program and his friend. Rick Stevens Seattle, Washington July 18, 2008

Mantle Convection on Modern Supercomputers

NASA Astrophysics Data System (ADS)

Weismüller, J.; Gmeiner, B.; Huber, M.; John, L.; Mohr, M.; Rüde, U.; Wohlmuth, B.; Bunge, H. P.

2015-12-01

Mantle convection is the cause for plate tectonics, the formation of mountains and oceans, and the main driving mechanism behind earthquakes. The convection process is modeled by a system of partial differential equations describing the conservation of mass, momentum and energy. Characteristic to mantle flow is the vast disparity of length scales from global to microscopic, turning mantle convection simulations into a challenging application for high-performance computing. As system size and technical complexity of the simulations continue to increase, design and implementation of simulation models for next generation large-scale architectures is handled successfully only in an interdisciplinary context. A new priority program - named SPPEXA - by the German Research Foundation (DFG) addresses this issue, and brings together computer scientists, mathematicians and application scientists around grand challenges in HPC. Here we report from the TERRA-NEO project, which is part of the high visibility SPPEXA program, and a joint effort of four research groups. TERRA-NEO develops algorithms for future HPC infrastructures, focusing on high computational efficiency and resilience in next generation mantle convection models. We present software that can resolve the Earth's mantle with up to 1012 grid points and scales efficiently to massively parallel hardware with more than 50,000 processors. We use our simulations to explore the dynamic regime of mantle convection and assess the impact of small scale processes on global mantle flow.

From Petascale to Exascale: Eight Focus Areas of R&D Challenges for HPC Simulation Environments

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

Springmeyer, R; Still, C; Schulz, M

2011-03-17

Programming models bridge the gap between the underlying hardware architecture and the supporting layers of software available to applications. Programming models are different from both programming languages and application programming interfaces (APIs). Specifically, a programming model is an abstraction of the underlying computer system that allows for the expression of both algorithms and data structures. In comparison, languages and APIs provide implementations of these abstractions and allow the algorithms and data structures to be put into practice - a programming model exists independently of the choice of both the programming language and the supporting APIs. Programming models are typically focusedmore » on achieving increased developer productivity, performance, and portability to other system designs. The rapidly changing nature of processor architectures and the complexity of designing an exascale platform provide significant challenges for these goals. Several other factors are likely to impact the design of future programming models. In particular, the representation and management of increasing levels of parallelism, concurrency and memory hierarchies, combined with the ability to maintain a progressive level of interoperability with today's applications are of significant concern. Overall the design of a programming model is inherently tied not only to the underlying hardware architecture, but also to the requirements of applications and libraries including data analysis, visualization, and uncertainty quantification. Furthermore, the successful implementation of a programming model is dependent on exposed features of the runtime software layers and features of the operating system. Successful use of a programming model also requires effective presentation to the software developer within the context of traditional and new software development tools. Consideration must also be given to the impact of programming models on both languages and the associated compiler infrastructure. Exascale programming models must reflect several, often competing, design goals. These design goals include desirable features such as abstraction and separation of concerns. However, some aspects are unique to large-scale computing. For example, interoperability and composability with existing implementations will prove critical. In particular, performance is the essential underlying goal for large-scale systems. A key evaluation metric for exascale models will be the extent to which they support these goals rather than merely enable them.« less

ISCR Annual Report: Fical Year 2004

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

McGraw, J R

2005-03-03

Large-scale scientific computation and all of the disciplines that support and help to validate it have been placed at the focus of Lawrence Livermore National Laboratory (LLNL) by the Advanced Simulation and Computing (ASC) program of the National Nuclear Security Administration (NNSA) and the Scientific Discovery through Advanced Computing (SciDAC) initiative of the Office of Science of the Department of Energy (DOE). The maturation of computational simulation as a tool of scientific and engineering research is underscored in the November 2004 statement of the Secretary of Energy that, ''high performance computing is the backbone of the nation's science and technologymore » enterprise''. LLNL operates several of the world's most powerful computers--including today's single most powerful--and has undertaken some of the largest and most compute-intensive simulations ever performed. Ultrascale simulation has been identified as one of the highest priorities in DOE's facilities planning for the next two decades. However, computers at architectural extremes are notoriously difficult to use efficiently. Furthermore, each successful terascale simulation only points out the need for much better ways of interacting with the resulting avalanche of data. Advances in scientific computing research have, therefore, never been more vital to LLNL's core missions than at present. Computational science is evolving so rapidly along every one of its research fronts that to remain on the leading edge, LLNL must engage researchers at many academic centers of excellence. In Fiscal Year 2004, the Institute for Scientific Computing Research (ISCR) served as one of LLNL's main bridges to the academic community with a program of collaborative subcontracts, visiting faculty, student internships, workshops, and an active seminar series. The ISCR identifies researchers from the academic community for computer science and computational science collaborations with LLNL and hosts them for short- and long-term visits with the aim of encouraging long-term academic research agendas that address LLNL's research priorities. Through such collaborations, ideas and software flow in both directions, and LLNL cultivates its future workforce. The Institute strives to be LLNL's ''eyes and ears'' in the computer and information sciences, keeping the Laboratory aware of and connected to important external advances. It also attempts to be the ''feet and hands'' that carry those advances into the Laboratory and incorporates them into practice. ISCR research participants are integrated into LLNL's Computing and Applied Research (CAR) Department, especially into its Center for Applied Scientific Computing (CASC). In turn, these organizations address computational challenges arising throughout the rest of the Laboratory. Administratively, the ISCR flourishes under LLNL's University Relations Program (URP). Together with the other five institutes of the URP, it navigates a course that allows LLNL to benefit from academic exchanges while preserving national security. While it is difficult to operate an academic-like research enterprise within the context of a national security laboratory, the results declare the challenges well met and worth the continued effort.« less

Computer-Based Methods for Collecting Peer Nomination Data: Utility, Practice, and Empirical Support.

PubMed

van den Berg, Yvonne H M; Gommans, Rob

2017-09-01

New technologies have led to several major advances in psychological research over the past few decades. Peer nomination research is no exception. Thanks to these technological innovations, computerized data collection is becoming more common in peer nomination research. However, computer-based assessment is more than simply programming the questionnaire and asking respondents to fill it in on computers. In this chapter the advantages and challenges of computer-based assessments are discussed. In addition, a list of practical recommendations and considerations is provided to inform researchers on how computer-based methods can be applied to their own research. Although the focus is on the collection of peer nomination data in particular, many of the requirements, considerations, and implications are also relevant for those who consider the use of other sociometric assessment methods (e.g., paired comparisons, peer ratings, peer rankings) or computer-based assessments in general. © 2017 Wiley Periodicals, Inc.

Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

NASA Technical Reports Server (NTRS)

Rose, Geoffrey K.; Nguyen, Duc T.; Newman, Brett A.

2017-01-01

Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.

Center for Center for Technology for Advanced Scientific Component Software (TASCS)

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

Kostadin, Damevski

A resounding success of the Scientific Discovery through Advanced Computing (SciDAC) program is that high-performance computational science is now universally recognized as a critical aspect of scientific discovery [71], complementing both theoretical and experimental research. As scientific communities prepare to exploit unprecedented computing capabilities of emerging leadership-class machines for multi-model simulations at the extreme scale [72], it is more important than ever to address the technical and social challenges of geographically distributed teams that combine expertise in domain science, applied mathematics, and computer science to build robust and flexible codes that can incorporate changes over time. The Center for Technologymore » for Advanced Scientific Component Software (TASCS)1 tackles these these issues by exploiting component-based software development to facilitate collaborative high-performance scientific computing.« less

An Advanced User Interface Approach for Complex Parameter Study Process Specification in the Information Power Grid

NASA Technical Reports Server (NTRS)

Yarrow, Maurice; McCann, Karen M.; Biswas, Rupak; VanderWijngaart, Rob; Yan, Jerry C. (Technical Monitor)

2000-01-01

The creation of parameter study suites has recently become a more challenging problem as the parameter studies have now become multi-tiered and the computational environment has become a supercomputer grid. The parameter spaces are vast, the individual problem sizes are getting larger, and researchers are now seeking to combine several successive stages of parameterization and computation. Simultaneously, grid-based computing offers great resource opportunity but at the expense of great difficulty of use. We present an approach to this problem which stresses intuitive visual design tools for parameter study creation and complex process specification, and also offers programming-free access to grid-based supercomputer resources and process automation.

[Activities of Research Institute for Advanced Computer Science

NASA Technical Reports Server (NTRS)

Gross, Anthony R. (Technical Monitor); Leiner, Barry M.

2001-01-01

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administrations missions. RIACS is located at the NASA Ames Research Center, Moffett Field, California. RIACS research focuses on the three cornerstones of IT research necessary to meet the future challenges of NASA missions: 1. Automated Reasoning for Autonomous Systems Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth. 2. Human-Centered Computing Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities. 3. High Performance Computing and Networking Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to analysis of large scientific datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply IT research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, visiting scientist programs and student summer programs, designed to encourage and facilitate collaboration between the university and NASA IT research communities.

Constraint Programming to Solve Maximal Density Still Life

NASA Astrophysics Data System (ADS)

Chu, Geoffrey; Petrie, Karen Elizabeth; Yorke-Smith, Neil

The Maximum Density Still Life problem fills a finite Game of Life board with a stable pattern of cells that has as many live cells as possible. Although simple to state, this problem is computationally challenging for any but the smallest sizes of board. Especially difficult is to prove that the maximum number of live cells has been found. Various approaches have been employed. The most successful are approaches based on Constraint Programming (CP). We describe the Maximum Density Still Life problem, introduce the concept of constraint programming, give an overview on how the problem can be modelled and solved with CP, and report on best-known results for the problem.

Accelerating 3D Elastic Wave Equations on Knights Landing based Intel Xeon Phi processors

NASA Astrophysics Data System (ADS)

Sourouri, Mohammed; Birger Raknes, Espen

2017-04-01

In advanced imaging methods like reverse-time migration (RTM) and full waveform inversion (FWI) the elastic wave equation (EWE) is numerically solved many times to create the seismic image or the elastic parameter model update. Thus, it is essential to optimize the solution time for solving the EWE as this will have a major impact on the total computational cost in running RTM or FWI. From a computational point of view applications implementing EWEs are associated with two major challenges. The first challenge is the amount of memory-bound computations involved, while the second challenge is the execution of such computations over very large datasets. So far, multi-core processors have not been able to tackle these two challenges, which eventually led to the adoption of accelerators such as Graphics Processing Units (GPUs). Compared to conventional CPUs, GPUs are densely populated with many floating-point units and fast memory, a type of architecture that has proven to map well to many scientific computations. Despite its architectural advantages, full-scale adoption of accelerators has yet to materialize. First, accelerators require a significant programming effort imposed by programming models such as CUDA or OpenCL. Second, accelerators come with a limited amount of memory, which also require explicit data transfers between the CPU and the accelerator over the slow PCI bus. The second generation of the Xeon Phi processor based on the Knights Landing (KNL) architecture, promises the computational capabilities of an accelerator but require the same programming effort as traditional multi-core processors. The high computational performance is realized through many integrated cores (number of cores and tiles and memory varies with the model) organized in tiles that are connected via a 2D mesh based interconnect. In contrary to accelerators, KNL is a self-hosted system, meaning explicit data transfers over the PCI bus are no longer required. However, like most accelerators, KNL sports a memory subsystem consisting of low-level caches and 16GB of high-bandwidth MCDRAM memory. For capacity computing, up to 400GB of conventional DDR4 memory is provided. Such a strict hierarchical memory layout means that data locality is imperative if the true potential of this product is to be harnessed. In this work, we study a series of optimizations specifically targeting KNL for our EWE based application to reduce the time-to-solution time for the following 3D model sizes in grid points: 1283, 2563 and 5123. We compare the results with an optimized version for multi-core CPUs running on a dual-socket Xeon E5 2680v3 system using OpenMP. Our initial naive implementation on the KNL is roughly 20% faster than the multi-core version, but by using only one thread per core and careful memory placement using the memkind library, we could achieve higher speedups. Additionally, by using the MCDRAM as cache for problem sizes that are smaller than 16 GB further performance improvements were unlocked. Depending on the problem size, our overall results indicate that the KNL based system is approximately 2.2x faster than the 24-core Xeon E5 2680v3 system, with only modest changes to the code.

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

Harms, Kevin; Oral, H. Sarp; Atchley, Scott

The Oak Ridge and Argonne Leadership Computing Facilities are both receiving new systems under the Collaboration of Oak Ridge, Argonne, and Livermore (CORAL) program. Because they are both part of the INCITE program, applications need to be portable between these two facilities. However, the Summit and Aurora systems will be vastly different architectures, including their I/O subsystems. While both systems will have POSIX-compliant parallel file systems, their Burst Buffer technologies will be different. This difference may pose challenges to application portability between facilities. Application developers need to pay attention to specific burst buffer implementations to maximize code portability.

Use of a hand-held computer observational tool to improve communication for care planning and psychosocial well-being

PubMed Central

Corazzini, Kirsten; Rapp, Carla Gene; McConnell, Eleanor S.; Anderson, Ruth A.

2013-01-01

Staff development nurses in long-term care are challenged to implement training programs that foster quality unlicensed assistive personnel (UAP) care and improve the transfer of their observations to licensed nursing staff for care planning. This study describes the outcomes of a program where UAP recorded behavioral problems of residents to inform care. Findings suggest staff development nurses who aim to improve UAP reporting without simultaneously targeting licensed nursing staff behaviors may worsen nursing staff relationships. PMID:19182546

Students with Special Needs and 1:1 Computing: A Teacher's Perspective

ERIC Educational Resources Information Center

Corn, Jenifer; Tagsold, Jennifer T.; Argueta, Rodolfo

2012-01-01

To better understand the growing trend of 1:1 learning, researchers conducted an evaluation of a laptop initiative in 18 North Carolina high schools. The goal of the study was to provide information about the value of the initiative to enhance student learning, as well as to identify challenges to the successful implementation of 1:1 programs,…

Computer Competencies of the Faculty Members of the College of Education at the United Arab Emirates University

ERIC Educational Resources Information Center

Alghazo, Iman Mohammad

2006-01-01

In its effort to obtain accreditation using NCATE standards, the College of Education at the United Arab Emirates University is integrating ISTE standards into its teacher education programs. The main challenge at this stage is preparing faculty members to integrate technology into their teaching in order to help their students meet ISTE…

Evolving Information Technology: A Case Study of the Effects of Constant Change on Information Technology Instructional Design Architecture

ERIC Educational Resources Information Center

Helps, Richard

2010-01-01

A major challenge for Information Technology (IT) programs is that the rapid pace of evolution of computing technology leads to frequent redesign of IT courses. The problem is exacerbated by several factors. Firstly, the changing technology is the subject matter of the discipline and is also frequently used to support instruction; secondly, this…

A meta-analysis of pedagogical tools used in introductory programming courses

NASA Astrophysics Data System (ADS)

Trees, Frances P.

Programming is recognized as being challenging for teachers to teach and difficult for students to learn. For decades, computer science educators have looked at innovative approaches by creating pedagogical software tools that attempt to facilitate both the teaching of and the learning of programming. This dissertation investigates the motivations for the integration of pedagogical tools in introductory programming courses and the characteristics that are perceived to contribute to the effectiveness of these tools. The study employs three research stages that examine the tool characteristics and their use. The first stage surveys teachers who use pedagogical tools in an introductory programming course. The second interviews teachers to explore the survey results in more detail and to add greater depth into the choice and use of pedagogical tools in the introductory programming class. The third interviews tool developers to provide an explanatory insight of the tool and the motivation for its creation. The results indicate that the pedagogical tools perceived to be effective share common characteristics: They provide an environment that is manageable, flexible and visual; they provide for active engagement in learning activities and support programming in small pieces; they allow for an easy transition to subsequent courses and more robust environments; they provide technical support and resource materials. The results of this study also indicate that recommendations from other computer science educators have a strong impact on a teacher's initial tool choice for an introductory programming course. This study informs present and future tool developers of the characteristics that the teachers perceive to contribute to the effectiveness of a pedagogical tool and how to present their tools to encourage a more efficient and more effective widespread adoption of the tool into the teacher's curriculum. The teachers involved in this study are actively involved in the computer science education community. The results of this study, based on the perceptions of these computer science educators, provide guidance to those educators choosing to introduce a new pedagogical tool into their programming course.

Computer-aided biochemical programming of synthetic microreactors as diagnostic devices.

PubMed

Courbet, Alexis; Amar, Patrick; Fages, François; Renard, Eric; Molina, Franck

2018-04-26

Biological systems have evolved efficient sensing and decision-making mechanisms to maximize fitness in changing molecular environments. Synthetic biologists have exploited these capabilities to engineer control on information and energy processing in living cells. While engineered organisms pose important technological and ethical challenges, de novo assembly of non-living biomolecular devices could offer promising avenues toward various real-world applications. However, assembling biochemical parts into functional information processing systems has remained challenging due to extensive multidimensional parameter spaces that must be sampled comprehensively in order to identify robust, specification compliant molecular implementations. We introduce a systematic methodology based on automated computational design and microfluidics enabling the programming of synthetic cell-like microreactors embedding biochemical logic circuits, or protosensors , to perform accurate biosensing and biocomputing operations in vitro according to temporal logic specifications. We show that proof-of-concept protosensors integrating diagnostic algorithms detect specific patterns of biomarkers in human clinical samples. Protosensors may enable novel approaches to medicine and represent a step toward autonomous micromachines capable of precise interfacing of human physiology or other complex biological environments, ecosystems, or industrial bioprocesses. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

Preface: SciDAC 2006

NASA Astrophysics Data System (ADS)

Tang, William M., Dr.

2006-01-01

The second annual Scientific Discovery through Advanced Computing (SciDAC) Conference was held from June 25-29, 2006 at the new Hyatt Regency Hotel in Denver, Colorado. This conference showcased outstanding SciDAC-sponsored computational science results achieved during the past year across many scientific domains, with an emphasis on science at scale. Exciting computational science that has been accomplished outside of the SciDAC program both nationally and internationally was also featured to help foster communication between SciDAC computational scientists and those funded by other agencies. This was illustrated by many compelling examples of how domain scientists collaborated productively with applied mathematicians and computer scientists to effectively take advantage of terascale computers (capable of performing trillions of calculations per second) not only to accelerate progress in scientific discovery in a variety of fields but also to show great promise for being able to utilize the exciting petascale capabilities in the near future. The SciDAC program was originally conceived as an interdisciplinary computational science program based on the guiding principle that strong collaborative alliances between domain scientists, applied mathematicians, and computer scientists are vital to accelerated progress and associated discovery on the world's most challenging scientific problems. Associated verification and validation are essential in this successful program, which was funded by the US Department of Energy Office of Science (DOE OS) five years ago. As is made clear in many of the papers in these proceedings, SciDAC has fundamentally changed the way that computational science is now carried out in response to the exciting challenge of making the best use of the rapid progress in the emergence of more and more powerful computational platforms. In this regard, Dr. Raymond Orbach, Energy Undersecretary for Science at the DOE and Director of the OS has stated: `SciDAC has strengthened the role of high-end computing in furthering science. It is defining whole new fields for discovery.' (SciDAC Review, Spring 2006, p8). Application domains within the SciDAC 2006 conference agenda encompassed a broad range of science including: (i) the DOE core mission of energy research involving combustion studies relevant to fuel efficiency and pollution issues faced today and magnetic fusion investigations impacting prospects for future energy sources; (ii) fundamental explorations into the building blocks of matter, ranging from quantum chromodynamics - the basic theory that describes how quarks make up the protons and neutrons of all matter - to the design of modern high-energy accelerators; (iii) the formidable challenges of predicting and controlling the behavior of molecules in quantum chemistry and the complex biomolecules determining the evolution of biological systems; (iv) studies of exploding stars for insights into the nature of the universe; and (v) integrated climate modeling to enable realistic analysis of earth's changing climate. Associated research has made it quite clear that advanced computation is often the only means by which timely progress is feasible when dealing with these complex, multi-component physical, chemical, and biological systems operating over huge ranges of temporal and spatial scales. Working with the domain scientists, applied mathematicians and computer scientists have continued to develop the discretizations of the underlying equations and the complementary algorithms to enable improvements in solutions on modern parallel computing platforms as they evolve from the terascale toward the petascale regime. Moreover, the associated tremendous growth of data generated from the terabyte to the petabyte range demands not only the advanced data analysis and visualization methods to harvest the scientific information but also the development of efficient workflow strategies which can deal with the data input/output, management, movement, and storage challenges. If scientific discovery is expected to keep apace with the continuing progression from tera- to petascale platforms, the vital alliance between domain scientists, applied mathematicians, and computer scientists will be even more crucial. During the SciDAC 2006 Conference, some of the future challenges and opportunities in interdisciplinary computational science were emphasized in the Advanced Architectures Panel and by Dr. Victor Reis, Senior Advisor to the Secretary of Energy, who gave a featured presentation on `Simulation, Computation, and the Global Nuclear Energy Partnership.' Overall, the conference provided an excellent opportunity to highlight the rising importance of computational science in the scientific enterprise and to motivate future investment in this area. As Michael Strayer, SciDAC Program Director, has noted: `While SciDAC may have started out as a specific program, Scientific Discovery through Advanced Computing has become a powerful concept for addressing some of the biggest challenges facing our nation and our world.' Looking forward to next year, the SciDAC 2007 Conference will be held from June 24-28 at the Westin Copley Plaza in Boston, Massachusetts. Chairman: David Keyes, Columbia University. The Organizing Committee for the SciDAC 2006 Conference would like to acknowledge the individuals whose talents and efforts were essential to the success of the meeting. Special thanks go to Betsy Riley for her leadership in building the infrastructure support for the conference, for identifying and then obtaining contributions from our corporate sponsors, for coordinating all media communications, and for her efforts in organizing and preparing the conference proceedings for publication; to Tim Jones for handling the hotel scouting, subcontracts, and exhibits and stage production; to Angela Harris for handling supplies, shipping, and tracking, poster sessions set-up, and for her efforts in coordinating and scheduling the promotional activities that took place during the conference; to John Bui and John Smith for their superb wireless networking and A/V set-up and support; to Cindy Latham for Web site design, graphic design, and quality control of proceedings submissions; and to Pamelia Nixon-Hartje of Ambassador for budget and quality control of catering. We are grateful for the highly professional dedicated efforts of all of these individuals, who were the cornerstones of the SciDAC 2006 Conference. Thanks also go to Angela Beach of the ORNL Conference Center for her efforts in executing the contracts with the hotel, Carolyn James of Colorado State for on-site registration supervision, Lora Wolfe and Brittany Hagen for administrative support at ORNL, and Dami Rich and Andrew Sproles for graphic design and production. We are also most grateful to the Oak Ridge National Laboratory, especially Jeff Nichols, and to our corporate sponsors, Data Direct Networks, Cray, IBM, SGI, and Institute of Physics Publishing for their support. We especially express our gratitude to the featured speakers, invited oral speakers, invited poster presenters, session chairs, and advanced architecture panelists and chair for their excellent contributions on behalf of SciDAC 2006. We would like to express our deep appreciation to Lali Chatterjee, Graham Douglas, Margaret Smith, and the production team of Institute of Physics Publishing, who worked tirelessly to publish the final conference proceedings in a timely manner. Finally, heartfelt thanks are extended to Michael Strayer, Associate Director for OASCR and SciDAC Director, and to the DOE program managers associated with SciDAC for their continuing enthusiasm and strong support for the annual SciDAC Conferences as a special venue to showcase the exciting scientific discovery achievements enabled by the interdisciplinary collaborations championed by the SciDAC program.

GPU COMPUTING FOR PARTICLE TRACKING

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

Nishimura, Hiroshi; Song, Kai; Muriki, Krishna

2011-03-25

This is a feasibility study of using a modern Graphics Processing Unit (GPU) to parallelize the accelerator particle tracking code. To demonstrate the massive parallelization features provided by GPU computing, a simplified TracyGPU program is developed for dynamic aperture calculation. Performances, issues, and challenges from introducing GPU are also discussed. General purpose Computation on Graphics Processing Units (GPGPU) bring massive parallel computing capabilities to numerical calculation. However, the unique architecture of GPU requires a comprehensive understanding of the hardware and programming model to be able to well optimize existing applications. In the field of accelerator physics, the dynamic aperture calculationmore » of a storage ring, which is often the most time consuming part of the accelerator modeling and simulation, can benefit from GPU due to its embarrassingly parallel feature, which fits well with the GPU programming model. In this paper, we use the Tesla C2050 GPU which consists of 14 multi-processois (MP) with 32 cores on each MP, therefore a total of 448 cores, to host thousands ot threads dynamically. Thread is a logical execution unit of the program on GPU. In the GPU programming model, threads are grouped into a collection of blocks Within each block, multiple threads share the same code, and up to 48 KB of shared memory. Multiple thread blocks form a grid, which is executed as a GPU kernel. A simplified code that is a subset of Tracy++ [2] is developed to demonstrate the possibility of using GPU to speed up the dynamic aperture calculation by having each thread track a particle.« less

The role of the host in a cooperating mainframe and workstation environment, volumes 1 and 2

NASA Technical Reports Server (NTRS)

Kusmanoff, Antone; Martin, Nancy L.

1989-01-01

In recent years, advancements made in computer systems have prompted a move from centralized computing based on timesharing a large mainframe computer to distributed computing based on a connected set of engineering workstations. A major factor in this advancement is the increased performance and lower cost of engineering workstations. The shift to distributed computing from centralized computing has led to challenges associated with the residency of application programs within the system. In a combined system of multiple engineering workstations attached to a mainframe host, the question arises as to how does a system designer assign applications between the larger mainframe host and the smaller, yet powerful, workstation. The concepts related to real time data processing are analyzed and systems are displayed which use a host mainframe and a number of engineering workstations interconnected by a local area network. In most cases, distributed systems can be classified as having a single function or multiple functions and as executing programs in real time or nonreal time. In a system of multiple computers, the degree of autonomy of the computers is important; a system with one master control computer generally differs in reliability, performance, and complexity from a system in which all computers share the control. This research is concerned with generating general criteria principles for software residency decisions (host or workstation) for a diverse yet coupled group of users (the clustered workstations) which may need the use of a shared resource (the mainframe) to perform their functions.

Solution of large nonlinear quasistatic structural mechanics problems on distributed-memory multiprocessor computers

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

Blanford, M.

1997-12-31

Most commercially-available quasistatic finite element programs assemble element stiffnesses into a global stiffness matrix, then use a direct linear equation solver to obtain nodal displacements. However, for large problems (greater than a few hundred thousand degrees of freedom), the memory size and computation time required for this approach becomes prohibitive. Moreover, direct solution does not lend itself to the parallel processing needed for today`s multiprocessor systems. This talk gives an overview of the iterative solution strategy of JAS3D, the nonlinear large-deformation quasistatic finite element program. Because its architecture is derived from an explicit transient-dynamics code, it does not ever assemblemore » a global stiffness matrix. The author describes the approach he used to implement the solver on multiprocessor computers, and shows examples of problems run on hundreds of processors and more than a million degrees of freedom. Finally, he describes some of the work he is presently doing to address the challenges of iterative convergence for ill-conditioned problems.« less

Experimental Evaluation and Workload Characterization for High-Performance Computer Architectures

NASA Technical Reports Server (NTRS)

El-Ghazawi, Tarek A.

1995-01-01

This research is conducted in the context of the Joint NSF/NASA Initiative on Evaluation (JNNIE). JNNIE is an inter-agency research program that goes beyond typical.bencbking to provide and in-depth evaluations and understanding of the factors that limit the scalability of high-performance computing systems. Many NSF and NASA centers have participated in the effort. Our research effort was an integral part of implementing JNNIE in the NASA ESS grand challenge applications context. Our research work under this program was composed of three distinct, but related activities. They include the evaluation of NASA ESS high- performance computing testbeds using the wavelet decomposition application; evaluation of NASA ESS testbeds using astrophysical simulation applications; and developing an experimental model for workload characterization for understanding workload requirements. In this report, we provide a summary of findings that covers all three parts, a list of the publications that resulted from this effort, and three appendices with the details of each of the studies using a key publication developed under the respective work.

When promotoras and technology meet: A qualitative analysis of promotoras’ use of small media to increase cancer screening among South Texas Latinos

PubMed Central

Fernandez, Maria E.; LaRue, Denise M.; Bartholomew, L. Kay

2012-01-01

Computer-based multimedia technologies can be used to tailor health messages, but promotoras (Spanish-speaking community health workers) rarely use these tools. Promotoras delivered health messages about colorectal cancer screening to medically underserved Latinos in South Texas using two small media formats: a “low-tech” format (flipchart and video); and a “high-tech” format consisting of a tailored, interactive computer program delivered on a tablet computer. Using qualitative methods, we observed promotora training and intervention delivery, and conducted interviews with five promotoras to compare and contrast program implementation of both formats. We discuss the ways each format aided or challenged promotoras’ intervention delivery. Findings reveal that some aspects of both formats enhanced intervention delivery by tapping into Latino health communication preferences and facilitating interpersonal communication, while other aspects hindered intervention delivery. This study contributes to our understanding of how community health workers use low- and high-tech small media formats when delivering health messages to Latinos. PMID:21986243

Case Study: The Role of eLearning in Midwifery Pre-Service Education in Ghana.

PubMed

Appiagyei, Martha; Trump, Alison; Danso, Evans; Yeboah, Alex; Searle, Sarah; Carr, Catherine

The issues and challenges of implementing eLearning in pre-service health education were explored through a pilot study conducted in six nurse-midwifery education programs in Ghana. Case-based, interactive computer mediated eLearning modules, targeted to basic emergency and obstetrical signal functions, were delivered both online and offline using a free-for-use eLearning platform, skoool HE(®). Key success factors included broad stakeholder support, an established curriculum and student and tutor interest. Challenges included infrastructure limitations, large class sizes and added workloads for tutors and information technology staff. National scale up is planned.

USRA/RIACS

NASA Technical Reports Server (NTRS)

Oliger, Joseph

1992-01-01

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on June 6, 1983. RIACS is privately operated by USRA, a consortium of universities with research programs in the aerospace sciences, under a cooperative agreement with NASA. The primary mission of RIACS is to provide research and expertise in computer science and scientific computing to support the scientific missions of NASA ARC. The research carried out at RIACS must change its emphasis from year to year in response to NASA ARC's changing needs and technological opportunities. A flexible scientific staff is provided through a university faculty visitor program, a post doctoral program, and a student visitor program. Not only does this provide appropriate expertise but it also introduces scientists outside of NASA to NASA problems. A small group of core RIACS staff provides continuity and interacts with an ARC technical monitor and scientific advisory group to determine the RIACS mission. RIACS activities are reviewed and monitored by a USRA advisory council and ARC technical monitor. Research at RIACS is currently being done in the following areas: (1) parallel computing; (2) advanced methods for scientific computing; (3) learning systems; (4) high performance networks and technology; and (5) graphics, visualization, and virtual environments. In the past year, parallel compiler techniques and adaptive numerical methods for flows in complicated geometries were identified as important problems to investigate for ARC's involvement in the Computational Grand Challenges of the next decade. We concluded a summer student visitors program during this six months. We had six visiting graduate students that worked on projects over the summer and presented seminars on their work at the conclusion of their visits. RIACS technical reports are usually preprints of manuscripts that have been submitted to research journals or conference proceedings. A list of these reports for the period July 1, 1992 through December 31, 1992 is provided.

Membrane proteins structures: A review on computational modeling tools.

PubMed

Almeida, Jose G; Preto, Antonio J; Koukos, Panagiotis I; Bonvin, Alexandre M J J; Moreira, Irina S

2017-10-01

Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights. This review highlights the importance of membrane proteins and how computational methods are capable of overcoming challenges associated with their experimental characterization. It covers various MP structural aspects, such as lipid interactions, allostery, and structure prediction, based on methods such as Molecular Dynamics (MD) and Machine-Learning (ML). Recent developments in algorithms, tools and hybrid approaches, together with the increase in both computational resources and the amount of available data have resulted in increasingly powerful and trustworthy approaches to model MPs. Even though MPs are elementary and important in nature, the determination of their 3D structure has proven to be a challenging endeavor. Computational methods provide a reliable alternative to experimental methods. In this review, we focus on computational techniques to determine the 3D structure of MP and characterize their binding interfaces. We also summarize the most relevant databases and software programs available for the study of MPs. Copyright © 2017 Elsevier B.V. All rights reserved.

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.

PubMed

Nakato, Ryuichiro; Itoh, Tahehiko; Shirahige, Katsuhiko

2013-07-01

Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) can identify genomic regions that bind proteins involved in various chromosomal functions. Although the development of next-generation sequencers offers the technology needed to identify these protein-binding sites, the analysis can be computationally challenging because sequencing data sometimes consist of >100 million reads/sample. Herein, we describe a cost-effective and time-efficient protocol that is generally applicable to ChIP-seq analysis; this protocol uses a novel peak-calling program termed DROMPA to identify peaks and an additional program, parse2wig, to preprocess read-map files. This two-step procedure drastically reduces computational time and memory requirements compared with other programs. DROMPA enables the identification of protein localization sites in repetitive sequences and efficiently identifies both broad and sharp protein localization peaks. Specifically, DROMPA outputs a protein-binding profile map in pdf or png format, which can be easily manipulated by users who have a limited background in bioinformatics. © 2013 The Authors Genes to Cells © 2013 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

Dropping Out of Computer Science: A Phenomenological Study of Student Lived Experiences in Community College Computer Science

NASA Astrophysics Data System (ADS)

Gilbert-Valencia, Daniel H.

California community colleges contribute alarmingly few computer science degree or certificate earners. While the literature shows clear K-12 impediments to CS matriculation in higher education, very little is known about the experiences of those who overcome initial impediments to CS yet do not persist through to program completion. This phenomenological study explores insights into that specific experience by interviewing underrepresented, low income, first-generation college students who began community college intending to transfer to 4-year institutions majoring in CS but switched to another field and remain enrolled or graduated. This study explores the lived experiences of students facing barriers, their avenues for developing interest in CS, and the persistence support systems they encountered, specifically looking at how students constructed their academic choice from these experiences. The growing diversity within California's population necessitates that experiences specific to underrepresented students be considered as part of this exploration. Ten semi-structured interviews and observations were conducted, transcribed and coded. Artifacts supporting student experiences were also collected. Data was analyzed through a social-constructivist lens to provide insight into experiences and how they can be navigated to create actionable strategies for community college computer science departments wishing to increase student success. Three major themes emerged from this research: (1) students shared pre-college characteristics; (2) faced similar challenges in college CS courses; and (3) shared similar reactions to the "work" of computer science. Results of the study included (1) CS interest development hinged on computer ownership in the home; (2) participants shared characteristics that were ideal for college success but not CS success; and (3) encounters in CS departments produced unique challenges for participants. Though CS interest was and remains abundant, opportunities for learning programming skills before college were non-existent and there were few opportunities in college to build skills or establish a peer support networks. Recommendations for institutional leaders and further research are also provided.

Spreadsheet-based program for alignment of overlapping DNA sequences.

PubMed

Anbazhagan, R; Gabrielson, E

1999-06-01

Molecular biology laboratories frequently face the challenge of aligning small overlapping DNA sequences derived from a long DNA segment. Here, we present a short program that can be used to adapt Excel spreadsheets as a tool for aligning DNA sequences, regardless of their orientation. The program runs on any Windows or Macintosh operating system computer with Excel 97 or Excel 98. The program is available for use as an Excel file, which can be downloaded from the BioTechniques Web site. Upon execution, the program opens a specially designed customized workbook and is capable of identifying overlapping regions between two sequence fragments and displaying the sequence alignment. It also performs a number of specialized functions such as recognition of restriction enzyme cutting sites and CpG island mapping without costly specialized software.

Display integration for ground combat vehicles

NASA Astrophysics Data System (ADS)

Busse, David J.

1998-09-01

The United States Army's requirement to employ high resolution target acquisition sensors and information warfare to increase its dominance over enemy forces has led to the need to integrate advanced display devices into ground combat vehicle crew stations. The Army's force structure require the integration of advanced displays on both existing and emerging ground combat vehicle systems. The fielding of second generation target acquisition sensors, color digital terrain maps and high volume digital command and control information networks on these platforms define display performance requirements. The greatest challenge facing the system integrator is the development and integration of advanced displays that meet operational, vehicle and human computer interface performance requirements for the ground combat vehicle fleet. The subject of this paper is to address those challenges: operational and vehicle performance, non-soldier centric crew station configurations, display performance limitations related to human computer interfaces and vehicle physical environments, display technology limitations and the Department of Defense (DOD) acquisition reform initiatives. How the ground combat vehicle Program Manager and system integrator are addressing these challenges are discussed through the integration of displays on fielded, current and future close combat vehicle applications.

Feedback-Driven Dynamic Invariant Discovery

NASA Technical Reports Server (NTRS)

Zhang, Lingming; Yang, Guowei; Rungta, Neha S.; Person, Suzette; Khurshid, Sarfraz

2014-01-01

Program invariants can help software developers identify program properties that must be preserved as the software evolves, however, formulating correct invariants can be challenging. In this work, we introduce iDiscovery, a technique which leverages symbolic execution to improve the quality of dynamically discovered invariants computed by Daikon. Candidate invariants generated by Daikon are synthesized into assertions and instrumented onto the program. The instrumented code is executed symbolically to generate new test cases that are fed back to Daikon to help further re ne the set of candidate invariants. This feedback loop is executed until a x-point is reached. To mitigate the cost of symbolic execution, we present optimizations to prune the symbolic state space and to reduce the complexity of the generated path conditions. We also leverage recent advances in constraint solution reuse techniques to avoid computing results for the same constraints across iterations. Experimental results show that iDiscovery converges to a set of higher quality invariants compared to the initial set of candidate invariants in a small number of iterations.

How robotics programs influence young women's career choices : a grounded theory model

NASA Astrophysics Data System (ADS)

Craig, Cecilia Dosh-Bluhm

The fields of engineering, computer science, and physics have a paucity of women despite decades of intervention by universities and organizations. Women's graduation rates in these fields continue to stagnate, posing a critical problem for society. This qualitative grounded theory (GT) study sought to understand how robotics programs influenced young women's career decisions and the program's effect on engineering, physics, and computer science career interests. To test this, a study was mounted to explore how the FIRST (For Inspiration and Recognition of Science and Technology) Robotics Competition (FRC) program influenced young women's college major and career choices. Career theories suggested that experiential programs coupled with supportive relationships strongly influence career decisions, especially for science, technology, engineering, and mathematics careers. The study explored how and when young women made career decisions and how the experiential program and! its mentors and role models influenced career choice. Online focus groups and interviews (online and face-to-face) with 10 female FRC alumnae and GT processes (inductive analysis, open coding, categorizations using mind maps and content clouds) were used to generate a general systems theory style model of the career decision process for these young women. The study identified gender stereotypes and other career obstacles for women. The study's conclusions include recommendations to foster connections to real-world challenges, to develop training programs for mentors, and to nurture social cohesion, a mostly untapped area. Implementing these recommendations could help grow a critical mass of women in engineering, physics, and computer science careers, a social change worth pursuing.

Projected phase-change memory devices.

PubMed

Koelmans, Wabe W; Sebastian, Abu; Jonnalagadda, Vara Prasad; Krebs, Daniel; Dellmann, Laurent; Eleftheriou, Evangelos

2015-09-03

Nanoscale memory devices, whose resistance depends on the history of the electric signals applied, could become critical building blocks in new computing paradigms, such as brain-inspired computing and memcomputing. However, there are key challenges to overcome, such as the high programming power required, noise and resistance drift. Here, to address these, we present the concept of a projected memory device, whose distinguishing feature is that the physical mechanism of resistance storage is decoupled from the information-retrieval process. We designed and fabricated projected memory devices based on the phase-change storage mechanism and convincingly demonstrate the concept through detailed experimentation, supported by extensive modelling and finite-element simulations. The projected memory devices exhibit remarkably low drift and excellent noise performance. We also demonstrate active control and customization of the programming characteristics of the device that reliably realize a multitude of resistance states.

Application of artificial intelligence to pharmacy and medicine.

PubMed

Dasta, J F

1992-04-01

Artificial intelligence (AI) is a branch of computer science dealing with solving problems using symbolic programming. It has evolved into a problem solving science with applications in business, engineering, and health care. One application of AI is expert system development. An expert system consists of a knowledge base and inference engine, coupled with a user interface. A crucial aspect of expert system development is knowledge acquisition and implementing computable ways to solve problems. There have been several expert systems developed in medicine to assist physicians with medical diagnosis. Recently, several programs focusing on drug therapy have been described. They provide guidance on drug interactions, drug therapy monitoring, and drug formulary selection. There are many aspects of pharmacy that AI can have an impact on and the reader is challenged to consider these possibilities because they may some day become a reality in pharmacy.

Enhancing computer literacy and information retrieval skills: A rural and remote nursing and midwifery workforce study.

PubMed

Mills, Jane; Francis, Karen; McLeod, Margaret; Al-Motlaq, Mohammad

2015-01-01

Nurses and midwives collectively, represent the largest workforce category in rural and remote areas of Australia. Maintaining currency of practice and attaining annual licensure with the Australian Health Practitioners Regulatory Authority (AHPRA) present challenges for individual nurses and midwives and for their health service managers. Engagement with information and communication technologies, in order for geographically isolated clinicians to access ongoing education and training, is considered a useful strategy to address such challenges. This paper presents a pre- and post-test study design. It examines the impact of an online continuing professional development (CPD) program on Australian rural nurses and midwives. The aims of the program were to increase basic skill acquisition in the utilisation of common computer software, the use of the Internet and the enhancement of email communication. Findings from the study demonstrate that participants who complete a relevant CPD program gain confidence in the use of information and communication technologies. Further, increased confidence leads to increased access to contemporary, reliable and important health care information on the Internet, in addition to clinicians adopting email as a regular method of communication. Health care employers commonly assume employees are skilled users of information and communication technologies. However, findings from this study contradict such assumptions. It is argued in the recommendations that health care employees should be given regular access to CPD programs designed to introduce them to information and communication technologies. Developing knowledge and skills in this area has the potential to improve staff productivity, raise health care standards and improve patient outcomes.

solveME: fast and reliable solution of nonlinear ME models.

PubMed

Yang, Laurence; Ma, Ding; Ebrahim, Ali; Lloyd, Colton J; Saunders, Michael A; Palsson, Bernhard O

2016-09-22

Genome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challenges: they are much (>30 times) larger than corresponding metabolic reconstructions (M models), are multiscale, and growth maximization is a nonlinear programming (NLP) problem, mainly due to macromolecule dilution constraints. Here, we address these computational challenges. We develop a fast and numerically reliable solution method for growth maximization in ME models using a quad-precision NLP solver (Quad MINOS). Our method was up to 45 % faster than binary search for six significant digits in growth rate. We also develop a fast, quad-precision flux variability analysis that is accelerated (up to 60× speedup) via solver warm-starts. Finally, we employ the tools developed to investigate growth-coupled succinate overproduction, accounting for proteome constraints. Just as genome-scale metabolic reconstructions have become an invaluable tool for computational and systems biologists, we anticipate that these fast and numerically reliable ME solution methods will accelerate the wide-spread adoption of ME models for researchers in these fields.

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

Underwood, Keith D; Ulmer, Craig D.; Thompson, David

Field programmable gate arrays (FPGAs) have been used as alternative computational de-vices for over a decade; however, they have not been used for traditional scientific com-puting due to their perceived lack of floating-point performance. In recent years, there hasbeen a surge of interest in alternatives to traditional microprocessors for high performancecomputing. Sandia National Labs began two projects to determine whether FPGAs wouldbe a suitable alternative to microprocessors for high performance scientific computing and,if so, how they should be integrated into the system. We present results that indicate thatFPGAs could have a significant impact on future systems. FPGAs have thepotentialtohave ordermore » of magnitude levels of performance wins on several key algorithms; however,there are serious questions as to whether the system integration challenge can be met. Fur-thermore, there remain challenges in FPGA programming and system level reliability whenusing FPGA devices.4 AcknowledgmentArun Rodrigues provided valuable support and assistance in the use of the Structural Sim-ulation Toolkit within an FPGA context. Curtis Janssen and Steve Plimpton provided valu-able insights into the workings of two Sandia applications (MPQC and LAMMPS, respec-tively).5« less

Parallel Processing of Images in Mobile Devices using BOINC

NASA Astrophysics Data System (ADS)

Curiel, Mariela; Calle, David F.; Santamaría, Alfredo S.; Suarez, David F.; Flórez, Leonardo

2018-04-01

Medical image processing helps health professionals make decisions for the diagnosis and treatment of patients. Since some algorithms for processing images require substantial amounts of resources, one could take advantage of distributed or parallel computing. A mobile grid can be an adequate computing infrastructure for this problem. A mobile grid is a grid that includes mobile devices as resource providers. In a previous step of this research, we selected BOINC as the infrastructure to build our mobile grid. However, parallel processing of images in mobile devices poses at least two important challenges: the execution of standard libraries for processing images and obtaining adequate performance when compared to desktop computers grids. By the time we started our research, the use of BOINC in mobile devices also involved two issues: a) the execution of programs in mobile devices required to modify the code to insert calls to the BOINC API, and b) the division of the image among the mobile devices as well as its merging required additional code in some BOINC components. This article presents answers to these four challenges.

GPU-based High-Performance Computing for Radiation Therapy

PubMed Central

Jia, Xun; Ziegenhein, Peter; Jiang, Steve B.

2014-01-01

Recent developments in radiotherapy therapy demand high computation powers to solve challenging problems in a timely fashion in a clinical environment. Graphics processing unit (GPU), as an emerging high-performance computing platform, has been introduced to radiotherapy. It is particularly attractive due to its high computational power, small size, and low cost for facility deployment and maintenance. Over the past a few years, GPU-based high-performance computing in radiotherapy has experienced rapid developments. A tremendous amount of studies have been conducted, in which large acceleration factors compared with the conventional CPU platform have been observed. In this article, we will first give a brief introduction to the GPU hardware structure and programming model. We will then review the current applications of GPU in major imaging-related and therapy-related problems encountered in radiotherapy. A comparison of GPU with other platforms will also be presented. PMID:24486639

Multi-media based education.

PubMed

Wurdack, C M

1997-01-01

Computers are changing the way we do everything from paying our bills to programming our home entertainment systems. If you thought that dental education was not likely to benefit from computers, consider this: Computer technology is revolutionizing dental instruction in ways that promise to improve the quality and efficiency of dental education. It is providing a challenging learning opportunity for dental educators as well. Since much of dental education involves the visual transfer of both concepts and procedures from the instructor to the student, it makes sense that using computer technology to enhance conventional teaching techniques--with materials that include clear, informative images and real-time demonstrations melding sound and animation to deliver to the student in the classroom material that complements textbooks, 35mm slides, and the lecture format. Use of computers at UOP is about teaching students to be competent dentists by making instruction more direct, better visualized, and more comprehensible.

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.

Automated a complex computer aided design concept generated using macros programming

NASA Astrophysics Data System (ADS)

Rizal Ramly, Mohammad; Asrokin, Azharrudin; Abd Rahman, Safura; Zulkifly, Nurul Ain Md

2013-12-01

Changing a complex Computer Aided design profile such as car and aircraft surfaces has always been difficult and challenging. The capability of CAD software such as AutoCAD and CATIA show that a simple configuration of a CAD design can be easily modified without hassle, but it is not the case with complex design configuration. Design changes help users to test and explore various configurations of the design concept before the production of a model. The purpose of this study is to look into macros programming as parametric method of the commercial aircraft design. Macros programming is a method where the configurations of the design are done by recording a script of commands, editing the data value and adding a certain new command line to create an element of parametric design. The steps and the procedure to create a macro programming are discussed, besides looking into some difficulties during the process of creation and advantage of its usage. Generally, the advantages of macros programming as a method of parametric design are; allowing flexibility for design exploration, increasing the usability of the design solution, allowing proper contained by the model while restricting others and real time feedback changes.

Challenges and potential solutions for big data implementations in developing countries.

PubMed

Luna, D; Mayan, J C; García, M J; Almerares, A A; Househ, M

2014-08-15

The volume of data, the velocity with which they are generated, and their variety and lack of structure hinder their use. This creates the need to change the way information is captured, stored, processed, and analyzed, leading to the paradigm shift called Big Data. To describe the challenges and possible solutions for developing countries when implementing Big Data projects in the health sector. A non-systematic review of the literature was performed in PubMed and Google Scholar. The following keywords were used: "big data", "developing countries", "data mining", "health information systems", and "computing methodologies". A thematic review of selected articles was performed. There are challenges when implementing any Big Data program including exponential growth of data, special infrastructure needs, need for a trained workforce, need to agree on interoperability standards, privacy and security issues, and the need to include people, processes, and policies to ensure their adoption. Developing countries have particular characteristics that hinder further development of these projects. The advent of Big Data promises great opportunities for the healthcare field. In this article, we attempt to describe the challenges developing countries would face and enumerate the options to be used to achieve successful implementations of Big Data programs.

Learning the Digital Way: Evaluating Progress, Tackling Challenges. Technology Counts, 2015. Education Week. Volume 34, Number 35

ERIC Educational Resources Information Center

Edwards, Virginia B., Ed.

2015-01-01

Lofty ed-tech visions are always tempered by reality. Unexpected problems that arose during a launch of a 1-to-1 computing program and ambitious digital curriculum initiative in Los Angeles led to the dialing back of the effort. Financial, legal, and managerial repercussions continue to swirl in the wake. These problems should not prevent schools…

Selecting a Benchmark Suite to Profile High-Performance Computing (HPC) Machines

DTIC Science & Technology

2014-11-01

architectures. Machines now contain central processing units (CPUs), graphics processing units (GPUs), and many integrated core ( MIC ) architecture all...evaluate the feasibility and applicability of a new architecture just released to the market . Researchers are often unsure how available resources will...architectures. Having a suite of programs running on different architectures, such as GPUs, MICs , and CPUs, adds complexity and technical challenges

An Overview of Recent Developments in Computational Aeroelasticity

NASA Technical Reports Server (NTRS)

Bennett, Robert M.; Edwards, John W.

2004-01-01

The motivation for Computational Aeroelasticity (CA) and the elements of one type of the analysis or simulation process are briefly reviewed. The need for streamlining and improving the overall process to reduce elapsed time and improve overall accuracy is discussed. Further effort is needed to establish the credibility of the methodology, obtain experience, and to incorporate the experience base to simplify the method for future use. Experience with the application of a variety of Computational Aeroelasticity programs is summarized for the transonic flutter of two wings, the AGARD 445.6 wing and a typical business jet wing. There is a compelling need for a broad range of additional flutter test cases for further comparisons. Some existing data sets that may offer CA challenges are presented.

Resources and Approaches for Teaching Quantitative and Computational Skills in the Geosciences and Allied Fields

NASA Astrophysics Data System (ADS)

Orr, C. H.; Mcfadden, R. R.; Manduca, C. A.; Kempler, L. A.

2016-12-01

Teaching with data, simulations, and models in the geosciences can increase many facets of student success in the classroom, and in the workforce. Teaching undergraduates about programming and improving students' quantitative and computational skills expands their perception of Geoscience beyond field-based studies. Processing data and developing quantitative models are critically important for Geoscience students. Students need to be able to perform calculations, analyze data, create numerical models and visualizations, and more deeply understand complex systems—all essential aspects of modern science. These skills require students to have comfort and skill with languages and tools such as MATLAB. To achieve comfort and skill, computational and quantitative thinking must build over a 4-year degree program across courses and disciplines. However, in courses focused on Geoscience content it can be challenging to get students comfortable with using computational methods to answers Geoscience questions. To help bridge this gap, we have partnered with MathWorks to develop two workshops focused on collecting and developing strategies and resources to help faculty teach students to incorporate data, simulations, and models into the curriculum at the course and program levels. We brought together faculty members from the sciences, including Geoscience and allied fields, who teach computation and quantitative thinking skills using MATLAB to build a resource collection for teaching. These materials, and the outcomes of the workshops are freely available on our website. The workshop outcomes include a collection of teaching activities, essays, and course descriptions that can help faculty incorporate computational skills at the course or program level. The teaching activities include in-class assignments, problem sets, labs, projects, and toolboxes. These activities range from programming assignments to creating and using models. The outcomes also include workshop syntheses that highlights best practices, a set of webpages to support teaching with software such as MATLAB, and an interest group actively discussing aspects these issues in Geoscience and allied fields. Learn more and view the resources at http://serc.carleton.edu/matlab_computation2016/index.html

Meeting the DHCP Challenge: A Model for Implementing a Decentralized Hospital Computer Program

PubMed Central

Catellier, Julie; Benway, Paula K.; Perez, Kathleen

1987-01-01

The James A. Haley Veterans' Hospital in Tampa has been a consistent leader in the implementation of automated systems within the VA. Our approach has been essentially to focus on obtaining maximum user involvement and contribution to the automation program within the Medical Center. Since clinical acceptance is vital to a viable program, a great deal of our efforts have been aimed at maximizing the training and participation of physicians, nurses and other clinical staff. The following is a description of our organization structure relative to this topic. We believe it to be a highly workable approach which can be easily implemented structurally at any hospital — public or private.

Women in computer science: An interpretative phenomenological analysis exploring common factors contributing to women's selection and persistence in computer science as an academic major

NASA Astrophysics Data System (ADS)

Thackeray, Lynn Roy

The purpose of this study is to understand the meaning that women make of the social and cultural factors that influence their reasons for entering and remaining in study of computer science. The twenty-first century presents many new challenges in career development and workforce choices for both men and women. Information technology has become the driving force behind many areas of the economy. As this trend continues, it has become essential that U.S. citizens need to pursue a career in technologies, including the computing sciences. Although computer science is a very lucrative profession, many Americans, especially women, are not choosing it as a profession. Recent studies have shown no significant differences in math, technical and science competency between men and women. Therefore, other factors, such as social, cultural, and environmental influences seem to affect women's decisions in choosing an area of study and career choices. A phenomenological method of qualitative research was used in this study, based on interviews of seven female students who are currently enrolled in a post-secondary computer science program. Their narratives provided meaning into the social and cultural environments that contribute to their persistence in their technical studies, as well as identifying barriers and challenges that are faced by female students who choose to study computer science. It is hoped that the data collected from this study may provide recommendations for the recruiting, retention and support for women in computer science departments of U.S. colleges and universities, and thereby increase the numbers of women computer scientists in industry. Keywords: gender access, self-efficacy, culture, stereotypes, computer education, diversity.

Challenges in accessing sexual and reproductive health services by people with physical disabilities in Kampala, Uganda

PubMed Central

2014-01-01

Introduction Despite the universal right to access the same range, quality and standard of free or affordable health care and programs as provided to other persons, people with physical disabilities (PWPDs) continue to experience challenges in accessing these services. This article presents the challenges faced by PWPDs in accessing sexual and reproductive health (SRH) services in Kampala, Uganda. Methods This was a qualitative study that was conducted with male and female PWPDs in Kampala in 2007. Data on the challenges experienced by PWPDs in accessing SRH services were collected using in-depth interviews with 40 PWPDs and key informant interviews with 10 PWPDs’ representatives, staff of agencies supporting PWPDs and health workers. All data were captured verbatim using an audio-tape recorder, entered into a Microsoft Word computer program and analyzed manually following a content thematic approach. Results The study findings show that PWPDs face a multitude of challenges in accessing SRH services including negative attitudes of service providers, long queues at health facilities, distant health facilities, high costs of services involved, unfriendly physical structures and the perception from able-bodied people that PWPDs should be asexual. Conclusion People with physical disabilities (PWPDs) face health facility-related (service provider and facility-related challenges), economic and societal challenges in accessing SRH services. These findings call for a need to sensitize service providers on SRH needs of PWPDs for better support and for the government to enforce the provision of PWPD-friendly services in all health facilities. PMID:25086444

Challenges in accessing sexual and reproductive health services by people with physical disabilities in Kampala, Uganda.

PubMed

Ahumuza, Sharon Eva; Matovu, Joseph K B; Ddamulira, John Bosco; Muhanguzi, Florence Kyoheirwe

2014-08-02

Despite the universal right to access the same range, quality and standard of free or affordable health care and programs as provided to other persons, people with physical disabilities (PWPDs) continue to experience challenges in accessing these services. This article presents the challenges faced by PWPDs in accessing sexual and reproductive health (SRH) services in Kampala, Uganda. This was a qualitative study that was conducted with male and female PWPDs in Kampala in 2007. Data on the challenges experienced by PWPDs in accessing SRH services were collected using in-depth interviews with 40 PWPDs and key informant interviews with 10 PWPDs' representatives, staff of agencies supporting PWPDs and health workers. All data were captured verbatim using an audio-tape recorder, entered into a Microsoft Word computer program and analyzed manually following a content thematic approach. The study findings show that PWPDs face a multitude of challenges in accessing SRH services including negative attitudes of service providers, long queues at health facilities, distant health facilities, high costs of services involved, unfriendly physical structures and the perception from able-bodied people that PWPDs should be asexual. People with physical disabilities (PWPDs) face health facility-related (service provider and facility-related challenges), economic and societal challenges in accessing SRH services. These findings call for a need to sensitize service providers on SRH needs of PWPDs for better support and for the government to enforce the provision of PWPD-friendly services in all health facilities.

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists

PubMed Central

Visser, Marco D.; McMahon, Sean M.; Merow, Cory; Dixon, Philip M.; Record, Sydne; Jongejans, Eelke

2015-01-01

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research. PMID:25811842

Space-Time Conservation Element and Solution Element Method Being Developed

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung; Himansu, Ananda; Jorgenson, Philip C. E.; Loh, Ching-Yuen; Wang, Xiao-Yen; Yu, Sheng-Tao

1999-01-01

The engineering research and design requirements of today pose great computer-simulation challenges to engineers and scientists who are called on to analyze phenomena in continuum mechanics. The future will bring even more daunting challenges, when increasingly complex phenomena must be analyzed with increased accuracy. Traditionally used numerical simulation methods have evolved to their present state by repeated incremental extensions to broaden their scope. They are reaching the limits of their applicability and will need to be radically revised, at the very least, to meet future simulation challenges. At the NASA Lewis Research Center, researchers have been developing a new numerical framework for solving conservation laws in continuum mechanics, namely, the Space-Time Conservation Element and Solution Element Method, or the CE/SE method. This method has been built from fundamentals and is not a modification of any previously existing method. It has been designed with generality, simplicity, robustness, and accuracy as cornerstones. The CE/SE method has thus far been applied in the fields of computational fluid dynamics, computational aeroacoustics, and computational electromagnetics. Computer programs based on the CE/SE method have been developed for calculating flows in one, two, and three spatial dimensions. Results have been obtained for numerous problems and phenomena, including various shock-tube problems, ZND detonation waves, an implosion and explosion problem, shocks over a forward-facing step, a blast wave discharging from a nozzle, various acoustic waves, and shock/acoustic-wave interactions. The method can clearly resolve shock/acoustic-wave interactions, wherein the difference of the magnitude between the acoustic wave and shock could be up to six orders. In two-dimensional flows, the reflected shock is as crisp as the leading shock. CE/SE schemes are currently being used for advanced applications to jet and fan noise prediction and to chemically reacting flows.

Multi-Strain Deterministic Chaos in Dengue Epidemiology, A Challenge for Computational Mathematics

NASA Astrophysics Data System (ADS)

Aguiar, Maíra; Kooi, Bob W.; Stollenwerk, Nico

2009-09-01

Recently, we have analysed epidemiological models of competing strains of pathogens and hence differences in transmission for first versus secondary infection due to interaction of the strains with previously aquired immunities, as has been described for dengue fever, known as antibody dependent enhancement (ADE). These models show a rich variety of dynamics through bifurcations up to deterministic chaos. Including temporary cross-immunity even enlarges the parameter range of such chaotic attractors, and also gives rise to various coexisting attractors, which are difficult to identify by standard numerical bifurcation programs using continuation methods. A combination of techniques, including classical bifurcation plots and Lyapunov exponent spectra has to be applied in comparison to get further insight into such dynamical structures. Especially, Lyapunov spectra, which quantify the predictability horizon in the epidemiological system, are computationally very demanding. We show ways to speed up computations of such Lyapunov spectra by a factor of more than ten by parallelizing previously used sequential C programs. Such fast computations of Lyapunov spectra will be especially of use in future investigations of seasonally forced versions of the present models, as they are needed for data analysis.

Directed Incremental Symbolic Execution

NASA Technical Reports Server (NTRS)

Person, Suzette; Yang, Guowei; Rungta, Neha; Khurshid, Sarfraz

2011-01-01

The last few years have seen a resurgence of interest in the use of symbolic execution -- a program analysis technique developed more than three decades ago to analyze program execution paths. Scaling symbolic execution and other path-sensitive analysis techniques to large systems remains challenging despite recent algorithmic and technological advances. An alternative to solving the problem of scalability is to reduce the scope of the analysis. One approach that is widely studied in the context of regression analysis is to analyze the differences between two related program versions. While such an approach is intuitive in theory, finding efficient and precise ways to identify program differences, and characterize their effects on how the program executes has proved challenging in practice. In this paper, we present Directed Incremental Symbolic Execution (DiSE), a novel technique for detecting and characterizing the effects of program changes. The novelty of DiSE is to combine the efficiencies of static analysis techniques to compute program difference information with the precision of symbolic execution to explore program execution paths and generate path conditions affected by the differences. DiSE is a complementary technique to other reduction or bounding techniques developed to improve symbolic execution. Furthermore, DiSE does not require analysis results to be carried forward as the software evolves -- only the source code for two related program versions is required. A case-study of our implementation of DiSE illustrates its effectiveness at detecting and characterizing the effects of program changes.

A component-based software environment for visualizing large macromolecular assemblies.

PubMed

Sanner, Michel F

2005-03-01

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Challenges and Opportunities in Interdisciplinary Materials Research Experiences for Undergraduates

NASA Astrophysics Data System (ADS)

Vohra, Yogesh; Nordlund, Thomas

2009-03-01

The University of Alabama at Birmingham (UAB) offer a broad range of interdisciplinary materials research experiences to undergraduate students with diverse backgrounds in physics, chemistry, applied mathematics, and engineering. The research projects offered cover a broad range of topics including high pressure physics, microelectronic materials, nano-materials, laser materials, bioceramics and biopolymers, cell-biomaterials interactions, planetary materials, and computer simulation of materials. The students welcome the opportunity to work with an interdisciplinary team of basic science, engineering, and biomedical faculty but the challenge is in learning the key vocabulary for interdisciplinary collaborations, experimental tools, and working in an independent capacity. The career development workshops dealing with the graduate school application process and the entrepreneurial business activities were found to be most effective. The interdisciplinary university wide poster session helped student broaden their horizons in research careers. The synergy of the REU program with other concurrently running high school summer programs on UAB campus will also be discussed.

Scalability and Validation of Big Data Bioinformatics Software.

PubMed

Yang, Andrian; Troup, Michael; Ho, Joshua W K

2017-01-01

This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs. Nonetheless the surge of volume and variety of biological and biomedical data has posed new challenges. We discuss how modern cloud computing and big data programming frameworks such as MapReduce and Spark are being used to effectively implement divide-and-conquer in a distributed computing environment. Validation of software is another important issue in big data bioinformatics that is often ignored. Software validation is the process of determining whether the program under test fulfils the task for which it was designed. Determining the correctness of the computational output of big data bioinformatics software is especially difficult due to the large input space and complex algorithms involved. We discuss how state-of-the-art software testing techniques that are based on the idea of multiple executions, such as metamorphic testing, can be used to implement an effective bioinformatics quality assurance strategy. We hope this review will raise awareness of these critical issues in bioinformatics.

FastChem: A computer program for efficient complex chemical equilibrium calculations in the neutral/ionized gas phase with applications to stellar and planetary atmospheres

NASA Astrophysics Data System (ADS)

Stock, Joachim W.; Kitzmann, Daniel; Patzer, A. Beate C.; Sedlmayr, Erwin

2018-06-01

For the calculation of complex neutral/ionized gas phase chemical equilibria, we present a semi-analytical versatile and efficient computer program, called FastChem. The applied method is based on the solution of a system of coupled nonlinear (and linear) algebraic equations, namely the law of mass action and the element conservation equations including charge balance, in many variables. Specifically, the system of equations is decomposed into a set of coupled nonlinear equations in one variable each, which are solved analytically whenever feasible to reduce computation time. Notably, the electron density is determined by using the method of Nelder and Mead at low temperatures. The program is written in object-oriented C++ which makes it easy to couple the code with other programs, although a stand-alone version is provided. FastChem can be used in parallel or sequentially and is available under the GNU General Public License version 3 at https://github.com/exoclime/FastChem together with several sample applications. The code has been successfully validated against previous studies and its convergence behavior has been tested even for extreme physical parameter ranges down to 100 K and up to 1000 bar. FastChem converges stable and robust in even most demanding chemical situations, which posed sometimes extreme challenges for previous algorithms.

Internet-based computer technology on radiotherapy.

PubMed

Chow, James C L

2017-01-01

Recent rapid development of Internet-based computer technologies has made possible many novel applications in radiation dose delivery. However, translational speed of applying these new technologies in radiotherapy could hardly catch up due to the complex commissioning process and quality assurance protocol. Implementing novel Internet-based technology in radiotherapy requires corresponding design of algorithm and infrastructure of the application, set up of related clinical policies, purchase and development of software and hardware, computer programming and debugging, and national to international collaboration. Although such implementation processes are time consuming, some recent computer advancements in the radiation dose delivery are still noticeable. In this review, we will present the background and concept of some recent Internet-based computer technologies such as cloud computing, big data processing and machine learning, followed by their potential applications in radiotherapy, such as treatment planning and dose delivery. We will also discuss the current progress of these applications and their impacts on radiotherapy. We will explore and evaluate the expected benefits and challenges in implementation as well.

Programming and Tuning a Quantum Annealing Device to Solve Real World Problems

NASA Astrophysics Data System (ADS)

Perdomo-Ortiz, Alejandro; O'Gorman, Bryan; Fluegemann, Joseph; Smelyanskiy, Vadim

2015-03-01

Solving real-world applications with quantum algorithms requires overcoming several challenges, ranging from translating the computational problem at hand to the quantum-machine language to tuning parameters of the quantum algorithm that have a significant impact on the performance of the device. In this talk, we discuss these challenges, strategies developed to enhance performance, and also a more efficient implementation of several applications. Although we will focus on applications of interest to NASA's Quantum Artificial Intelligence Laboratory, the methods and concepts presented here apply to a broader family of hard discrete optimization problems, including those that occur in many machine-learning algorithms.

"Finding my own time": examining the spatially produced experiences of rural RNs in the rural nursing certificate program.

PubMed

Place, Jessica; MacLeod, Martha; John, Norma; Adamack, Monica; Lindsey, A Elizabeth

2012-07-01

Rural nurses require access to education that exposes them to the most up-to-date information and skill development. However, since most education opportunities are located in urban centers and focused on providing skills to urban nurses, geography effectively acts as a barrier to accessing education that meets the needs of rural nurses. The Rural Nursing Certificate Program is a post-basic education program that addresses these concerns by providing rural-relevant content online, with limited campus sessions. Does online delivery of rural nursing curriculum overcome challenges related to geography? This study employed surveys with some open-ended questions. Analysis included descriptive statistics and content analysis. Students reported that online delivery improved access. Benefits included not having to relocate; being able to continue working; and, flexibility. Challenges included travel for practical experiences and time management related to staffing shortages, personal-professional overlap and family responsibilities. Online learning improved access to nursing education. However, the realities of rural nursing made it impossible to completely overcome geography: sense of obligation to work overtime, cost and time of traveling to workshops and practicums, uneven access to the Internet and computer services, and distance from peer and university support remained challenges. Copyright © 2011 Elsevier Ltd. All rights reserved.

Challenges facing the development of the Arabic chatbot

NASA Astrophysics Data System (ADS)

AlHagbani, Eman Saad; Khan, Muhammad Badruddin

2016-07-01

The future information systems are expected to be more intelligent and will take human queries in natural language as input and answer them promptly. To develop a chatbot or a computer program that can chat with humans in realistic manner to extent that human get impressions that he/she is talking with other human is a challenging task. To make such chatbots, different technologies will work together ranging from artificial intelligence to development of semantic resources. Sophisticated chatbots are developed to perform conversation in number of languages. Arabic chatbots can be helpful in automating many operations and serve people who only know Arabic language. However, the technology for Arabic language is still in its infancy stage due to some challenges surrounding the Arabic language. This paper offers an overview of the chatbot application and the several obstacles and challenges that need to be resolved to develop an effective Arabic chatbot.

Adaptation and Feasibility Study of a Digital Health Program to Prevent Diabetes among Low-Income Patients: Results from a Partnership between a Digital Health Company and an Academic Research Team

PubMed Central

McDermott, Kelly; Tieu, Lina; Rios, Christina; Gibson, Eliza; Sweet, Cynthia Castro; Payne, Mike

2016-01-01

Background. The feasibility of digital health programs to prevent and manage diabetes in low-income patients has not been adequately explored. Methods. Researchers collaborated with a digital health company to adapt a diabetes prevention program for low-income prediabetes patients at a large safety net clinic. We conducted focus groups to assess patient perspectives, revised lessons for improved readability and cultural relevance to low-income and Hispanic patients, conducted a feasibility study of the adapted program in English and Spanish speaking cohorts, and implemented real-time adaptations to the program for commercial use and for a larger trial of in multiple safety net clinics. Results. The majority of focus group participants were receptive to the program. We modified the curriculum to a 5th-grade reading level and adapted content based on patient feedback. In the feasibility study, 54% of eligible contacted patients expressed interest in enrolling (n = 23). Although some participants' computer access and literacy made registration challenging, they were highly satisfied and engaged (80% logged in at least once/week). Conclusions. Underserved prediabetic patients displayed high engagement and satisfaction with a digital diabetes prevention program despite lower digital literacy skills. The collaboration between researchers and a digital health company enabled iterative improvements in technology implementation to address challenges in low-income populations. PMID:27868070

Progress and challenges in bioinformatics approaches for enhancer identification

PubMed Central

Kleftogiannis, Dimitrios; Kalnis, Panos

2016-01-01

Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration. PMID:26634919

Recent advances at NASA in calculating the electronic spectra of diatomic molecules

NASA Technical Reports Server (NTRS)

Whiting, Ellis E.; Paterson, John A.

1988-01-01

Advanced entry vehicles, such as the proposed Aero-assisted Orbital Transfer Vehicle, provide new and challenging problems for spectroscopy. Large portions of the flow field about such vehicles will be characterized by chemical and thermal nonequilibrium. Only by considering the actual overlap of the atomic and rotational lines emitted by the species present can the impact of radiative transport within the flow field be assessed correctly. To help make such an assessment, a new computer program is described that can generate high-resolution, line-by-line spectra for any spin-allowed transitions in diatomic molecules. The program includes the matrix elements for the rotational energy and distortion to the fourth order; the spin-orbit, spin-spin, and spin-rotation interactions to first order; and the lambda splitting by a perturbation calculation. An overview of the Computational Chemistry Branch at Ames Research Center is also presented.

Analytical modeling of helicopter static and dynamic induced velocity in GRASP

NASA Technical Reports Server (NTRS)

Kunz, Donald L.; Hodges, Dewey H.

1987-01-01

The methodology used by the General Rotorcraft Aeromechanical Stability Program (GRASP) to model the characteristics of the flow through a helicopter rotor in hovering or axial flight is described. Since the induced flow plays a significant role in determining the aeroelastic properties of rotorcraft, the computation of the induced flow is an important aspect of the program. Because of the combined finite-element/multibody methodology used as the basis for GRASP, the implementation of induced velocity calculations presented an unusual challenge to the developers. To preserve the modelling flexibility and generality of the code, it was necessary to depart from the traditional methods of computing the induced velocity. This is accomplished by calculating the actuator disc contributions to the rotor loads in a separate element called the air mass element, and then performing the calculations of the aerodynamic forces on individual blade elements within the aeroelastic beam element.

DARPA-funded efforts in the development of novel brain-computer interface technologies.

PubMed

Miranda, Robbin A; Casebeer, William D; Hein, Amy M; Judy, Jack W; Krotkov, Eric P; Laabs, Tracy L; Manzo, Justin E; Pankratz, Kent G; Pratt, Gill A; Sanchez, Justin C; Weber, Douglas J; Wheeler, Tracey L; Ling, Geoffrey S F

2015-04-15

The Defense Advanced Research Projects Agency (DARPA) has funded innovative scientific research and technology developments in the field of brain-computer interfaces (BCI) since the 1970s. This review highlights some of DARPA's major advances in the field of BCI, particularly those made in recent years. Two broad categories of DARPA programs are presented with respect to the ultimate goals of supporting the nation's warfighters: (1) BCI efforts aimed at restoring neural and/or behavioral function, and (2) BCI efforts aimed at improving human training and performance. The programs discussed are synergistic and complementary to one another, and, moreover, promote interdisciplinary collaborations among researchers, engineers, and clinicians. Finally, this review includes a summary of some of the remaining challenges for the field of BCI, as well as the goals of new DARPA efforts in this domain. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

The Effect of Interchanging the Polarity of the Dense Plasma Focus on Neutron Yield

NASA Astrophysics Data System (ADS)

Jiang, Sheng; Higginson, Drew; Link, Anthony; Schmidt, Andrea

2017-10-01

The dense plasma focus (DPF) Z-pinch devices can serve as portable neutron sources when deuterium is used as the filling gas. DPF devices are normally operated with the inner electrode as the anode. It has been found that interchanging the polarity of the electrodes can cause orders of magnitude decrease in the neutron yield. Here we use the particle-in-cell (PIC) code LSP to model a DPF with both polarities. We have found the difference in the shape of the sheath, the voltage and current traces, and the electric and magnetic fields in the pinch region due to different polarities. A detailed comparison will be presented. Prepared by LLNL under Contract DE-AC52-07NA27344 and supported by the Laboratory Directed Research and Development Program (15-ERD-034) at LLNL. Computing support for this work came from the LLNL Institutional Computing Grand Challenge program.

Mobile, Cloud, and Big Data Computing: Contributions, Challenges, and New Directions in Telecardiology

PubMed Central

Hsieh, Jui-Chien; Li, Ai-Hsien; Yang, Chung-Chi

2013-01-01

Many studies have indicated that computing technology can enable off-site cardiologists to read patients’ electrocardiograph (ECG), echocardiography (ECHO), and relevant images via smart phones during pre-hospital, in-hospital, and post-hospital teleconsultation, which not only identifies emergency cases in need of immediate treatment, but also prevents the unnecessary re-hospitalizations. Meanwhile, several studies have combined cloud computing and mobile computing to facilitate better storage, delivery, retrieval, and management of medical files for telecardiology. In the future, the aggregated ECG and images from hospitals worldwide will become big data, which should be used to develop an e-consultation program helping on-site practitioners deliver appropriate treatment. With information technology, real-time tele-consultation and tele-diagnosis of ECG and images can be practiced via an e-platform for clinical, research, and educational purposes. While being devoted to promote the application of information technology onto telecardiology, we need to resolve several issues: (1) data confidentiality in the cloud, (2) data interoperability among hospitals, and (3) network latency and accessibility. If these challenges are overcome, tele-consultation will be ubiquitous, easy to perform, inexpensive, and beneficial. Most importantly, these services will increase global collaboration and advance clinical practice, education, and scientific research in cardiology. PMID:24232290

Information science and technology developments within the National Biological Information Infrastructure

USGS Publications Warehouse

Frame, M.T.; Cotter, G.; Zolly, L.; Little, J.

2002-01-01

Whether your vantage point is that of an office window or a national park, your view undoubtedly encompasses a rich diversity of life forms, all carefully studied or managed by some scientist, resource manager, or planner. A few simple calculations - the number of species, their interrelationships, and the many researchers studying them - and you can easily see the tremendous challenges that the resulting biological data presents to the information and computer science communities. Biological information varies in format and content: it may pertain to a particular species or an entire ecosystem; it can contain land use characteristics, and geospatially referenced information. The complexity and uniqueness of each individual species or ecosystem do not easily lend themselves to today's computer science tools and applications. To address the challenges that the biological enterprise presents, the National Biological Information Infrastructure (NBII) (http://www.nbii.gov) was established in 1993 on the recommendation of the National Research Council (National Research Council 1993). The NBII is designed to address these issues on a national scale, and through international partnerships. This paper discusses current information and computer science efforts within the National Biological Information Infrastructure Program, and future computer science research endeavors that are needed to address the ever-growing issues related to our nation's biological concerns. ?? 2003 by The Haworth Press, Inc. All rights reserved.

Computational Aspects of Data Assimilation and the ESMF

NASA Technical Reports Server (NTRS)

daSilva, A.

2003-01-01

The scientific challenge of developing advanced data assimilation applications is a daunting task. Independently developed components may have incompatible interfaces or may be written in different computer languages. The high-performance computer (HPC) platforms required by numerically intensive Earth system applications are complex, varied, rapidly evolving and multi-part systems themselves. Since the market for high-end platforms is relatively small, there is little robust middleware available to buffer the modeler from the difficulties of HPC programming. To complicate matters further, the collaborations required to develop large Earth system applications often span initiatives, institutions and agencies, involve geoscience, software engineering, and computer science communities, and cross national borders.The Earth System Modeling Framework (ESMF) project is a concerted response to these challenges. Its goal is to increase software reuse, interoperability, ease of use and performance in Earth system models through the use of a common software framework, developed in an open manner by leaders in the modeling community. The ESMF addresses the technical and to some extent the cultural - aspects of Earth system modeling, laying the groundwork for addressing the more difficult scientific aspects, such as the physical compatibility of components, in the future. In this talk we will discuss the general philosophy and architecture of the ESMF, focussing on those capabilities useful for developing advanced data assimilation applications.

A New Biogeochemical Computational Framework Integrated within the Community Land Model

NASA Astrophysics Data System (ADS)

Fang, Y.; Li, H.; Liu, C.; Huang, M.; Leung, L.

2012-12-01

Terrestrial biogeochemical processes, particularly carbon cycle dynamics, have been shown to significantly influence regional and global climate changes. Modeling terrestrial biogeochemical processes within the land component of Earth System Models such as the Community Land model (CLM), however, faces three major challenges: 1) extensive efforts in modifying modeling structures and rewriting computer programs to incorporate biogeochemical processes with increasing complexity, 2) expensive computational cost to solve the governing equations due to numerical stiffness inherited from large variations in the rates of biogeochemical processes, and 3) lack of an efficient framework to systematically evaluate various mathematical representations of biogeochemical processes. To address these challenges, we introduce a new computational framework to incorporate biogeochemical processes into CLM, which consists of a new biogeochemical module with a generic algorithm and reaction database. New and updated biogeochemical processes can be incorporated into CLM without significant code modification. To address the stiffness issue, algorithms and criteria will be developed to identify fast processes, which will be replaced with algebraic equations and decoupled from slow processes. This framework can serve as a generic and user-friendly platform to test out different mechanistic process representations and datasets and gain new insight on the behavior of the terrestrial ecosystems in response to climate change in a systematic way.

Mobile, cloud, and big data computing: contributions, challenges, and new directions in telecardiology.

PubMed

Hsieh, Jui-Chien; Li, Ai-Hsien; Yang, Chung-Chi

2013-11-13

Many studies have indicated that computing technology can enable off-site cardiologists to read patients' electrocardiograph (ECG), echocardiography (ECHO), and relevant images via smart phones during pre-hospital, in-hospital, and post-hospital teleconsultation, which not only identifies emergency cases in need of immediate treatment, but also prevents the unnecessary re-hospitalizations. Meanwhile, several studies have combined cloud computing and mobile computing to facilitate better storage, delivery, retrieval, and management of medical files for telecardiology. In the future, the aggregated ECG and images from hospitals worldwide will become big data, which should be used to develop an e-consultation program helping on-site practitioners deliver appropriate treatment. With information technology, real-time tele-consultation and tele-diagnosis of ECG and images can be practiced via an e-platform for clinical, research, and educational purposes. While being devoted to promote the application of information technology onto telecardiology, we need to resolve several issues: (1) data confidentiality in the cloud, (2) data interoperability among hospitals, and (3) network latency and accessibility. If these challenges are overcome, tele-consultation will be ubiquitous, easy to perform, inexpensive, and beneficial. Most importantly, these services will increase global collaboration and advance clinical practice, education, and scientific research in cardiology.

Mining Videos for Features that Drive Attention

DTIC Science & Technology

2015-04-01

Psychology & Neuroscience Graduate Program, University of Southern California, 3641 Watt Way, HNB 10, Los Angeles, CA 90089, USA e-mail: itti@usc.edu...challenging question in neuroscience . Since the onset of visual experience, a human or animal begins to form a subjective percept which, depending on...been added based on neuroscience discoveries of mechanisms of vision in the brain as well as useful features based on computer vision. Figure14.1 illus

The Future: Challenges and Opportunities for Air War College.

DTIC Science & Technology

1990-04-01

for commuters and other travel.(155:l; 2:--; 42:748; 125:--; 47:31) Magnetically levitating ( maglev ) trains were developed 20 years ago, and reach...These trains began operation in Japan and France in the 1970s. Page 132 Florida is considering using a maglev system for train connections among Miami...Ballistic Missile Maglev : Magnetic Levitation MPC/DPMYI: Air Force Military Personnel Center, Directorate of Plans. Programs and Analysis, Computer Support

The 1987 RIACS annual report

NASA Technical Reports Server (NTRS)

1987-01-01

The Research Institute for Advanced Computer Science (RIACS) was established at the NASA Ames Research Center in June of 1983. RIACS is privately operated by the Universities Space Research Association (USRA), a consortium of 64 universities with graduate programs in the aerospace sciences, under several Cooperative Agreements with NASA. RIACS's goal is to provide preeminent leadership in basic and applied computer science research as partners in support of NASA's goals and missions. In pursuit of this goal, RIACS contributes to several of the grand challenges in science and engineering facing NASA: flying an airplane inside a computer; determining the chemical properties of materials under hostile conditions in the atmospheres of earth and the planets; sending intelligent machines on unmanned space missions; creating a one-world network that makes all scientific resources, including those in space, accessible to all the world's scientists; providing intelligent computational support to all stages of the process of scientific investigation from problem formulation to results dissemination; and developing accurate global models for climatic behavior throughout the world. In working with these challenges, we seek novel architectures, and novel ways to use them, that exploit the potential of parallel and distributed computation and make possible new functions that are beyond the current reach of computing machines. The investigation includes pattern computers as well as the more familiar numeric and symbolic computers, and it includes networked systems of resources distributed around the world. We believe that successful computer science research is interdisciplinary: it is driven by (and drives) important problems in other disciplines. We believe that research should be guided by a clear long-term vision with planned milestones. And we believe that our environment must foster and exploit innovation. Our activities and accomplishments for the calendar year 1987 and our plans for 1988 are reported.

SCEAPI: A unified Restful Web API for High-Performance Computing

NASA Astrophysics Data System (ADS)

Rongqiang, Cao; Haili, Xiao; Shasha, Lu; Yining, Zhao; Xiaoning, Wang; Xuebin, Chi

2017-10-01

The development of scientific computing is increasingly moving to collaborative web and mobile applications. All these applications need high-quality programming interface for accessing heterogeneous computing resources consisting of clusters, grid computing or cloud computing. In this paper, we introduce our high-performance computing environment that integrates computing resources from 16 HPC centers across China. Then we present a bundle of web services called SCEAPI and describe how it can be used to access HPC resources with HTTP or HTTPs protocols. We discuss SCEAPI from several aspects including architecture, implementation and security, and address specific challenges in designing compatible interfaces and protecting sensitive data. We describe the functions of SCEAPI including authentication, file transfer and job management for creating, submitting and monitoring, and how to use SCEAPI in an easy-to-use way. Finally, we discuss how to exploit more HPC resources quickly for the ATLAS experiment by implementing the custom ARC compute element based on SCEAPI, and our work shows that SCEAPI is an easy-to-use and effective solution to extend opportunistic HPC resources.

Applied Mathematics at the U.S. Department of Energy: Past, Present and a View to the Future

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

Brown, D L; Bell, J; Estep, D

2008-02-15

Over the past half-century, the Applied Mathematics program in the U.S. Department of Energy's Office of Advanced Scientific Computing Research has made significant, enduring advances in applied mathematics that have been essential enablers of modern computational science. Motivated by the scientific needs of the Department of Energy and its predecessors, advances have been made in mathematical modeling, numerical analysis of differential equations, optimization theory, mesh generation for complex geometries, adaptive algorithms and other important mathematical areas. High-performance mathematical software libraries developed through this program have contributed as much or more to the performance of modern scientific computer codes as themore » high-performance computers on which these codes run. The combination of these mathematical advances and the resulting software has enabled high-performance computers to be used for scientific discovery in ways that could only be imagined at the program's inception. Our nation, and indeed our world, face great challenges that must be addressed in coming years, and many of these will be addressed through the development of scientific understanding and engineering advances yet to be discovered. The U.S. Department of Energy (DOE) will play an essential role in providing science-based solutions to many of these problems, particularly those that involve the energy, environmental and national security needs of the country. As the capability of high-performance computers continues to increase, the types of questions that can be answered by applying this huge computational power become more varied and more complex. It will be essential that we find new ways to develop and apply the mathematics necessary to enable the new scientific and engineering discoveries that are needed. In August 2007, a panel of experts in applied, computational and statistical mathematics met for a day and a half in Berkeley, California to understand the mathematical developments required to meet the future science and engineering needs of the DOE. It is important to emphasize that the panelists were not asked to speculate only on advances that might be made in their own research specialties. Instead, the guidance this panel was given was to consider the broad science and engineering challenges that the DOE faces and identify the corresponding advances that must occur across the field of mathematics for these challenges to be successfully addressed. As preparation for the meeting, each panelist was asked to review strategic planning and other informational documents available for one or more of the DOE Program Offices, including the Offices of Science, Nuclear Energy, Fossil Energy, Environmental Management, Legacy Management, Energy Efficiency & Renewable Energy, Electricity Delivery & Energy Reliability and Civilian Radioactive Waste Management as well as the National Nuclear Security Administration. The panelists reported on science and engineering needs for each of these offices, and then discussed and identified mathematical advances that will be required if these challenges are to be met. A review of DOE challenges in energy, the environment and national security brings to light a broad and varied array of questions that the DOE must answer in the coming years. A representative subset of such questions includes: (1) Can we predict the operating characteristics of a clean coal power plant? (2) How stable is the plasma containment in a tokamak? (3) How quickly is climate change occurring and what are the uncertainties in the predicted time scales? (4) How quickly can an introduced bio-weapon contaminate the agricultural environment in the US? (5) How do we modify models of the atmosphere and clouds to incorporate newly collected data of possibly of new types? (6) How quickly can the United States recover if part of the power grid became inoperable? (7) What are optimal locations and communication protocols for sensing devices in a remote-sensing network? (8) How can new materials be designed with a specified desirable set of properties? In comparing and contrasting these and other questions of importance to DOE, the panel found that while the scientific breadth of the requirements is enormous, a central theme emerges: Scientists are being asked to identify or provide technology, or to give expert analysis to inform policy-makers that requires the scientific understanding of increasingly complex physical and engineered systems. In addition, as the complexity of the systems of interest increases, neither experimental observation nor mathematical and computational modeling alone can access all components of the system over the entire range of scales or conditions needed to provide the required scientific understanding.« less

Beyond the Renderer: Software Architecture for Parallel Graphics and Visualization

NASA Technical Reports Server (NTRS)

Crockett, Thomas W.

1996-01-01

As numerous implementations have demonstrated, software-based parallel rendering is an effective way to obtain the needed computational power for a variety of challenging applications in computer graphics and scientific visualization. To fully realize their potential, however, parallel renderers need to be integrated into a complete environment for generating, manipulating, and delivering visual data. We examine the structure and components of such an environment, including the programming and user interfaces, rendering engines, and image delivery systems. We consider some of the constraints imposed by real-world applications and discuss the problems and issues involved in bringing parallel rendering out of the lab and into production.

Using RxNorm for cross-institutional formulary data normalization within a distributed grid-computing environment.

PubMed

Wynden, Rob; Anderson, Nick; Casale, Marco; Lakshminarayanan, Prakash; Anderson, Kent; Prosser, Justin; Errecart, Larry; Livshits, Alice; Thimman, Tim; Weiner, Mark

2011-01-01

Within the CTSA (Clinical Translational Sciences Awards) program, academic medical centers are tasked with the storage of clinical formulary data within an Integrated Data Repository (IDR) and the subsequent exposure of that data over grid computing environments for hypothesis generation and cohort selection. Formulary data collected over long periods of time across multiple institutions requires normalization of terms before those data sets can be aggregated and compared. This paper sets forth a solution to the challenge of generating derived aggregated normalized views from large, distributed data sets of clinical formulary data intended for re-use within clinical translational research.

Finding Tropical Cyclones on a Cloud Computing Cluster: Using Parallel Virtualization for Large-Scale Climate Simulation Analysis

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

Hasenkamp, Daren; Sim, Alexander; Wehner, Michael

Extensive computing power has been used to tackle issues such as climate changes, fusion energy, and other pressing scientific challenges. These computations produce a tremendous amount of data; however, many of the data analysis programs currently only run a single processor. In this work, we explore the possibility of using the emerging cloud computing platform to parallelize such sequential data analysis tasks. As a proof of concept, we wrap a program for analyzing trends of tropical cyclones in a set of virtual machines (VMs). This approach allows the user to keep their familiar data analysis environment in the VMs, whilemore » we provide the coordination and data transfer services to ensure the necessary input and output are directed to the desired locations. This work extensively exercises the networking capability of the cloud computing systems and has revealed a number of weaknesses in the current cloud system software. In our tests, we are able to scale the parallel data analysis job to a modest number of VMs and achieve a speedup that is comparable to running the same analysis task using MPI. However, compared to MPI based parallelization, the cloud-based approach has a number of advantages. The cloud-based approach is more flexible because the VMs can capture arbitrary software dependencies without requiring the user to rewrite their programs. The cloud-based approach is also more resilient to failure; as long as a single VM is running, it can make progress while as soon as one MPI node fails the whole analysis job fails. In short, this initial work demonstrates that a cloud computing system is a viable platform for distributed scientific data analyses traditionally conducted on dedicated supercomputing systems.« less

Using Python as a first programming environment for computational physics in developing countries

NASA Astrophysics Data System (ADS)

Akpojotor, Godfrey; Ehwerhemuepha, Louis; Echenim, Myron; Akpojotor, Famous

2011-03-01

Python unique features such its interpretative, multiplatform and object oriented nature as well as being a free and open source software creates the possibility that any user connected to the internet can download the entire package into any platform, install it and immediately begin to use it. Thus Python is gaining reputation as a preferred environment for introducing students and new beginners to programming. Therefore in Africa, the Python African Tour project has been launched and we are coordinating its use in computational science. We examine here the challenges and prospects of using Python for computational physics (CP) education in developing countries (DC). Then we present our project on using Python to simulate and aid the learning of laboratory experiments illustrated here by modeling of the simple pendulum and also to visualize phenomena in physics illustrated here by demonstrating the wave motion of a particle in a varying potential. This project which is to train both the teachers and our students on CP using Python can easily be adopted in other DC.

Verification of Electromagnetic Physics Models for Parallel Computing Architectures in the GeantV Project

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

Amadio, G.; et al.

An intensive R&D and programming effort is required to accomplish new challenges posed by future experimental high-energy particle physics (HEP) programs. The GeantV project aims to narrow the gap between the performance of the existing HEP detector simulation software and the ideal performance achievable, exploiting latest advances in computing technology. The project has developed a particle detector simulation prototype capable of transporting in parallel particles in complex geometries exploiting instruction level microparallelism (SIMD and SIMT), task-level parallelism (multithreading) and high-level parallelism (MPI), leveraging both the multi-core and the many-core opportunities. We present preliminary verification results concerning the electromagnetic (EM) physicsmore » models developed for parallel computing architectures within the GeantV project. In order to exploit the potential of vectorization and accelerators and to make the physics model effectively parallelizable, advanced sampling techniques have been implemented and tested. In this paper we introduce a set of automated statistical tests in order to verify the vectorized models by checking their consistency with the corresponding Geant4 models and to validate them against experimental data.« less

Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach

PubMed Central

Cheung, Mike W.-L.; Jak, Suzanne

2016-01-01

Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists—and probably the most crucial one—is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study. PMID:27242639

Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach.

PubMed

Cheung, Mike W-L; Jak, Suzanne

2016-01-01

Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists-and probably the most crucial one-is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

A Combination of Hand-held Models and Computer Imaging Programs Helps Students Answer Oral Questions about Molecular Structure and Function: A Controlled Investigation of Student Learning

PubMed Central

Peck, Ronald F.; Colton, Shannon; Morris, Jennifer; Chaibub Neto, Elias; Kallio, Julie

2009-01-01

We conducted a controlled investigation to examine whether a combination of computer imagery and tactile tools helps introductory cell biology laboratory undergraduate students better learn about protein structure/function relationships as compared with computer imagery alone. In all five laboratory sections, students used the molecular imaging program, Protein Explorer (PE). In the three experimental sections, three-dimensional physical models were made available to the students, in addition to PE. Student learning was assessed via oral and written research summaries and videotaped interviews. Differences between the experimental and control group students were not found in our typical course assessments such as research papers, but rather were revealed during one-on-one interviews with students at the end of the semester. A subset of students in the experimental group produced superior answers to some higher-order interview questions as compared with students in the control group. During the interview, students in both groups preferred to use either the hand-held models alone or in combination with the PE imaging program. Students typically did not use any tools when answering knowledge (lower-level thinking) questions, but when challenged with higher-level thinking questions, students in both the control and experimental groups elected to use the models. PMID:19255134

Heterogeneous computing architecture for fast detection of SNP-SNP interactions.

PubMed

Sluga, Davor; Curk, Tomaz; Zupan, Blaz; Lotric, Uros

2014-06-25

The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort. General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems.

Heterogeneous computing architecture for fast detection of SNP-SNP interactions

PubMed Central

2014-01-01

Background The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. Results We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort. Conclusions General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems. PMID:24964802

Water Exploration: An Online High School Water Resource Education Program

NASA Astrophysics Data System (ADS)

Ellins, K. K.; McCall, L. R.; Amos, S.; McGowan, R. F.; Mote, A.; Negrito, K.; Paloski, B.; Ryan, C.; Cameron, B.

2010-12-01

The Institute for Geophysics at The University of Texas at Austin and 4empowerment.com, a Texas-based for-profit educational enterprise, teamed up with the Texas Water Development Board to develop and implement a Web-based water resources education program for Texas high school students. The program, Water Exploration uses a project-based learning approach called the Legacy Cycle model to permit students to conduct research and build an understanding about water science and critical water-related issues, using the Internet and computer technology. The three Legacy Cycle modules in the Water Exploration curriculum are: Water Basics, Water-Earth Dynamics and People Need Water. Within each Legacy Cycle there are three different challenges, or instructional modules, laid out as projects with clearly stated goals for students to carry out. Each challenge address themes that map to the water-related “Big Ideas” and supporting concepts found in the new Earth Science Literacy Principles: The Big Ideas and Supporting Concepts of Earth Science. As students work through a challenge they follow a series of steps, each of which is associated (i.e., linked online) with a manageable number of corresponding, high quality, research-based learning activities and Internet resources, including scholarly articles, cyber tools, and visualizations intended to enhance understanding of the concepts presented. The culmination of each challenge is a set of “Go Public” products that are the students’ answers to the challenge and which serve as the final assessment for the challenge. The “Go Public” products are posted to a collaborative workspace on the Internet as the “legacy” of the students’ work, thereby allowing subsequent groups of students who take the challenge to add new products. Twenty-two science educators have been trained on the implementation of the Water Exploration curriculum. A graduate student pursuing a master’s degree in science education through The University of Texas’ UTEACH program is conducting research to track the teachers’ implementation of Water Exploration and assess their comfort with cyber-education through classroom observations, students and teacher surveys, and evaluation of students’ “Go Public” products.

Decision support methods for the detection of adverse events in post-marketing data.

PubMed

Hauben, M; Bate, A

2009-04-01

Spontaneous reporting is a crucial component of post-marketing drug safety surveillance despite its significant limitations. The size and complexity of some spontaneous reporting system databases represent a challenge for drug safety professionals who traditionally have relied heavily on the scientific and clinical acumen of the prepared mind. Computer algorithms that calculate statistical measures of reporting frequency for huge numbers of drug-event combinations are increasingly used to support pharamcovigilance analysts screening large spontaneous reporting system databases. After an overview of pharmacovigilance and spontaneous reporting systems, we discuss the theory and application of contemporary computer algorithms in regular use, those under development, and the practical considerations involved in the implementation of computer algorithms within a comprehensive and holistic drug safety signal detection program.

Rational, computer-enabled peptide drug design: principles, methods, applications and future directions.

PubMed

Diller, David J; Swanson, Jon; Bayden, Alexander S; Jarosinski, Mark; Audie, Joseph

2015-01-01

Peptides provide promising templates for developing drugs to occupy a middle space between small molecules and antibodies and for targeting 'undruggable' intracellular protein-protein interactions. Importantly, rational or in cerebro design, especially when coupled with validated in silico tools, can be used to efficiently explore chemical space and identify islands of 'drug-like' peptides to satisfy diverse drug discovery program objectives. Here, we consider the underlying principles of and recent advances in rational, computer-enabled peptide drug design. In particular, we consider the impact of basic physicochemical properties, potency and ADME/Tox opportunities and challenges, and recently developed computational tools for enabling rational peptide drug design. Key principles and practices are spotlighted by recent case studies. We close with a hypothetical future case study.

Template Interfaces for Agile Parallel Data-Intensive Science

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

Ramakrishnan, Lavanya; Gunter, Daniel; Pastorello, Gilerto Z.

Tigres provides a programming library to compose and execute large-scale data-intensive scientific workflows from desktops to supercomputers. DOE User Facilities and large science collaborations are increasingly generating large enough data sets that it is no longer practical to download them to a desktop to operate on them. They are instead stored at centralized compute and storage resources such as high performance computing (HPC) centers. Analysis of this data requires an ability to run on these facilities, but with current technologies, scaling an analysis to an HPC center and to a large data set is difficult even for experts. Tigres ismore » addressing the challenge of enabling collaborative analysis of DOE Science data through a new concept of reusable "templates" that enable scientists to easily compose, run and manage collaborative computational tasks. These templates define common computation patterns used in analyzing a data set.« less

Educating the next generation of explorers at an historically Black University

NASA Astrophysics Data System (ADS)

Chaudhury, S.; Rodriguez, W. J.

2003-04-01

This paper describes the development of an innovative undergraduate research training model based at an Historically Black University in the USA that involves students with majors in diverse scientific disciplines in authentic Earth Systems Science research. Educating those who will be the next generation of explorers of earth and space poses several challenges at smaller academic institutions that might lack dedicated resources for this area of study. Over a 5-year span, Norfolk State University has been developing a program that has afforded the opportunity for students majoring in biology, chemistry, mathematics, computer science, physics, engineering and science education to work collaboratively in teams on research projects that emphasize the use of scientific visualization in studying the environment. Recently, a hands-on component has been added through partnerships with local K-12 school teachers in data collection and reporting for the GLOBE Program (GLobal Observations to Benefit the Environment). The successes and challenges of this program along with some innovative uses of technology to promote inquiry learning will be presented in this paper.

Mastering the game of Go with deep neural networks and tree search

NASA Astrophysics Data System (ADS)

Silver, David; Huang, Aja; Maddison, Chris J.; Guez, Arthur; Sifre, Laurent; van den Driessche, George; Schrittwieser, Julian; Antonoglou, Ioannis; Panneershelvam, Veda; Lanctot, Marc; Dieleman, Sander; Grewe, Dominik; Nham, John; Kalchbrenner, Nal; Sutskever, Ilya; Lillicrap, Timothy; Leach, Madeleine; Kavukcuoglu, Koray; Graepel, Thore; Hassabis, Demis

2016-01-01

The game of Go has long been viewed as the most challenging of classic games for artificial intelligence owing to its enormous search space and the difficulty of evaluating board positions and moves. Here we introduce a new approach to computer Go that uses ‘value networks’ to evaluate board positions and ‘policy networks’ to select moves. These deep neural networks are trained by a novel combination of supervised learning from human expert games, and reinforcement learning from games of self-play. Without any lookahead search, the neural networks play Go at the level of state-of-the-art Monte Carlo tree search programs that simulate thousands of random games of self-play. We also introduce a new search algorithm that combines Monte Carlo simulation with value and policy networks. Using this search algorithm, our program AlphaGo achieved a 99.8% winning rate against other Go programs, and defeated the human European Go champion by 5 games to 0. This is the first time that a computer program has defeated a human professional player in the full-sized game of Go, a feat previously thought to be at least a decade away.

Mastering the game of Go with deep neural networks and tree search.

PubMed

Silver, David; Huang, Aja; Maddison, Chris J; Guez, Arthur; Sifre, Laurent; van den Driessche, George; Schrittwieser, Julian; Antonoglou, Ioannis; Panneershelvam, Veda; Lanctot, Marc; Dieleman, Sander; Grewe, Dominik; Nham, John; Kalchbrenner, Nal; Sutskever, Ilya; Lillicrap, Timothy; Leach, Madeleine; Kavukcuoglu, Koray; Graepel, Thore; Hassabis, Demis

2016-01-28

The game of Go has long been viewed as the most challenging of classic games for artificial intelligence owing to its enormous search space and the difficulty of evaluating board positions and moves. Here we introduce a new approach to computer Go that uses 'value networks' to evaluate board positions and 'policy networks' to select moves. These deep neural networks are trained by a novel combination of supervised learning from human expert games, and reinforcement learning from games of self-play. Without any lookahead search, the neural networks play Go at the level of state-of-the-art Monte Carlo tree search programs that simulate thousands of random games of self-play. We also introduce a new search algorithm that combines Monte Carlo simulation with value and policy networks. Using this search algorithm, our program AlphaGo achieved a 99.8% winning rate against other Go programs, and defeated the human European Go champion by 5 games to 0. This is the first time that a computer program has defeated a human professional player in the full-sized game of Go, a feat previously thought to be at least a decade away.

Binary Image Classification: A Genetic Programming Approach to the Problem of Limited Training Instances.

PubMed

Al-Sahaf, Harith; Zhang, Mengjie; Johnston, Mark

2016-01-01

In the computer vision and pattern recognition fields, image classification represents an important yet difficult task. It is a challenge to build effective computer models to replicate the remarkable ability of the human visual system, which relies on only one or a few instances to learn a completely new class or an object of a class. Recently we proposed two genetic programming (GP) methods, one-shot GP and compound-GP, that aim to evolve a program for the task of binary classification in images. The two methods are designed to use only one or a few instances per class to evolve the model. In this study, we investigate these two methods in terms of performance, robustness, and complexity of the evolved programs. We use ten data sets that vary in difficulty to evaluate these two methods. We also compare them with two other GP and six non-GP methods. The results show that one-shot GP and compound-GP outperform or achieve results comparable to competitor methods. Moreover, the features extracted by these two methods improve the performance of other classifiers with handcrafted features and those extracted by a recently developed GP-based method in most cases.

Institute for scientific computing research;fiscal year 1999 annual report

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

Keyes, D

2000-03-28

Large-scale scientific computation, and all of the disciplines that support it and help to validate it, have been placed at the focus of Lawrence Livermore National Laboratory by the Accelerated Strategic Computing Initiative (ASCI). The Laboratory operates the computer with the highest peak performance in the world and has undertaken some of the largest and most compute-intensive simulations ever performed. Computers at the architectural extremes, however, are notoriously difficult to use efficiently. Even such successes as the Laboratory's two Bell Prizes awarded in November 1999 only emphasize the need for much better ways of interacting with the results of large-scalemore » simulations. Advances in scientific computing research have, therefore, never been more vital to the core missions of the Laboratory than at present. Computational science is evolving so rapidly along every one of its research fronts that to remain on the leading edge, the Laboratory must engage researchers at many academic centers of excellence. In FY 1999, the Institute for Scientific Computing Research (ISCR) has expanded the Laboratory's bridge to the academic community in the form of collaborative subcontracts, visiting faculty, student internships, a workshop, and a very active seminar series. ISCR research participants are integrated almost seamlessly with the Laboratory's Center for Applied Scientific Computing (CASC), which, in turn, addresses computational challenges arising throughout the Laboratory. Administratively, the ISCR flourishes under the Laboratory's University Relations Program (URP). Together with the other four Institutes of the URP, it must navigate a course that allows the Laboratory to benefit from academic exchanges while preserving national security. Although FY 1999 brought more than its share of challenges to the operation of an academic-like research enterprise within the context of a national security laboratory, the results declare the challenges well met and well worth the continued effort. A change of administration for the ISCR occurred during FY 1999. Acting Director John Fitzgerald retired from LLNL in August after 35 years of service, including the last two at helm of the ISCR. David Keyes, who has been a regular visitor in conjunction with ASCI scalable algorithms research since October 1997, overlapped with John for three months and serves half-time as the new Acting Director.« less

Parallel Programming Strategies for Irregular Adaptive Applications

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

Achieving scalable performance for dynamic irregular applications is eminently challenging. Traditional message-passing approaches have been making steady progress towards this goal; however, they suffer from complex implementation requirements. The use of a global address space greatly simplifies the programming task, but can degrade the performance for such computations. In this work, we examine two typical irregular adaptive applications, Dynamic Remeshing and N-Body, under competing programming methodologies and across various parallel architectures. The Dynamic Remeshing application simulates flow over an airfoil, and refines localized regions of the underlying unstructured mesh. The N-Body experiment models two neighboring Plummer galaxies that are about to undergo a merger. Both problems demonstrate dramatic changes in processor workloads and interprocessor communication with time; thus, dynamic load balancing is a required component.

Variable Complexity Structural Optimization of Shells

NASA Technical Reports Server (NTRS)

Haftka, Raphael T.; Venkataraman, Satchi

1999-01-01

Structural designers today face both opportunities and challenges in a vast array of available analysis and optimization programs. Some programs such as NASTRAN, are very general, permitting the designer to model any structure, to any degree of accuracy, but often at a higher computational cost. Additionally, such general procedures often do not allow easy implementation of all constraints of interest to the designer. Other programs, based on algebraic expressions used by designers one generation ago, have limited applicability for general structures with modem materials. However, when applicable, they provide easy understanding of design decisions trade-off. Finally, designers can also use specialized programs suitable for designing efficiently a subset of structural problems. For example, PASCO and PANDA2 are panel design codes, which calculate response and estimate failure much more efficiently than general-purpose codes, but are narrowly applicable in terms of geometry and loading. Therefore, the problem of optimizing structures based on simultaneous use of several models and computer programs is a subject of considerable interest. The problem of using several levels of models in optimization has been dubbed variable complexity modeling. Work under NASA grant NAG1-2110 has been concerned with the development of variable complexity modeling strategies with special emphasis on response surface techniques. In addition, several modeling issues for the design of shells of revolution were studied.

Variable Complexity Structural Optimization of Shells

NASA Technical Reports Server (NTRS)

Haftka, Raphael T.; Venkataraman, Satchi

1998-01-01

Structural designers today face both opportunities and challenges in a vast array of available analysis and optimization programs. Some programs such as NASTRAN, are very general, permitting the designer to model any structure, to any degree of accuracy, but often at a higher computational cost. Additionally, such general procedures often do not allow easy implementation of all constraints of interest to the designer. Other programs, based on algebraic expressions used by designers one generation ago, have limited applicability for general structures with modem materials. However, when applicable, they provide easy understanding of design decisions trade-off. Finally, designers can also use specialized programs suitable for designing efficiently a subset of structural problems. For example, PASCO and PANDA2 are panel design codes, which calculate response and estimate failure much more efficiently than general-purpose codes, but are narrowly applicable in terms of geometry and loading. Therefore, the problem of optimizing structures based on simultaneous use of several models and computer programs is a subject of considerable interest. The problem of using several levels of models in optimization has been dubbed variable complexity modeling. Work under NASA grant NAG1-1808 has been concerned with the development of variable complexity modeling strategies with special emphasis on response surface techniques. In addition several modeling issues for the design of shells of revolution were studied.

Challenges and Potential Solutions for Big Data Implementations in Developing Countries

PubMed Central

Mayan, J.C; García, M.J.; Almerares, A.A.; Househ, M.

2014-01-01

Summary Background The volume of data, the velocity with which they are generated, and their variety and lack of structure hinder their use. This creates the need to change the way information is captured, stored, processed, and analyzed, leading to the paradigm shift called Big Data. Objectives To describe the challenges and possible solutions for developing countries when implementing Big Data projects in the health sector. Methods A non-systematic review of the literature was performed in PubMed and Google Scholar. The following keywords were used: “big data”, “developing countries”, “data mining”, “health information systems”, and “computing methodologies”. A thematic review of selected articles was performed. Results There are challenges when implementing any Big Data program including exponential growth of data, special infrastructure needs, need for a trained workforce, need to agree on interoperability standards, privacy and security issues, and the need to include people, processes, and policies to ensure their adoption. Developing countries have particular characteristics that hinder further development of these projects. Conclusions The advent of Big Data promises great opportunities for the healthcare field. In this article, we attempt to describe the challenges developing countries would face and enumerate the options to be used to achieve successful implementations of Big Data programs. PMID:25123719

Argonne National Laboratory Annual Report of Laboratory Directed Research and Development program activities FY 2011.

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

Office of The Director)

As a national laboratory Argonne concentrates on scientific and technological challenges that can only be addressed through a sustained, interdisciplinary focus at a national scale. Argonne's eight major initiatives, as enumerated in its strategic plan, are Hard X-ray Sciences, Leadership Computing, Materials and Molecular Design and Discovery, Energy Storage, Alternative Energy and Efficiency, Nuclear Energy, Biological and Environmental Systems, and National Security. The purposes of Argonne's Laboratory Directed Research and Development (LDRD) Program are to encourage the development of novel technical concepts, enhance the Laboratory's research and development (R and D) capabilities, and pursue its strategic goals. projects are selectedmore » from proposals for creative and innovative R and D studies that require advance exploration before they are considered to be sufficiently developed to obtain support through normal programmatic channels. Among the aims of the projects supported by the LDRD Program are the following: establishment of engineering proof of principle, assessment of design feasibility for prospective facilities, development of instrumentation or computational methods or systems, and discoveries in fundamental science and exploratory development.« less

DNA context represents transcription regulation of the gene in mouse embryonic stem cells

NASA Astrophysics Data System (ADS)

Ha, Misook; Hong, Soondo

2016-04-01

Understanding gene regulatory information in DNA remains a significant challenge in biomedical research. This study presents a computational approach to infer gene regulatory programs from primary DNA sequences. Using DNA around transcription start sites as attributes, our model predicts gene regulation in the gene. We find that H3K27ac around TSS is an informative descriptor of the transcription program in mouse embryonic stem cells. We build a computational model inferring the cell-type-specific H3K27ac signatures in the DNA around TSS. A comparison of embryonic stem cell and liver cell-specific H3K27ac signatures in DNA shows that the H3K27ac signatures in DNA around TSS efficiently distinguish the cell-type specific H3K27ac peaks and the gene regulation. The arrangement of the H3K27ac signatures inferred from the DNA represents the transcription regulation of the gene in mESC. We show that the DNA around transcription start sites is associated with the gene regulatory program by specific interaction with H3K27ac.

DNA context represents transcription regulation of the gene in mouse embryonic stem cells.

PubMed

Ha, Misook; Hong, Soondo

2016-04-14

Understanding gene regulatory information in DNA remains a significant challenge in biomedical research. This study presents a computational approach to infer gene regulatory programs from primary DNA sequences. Using DNA around transcription start sites as attributes, our model predicts gene regulation in the gene. We find that H3K27ac around TSS is an informative descriptor of the transcription program in mouse embryonic stem cells. We build a computational model inferring the cell-type-specific H3K27ac signatures in the DNA around TSS. A comparison of embryonic stem cell and liver cell-specific H3K27ac signatures in DNA shows that the H3K27ac signatures in DNA around TSS efficiently distinguish the cell-type specific H3K27ac peaks and the gene regulation. The arrangement of the H3K27ac signatures inferred from the DNA represents the transcription regulation of the gene in mESC. We show that the DNA around transcription start sites is associated with the gene regulatory program by specific interaction with H3K27ac.

Configuration Aerodynamics: Past - Present - Future

NASA Technical Reports Server (NTRS)

Wood, Richard M.; Agrawal, Shreekant; Bencze, Daniel P.; Kulfan, Robert M.; Wilson, Douglas L.

1999-01-01

The Configuration Aerodynamics (CA) element of the High Speed Research (HSR) program is managed by a joint NASA and Industry team, referred to as the Technology Integration Development (ITD) team. This team is responsible for the development of a broad range of technologies for improved aerodynamic performance and stability and control characteristics at subsonic to supersonic flight conditions. These objectives are pursued through the aggressive use of advanced experimental test techniques and state of the art computational methods. As the HSR program matures and transitions into the next phase the objectives of the Configuration Aerodynamics ITD are being refined to address the drag reduction needs and stability and control requirements of High Speed Civil Transport (HSCT) aircraft. In addition, the experimental and computational tools are being refined and improved to meet these challenges. The presentation will review the work performed within the Configuration Aerodynamics element in 1994 and 1995 and then discuss the plans for the 1996-1998 time period. The final portion of the presentation will review several observations of the HSR program and the design activity within Configuration Aerodynamics.

The MUSOS (MUsic SOftware System) Toolkit: A computer-based, open source application for testing memory for melodies.

PubMed

Rainsford, M; Palmer, M A; Paine, G

2018-04-01

Despite numerous innovative studies, rates of replication in the field of music psychology are extremely low (Frieler et al., 2013). Two key methodological challenges affecting researchers wishing to administer and reproduce studies in music cognition are the difficulty of measuring musical responses, particularly when conducting free-recall studies, and access to a reliable set of novel stimuli unrestricted by copyright or licensing issues. In this article, we propose a solution for these challenges in computer-based administration. We present a computer-based application for testing memory for melodies. Created using the software Max/MSP (Cycling '74, 2014a), the MUSOS (Music Software System) Toolkit uses a simple modular framework configurable for testing common paradigms such as recall, old-new recognition, and stem completion. The program is accompanied by a stimulus set of 156 novel, copyright-free melodies, in audio and Max/MSP file formats. Two pilot tests were conducted to establish the properties of the accompanying stimulus set that are relevant to music cognition and general memory research. By using this software, a researcher without specialist musical training may administer and accurately measure responses from common paradigms used in the study of memory for music.

Designing and using computer simulations in medical education and training: an introduction.

PubMed

Friedl, Karl E; O'Neil, Harold F

2013-10-01

Computer-based technologies informed by the science of learning are becoming increasingly prevalent in education and training. For the Department of Defense (DoD), this presents a great potential advantage to the effective preparation of a new generation of technologically enabled service members. Military medicine has broad education and training challenges ranging from first aid and personal protective skills for every service member to specialized combat medic training; many of these challenges can be met with gaming and simulation technologies that this new generation has embraced. However, comprehensive use of medical games and simulation to augment expert mentorship is still limited to elite medical provider training programs, but can be expected to become broadly used in the training of first responders and allied health care providers. The purpose of this supplement is to review the use of computer games and simulation to teach and assess medical knowledge and skills. This review and other DoD research policy sources will form the basis for development of a research and development road map and guidelines for use of this technology in military medicine. Reprint & Copyright © 2013 Association of Military Surgeons of the U.S.

RIACS FY2002 Annual Report

NASA Technical Reports Server (NTRS)

Leiner, Barry M.; Gross, Anthony R. (Technical Monitor)

2002-01-01

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administration's missions. Operated by the Universities Space Research Association (a non-profit university consortium), RIACS is located at the NASA Ames Research Center, Moffett Field, California. It currently operates under a multiple year grant/cooperative agreement that began on October 1, 1997 and is up for renewal in September 2003. Ames has been designated NASA's Center of Excellence in Information Technology. In this capacity, Ames is charged with the responsibility to build an Information Technology (IT) Research Program that is preeminent within NASA. RIACS serves as a bridge between NASA Ames and the academic community, and RIACS scientists and visitors work in close collaboration with NASA scientists. RIACS has the additional goal of broadening the base of researchers in these areas of importance to the nation's space and aeronautics enterprises. RIACS research focuses on the three cornerstones of IT research necessary to meet the future challenges of NASA missions: 1) Automated Reasoning for Autonomous Systems; 2) Human-Centered Computing; and 3) High Performance Computing and Networking. In addition, RIACS collaborates with NASA scientists to apply IT research to a variety of NASA application domains including aerospace technology, earth science, life sciences, and astrobiology. RIACS also engages in other activities, such as workshops, seminars, visiting scientist programs and student summer programs, designed to encourage and facilitate collaboration between the university and NASA IT research communities.

ISCR FY2005 Annual Report

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

Keyes, D E; McGraw, J R

2006-02-02

Large-scale scientific computation and all of the disciplines that support and help validate it have been placed at the focus of Lawrence Livermore National Laboratory (LLNL) by the Advanced Simulation and Computing (ASC) program of the National Nuclear Security Administration (NNSA) and the Scientific Discovery through Advanced Computing (SciDAC) initiative of the Office of Science of the Department of Energy (DOE). The maturation of simulation as a fundamental tool of scientific and engineering research is underscored in the President's Information Technology Advisory Committee (PITAC) June 2005 finding that ''computational science has become critical to scientific leadership, economic competitiveness, and nationalmore » security''. LLNL operates several of the world's most powerful computers--including today's single most powerful--and has undertaken some of the largest and most compute-intensive simulations ever performed, most notably the molecular dynamics simulation that sustained more than 100 Teraflop/s and won the 2005 Gordon Bell Prize. Ultrascale simulation has been identified as one of the highest priorities in DOE's facilities planning for the next two decades. However, computers at architectural extremes are notoriously difficult to use in an efficient manner. Furthermore, each successful terascale simulation only points out the need for much better ways of interacting with the resulting avalanche of data. Advances in scientific computing research have, therefore, never been more vital to the core missions of LLNL than at present. Computational science is evolving so rapidly along every one of its research fronts that to remain on the leading edge, LLNL must engage researchers at many academic centers of excellence. In FY 2005, the Institute for Scientific Computing Research (ISCR) served as one of LLNL's main bridges to the academic community with a program of collaborative subcontracts, visiting faculty, student internships, workshops, and an active seminar series. The ISCR identifies researchers from the academic community for computer science and computational science collaborations with LLNL and hosts them for both brief and extended visits with the aim of encouraging long-term academic research agendas that address LLNL research priorities. Through these collaborations, ideas and software flow in both directions, and LLNL cultivates its future workforce. The Institute strives to be LLNL's ''eyes and ears'' in the computer and information sciences, keeping the Laboratory aware of and connected to important external advances. It also attempts to be the ''hands and feet'' that carry those advances into the Laboratory and incorporate them into practice. ISCR research participants are integrated into LLNL's Computing Applications and Research (CAR) Department, especially into its Center for Applied Scientific Computing (CASC). In turn, these organizations address computational challenges arising throughout the rest of the Laboratory. Administratively, the ISCR flourishes under LLNL's University Relations Program (URP). Together with the other four institutes of the URP, the ISCR navigates a course that allows LLNL to benefit from academic exchanges while preserving national security. While it is difficult to operate an academic-like research enterprise within the context of a national security laboratory, the results declare the challenges well met and worth the continued effort. The pages of this annual report summarize the activities of the faculty members, postdoctoral researchers, students, and guests from industry and other laboratories who participated in LLNL's computational mission under the auspices of the ISCR during FY 2005.« less

Simulation: Moving from Technology Challenge to Human Factors Success

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

Gould, Derek A., E-mail: dgould@liv.ac.uk; Chalmers, Nicholas; Johnson, Sheena J.

2012-06-15

Recognition of the many limitations of traditional apprenticeship training is driving new approaches to learning medical procedural skills. Among simulation technologies and methods available today, computer-based systems are topical and bring the benefits of automated, repeatable, and reliable performance assessments. Human factors research is central to simulator model development that is relevant to real-world imaging-guided interventional tasks and to the credentialing programs in which it would be used.

Three-Dimensional Cloud Visualization Based on Satellite Imagery

DTIC Science & Technology

1992-12-01

that information. As assessed by Schiavone and Papathomas (1990), a major challenge in meteorology today is the need to optimize the human/computer...program used on SGI system. Author: Eric Pepke, Jim Murray, John Lyons, August 1992, Florida State University. 58 S...Oceanography, and Hydrology. Amer. Meteor. Soc., Boston, MA, pp. 93-99 60 • • • • •• ,••’ "O Schiavone , J. A., and T. V. Papathomas, 1990

2009 High Performance Computing Modernization Program Users Group Conference

DTIC Science & Technology

2009-06-17

Asymmetric Threats Future Peer GWoT / ungoverned areas Irregular Warfare Low-end Asymmetric 1-4-2-1 (State-to-State War) Disruptive technologies Superiority...2008 “As changes in this century’s threat environment create strategic challenges – irregular warfare, weapons of mass destruction, disruptive ... technologies – this request places greater emphasis on basic research, which in recent years has not kept pace with other parts of the budget.” • Personnel

Mixed-Integer Conic Linear Programming: Challenges and Perspectives

DTIC Science & Technology

2013-10-01

The novel DCCs for MISOCO may be used in branch- and-cut algorithms when solving MISOCO problems. The experimental software CICLO was developed to...perform limited, but rigorous computational experiments. The CICLO solver utilizes continuous SOCO solvers, MOSEK, CPLES or SeDuMi, builds on the open...submitted Fall 2013. Software: 1. CICLO : Integer conic linear optimization package. Authors: J.C. Góez, T.K. Ralphs, Y. Fu, and T. Terlaky

A survey of GPU-based medical image computing techniques

PubMed Central

Shi, Lin; Liu, Wen; Zhang, Heye; Xie, Yongming

2012-01-01

Medical imaging currently plays a crucial role throughout the entire clinical applications from medical scientific research to diagnostics and treatment planning. However, medical imaging procedures are often computationally demanding due to the large three-dimensional (3D) medical datasets to process in practical clinical applications. With the rapidly enhancing performances of graphics processors, improved programming support, and excellent price-to-performance ratio, the graphics processing unit (GPU) has emerged as a competitive parallel computing platform for computationally expensive and demanding tasks in a wide range of medical image applications. The major purpose of this survey is to provide a comprehensive reference source for the starters or researchers involved in GPU-based medical image processing. Within this survey, the continuous advancement of GPU computing is reviewed and the existing traditional applications in three areas of medical image processing, namely, segmentation, registration and visualization, are surveyed. The potential advantages and associated challenges of current GPU-based medical imaging are also discussed to inspire future applications in medicine. PMID:23256080

Development and Validation of a Novel Fusion Algorithm for Continuous, Accurate and Automated R-wave Detection and Calculation of Signal-Derived Metrics

DTIC Science & Technology

2013-01-01

Predicting the onset of atrial fibrillation : the Computers in Cardiology Challenge 2001. Comput Cardiol 2001;28:113-6. [22] Moody GB, Mark RG, Goldberger AL...Computers in Cardiology Challenge 2006: QT interval measurement. Comput Cardiol 2006;33:313-6. [18] Moody GB. Spontaneous termination of atrial ... fibrillation : a challenge from PhysioNet and Computers in Cardiology 2004. Comput Cardiol 2004;31:101-4. [19] Moody GB, Jager F. Distinguishing ischemic from non

Southern California Earthquake Center/Undergraduate Studies in Earthquake Information Technology (SCEC/UseIT): Towards the Next Generation of Internship

NASA Astrophysics Data System (ADS)

Perry, S.; Benthien, M.; Jordan, T. H.

2005-12-01

The SCEC/UseIT internship program is training the next generation of earthquake scientist, with methods that can be adapted to other disciplines. UseIT interns work collaboratively, in multi-disciplinary teams, conducting computer science research that is needed by earthquake scientists. Since 2002, the UseIT program has welcomed 64 students, in some two dozen majors, at all class levels, from schools around the nation. Each summer''s work is posed as a ``Grand Challenge.'' The students then organize themselves into project teams, decide how to proceed, and pool their diverse talents and backgrounds. They have traditional mentors, who provide advice and encouragement, but they also mentor one another, and this has proved to be a powerful relationship. Most begin with fear that their Grand Challenge is impossible, and end with excitement and pride about what they have accomplished. The 22 UseIT interns in summer, 2005, were primarily computer science and engineering majors, with others in geology, mathematics, English, digital media design, physics, history, and cinema. The 2005 Grand Challenge was to "build an earthquake monitoring system" to aid scientists who must visualize rapidly evolving earthquake sequences and convey information to emergency personnel and the public. Most UseIT interns were engaged in software engineering, bringing new datasets and functionality to SCEC-VDO (Virtual Display of Objects), a 3D visualization software that was prototyped by interns last year, using Java3D and an extensible, plug-in architecture based on the Eclipse Integrated Development Environment. Other UseIT interns used SCEC-VDO to make animated movies, and experimented with imagery in order to communicate concepts and events in earthquake science. One movie-making project included the creation of an assessment to test the effectiveness of the movie''s educational message. Finally, one intern created an interactive, multimedia presentation of the UseIT program.

Accelerating scientific discovery : 2007 annual report.

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

Beckman, P.; Dave, P.; Drugan, C.

2008-11-14

As a gateway for scientific discovery, the Argonne Leadership Computing Facility (ALCF) works hand in hand with the world's best computational scientists to advance research in a diverse span of scientific domains, ranging from chemistry, applied mathematics, and materials science to engineering physics and life sciences. Sponsored by the U.S. Department of Energy's (DOE) Office of Science, researchers are using the IBM Blue Gene/L supercomputer at the ALCF to study and explore key scientific problems that underlie important challenges facing our society. For instance, a research team at the University of California-San Diego/ SDSC is studying the molecular basis ofmore » Parkinson's disease. The researchers plan to use the knowledge they gain to discover new drugs to treat the disease and to identify risk factors for other diseases that are equally prevalent. Likewise, scientists from Pratt & Whitney are using the Blue Gene to understand the complex processes within aircraft engines. Expanding our understanding of jet engine combustors is the secret to improved fuel efficiency and reduced emissions. Lessons learned from the scientific simulations of jet engine combustors have already led Pratt & Whitney to newer designs with unprecedented reductions in emissions, noise, and cost of ownership. ALCF staff members provide in-depth expertise and assistance to those using the Blue Gene/L and optimizing user applications. Both the Catalyst and Applications Performance Engineering and Data Analytics (APEDA) teams support the users projects. In addition to working with scientists running experiments on the Blue Gene/L, we have become a nexus for the broader global community. In partnership with the Mathematics and Computer Science Division at Argonne National Laboratory, we have created an environment where the world's most challenging computational science problems can be addressed. Our expertise in high-end scientific computing enables us to provide guidance for applications that are transitioning to petascale as well as to produce software that facilitates their development, such as the MPICH library, which provides a portable and efficient implementation of the MPI standard--the prevalent programming model for large-scale scientific applications--and the PETSc toolkit that provides a programming paradigm that eases the development of many scientific applications on high-end computers.« less

XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Lonie, David C.; Zurek, Eva

2011-02-01

The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely available to the scientific community for use and collaboration under the GNU Public License. Running time: User dependent. The program runs until stopped by the user.

Computer use in primary care and patient-physician communication.

PubMed

Sobral, Dilermando; Rosenbaum, Marcy; Figueiredo-Braga, Margarida

2015-07-08

This study evaluated how physicians and patients perceive the impact of computer use on clinical communication, and how a patient-centered orientation can influence this impact. The study followed a descriptive cross-sectional design and included 106 family physicians and 392 patients. An original questionnaire assessed computer use, participants' perspective of its impact, and patient centered strategies. Physicians reported spending 42% of consultation time in contact with the computer. A negative impact of computer in patient-physician communication regarding the consultation length, confidentiality, maintaining eye contact, active listening to the patient, and ability to understand the patient was reported by physicians, while patients reported a positive effect for all the items. Physicians considered that the usual computer placement in their consultation room was significantly unfavorable to patient-physician communication. Physicians perceive the impact of computer use on patient-physician communication as negative, while patients have a positive perception of computer use on patient-physician communication. Consultation support can represent a challenge to physicians who recognize its negative impact in patient centered orientation. Medical education programs aiming to enhance specific communication skills and to better integrate computer use in primary care settings are needed. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Sawja: Static Analysis Workshop for Java

NASA Astrophysics Data System (ADS)

Hubert, Laurent; Barré, Nicolas; Besson, Frédéric; Demange, Delphine; Jensen, Thomas; Monfort, Vincent; Pichardie, David; Turpin, Tiphaine

Static analysis is a powerful technique for automatic verification of programs but raises major engineering challenges when developing a full-fledged analyzer for a realistic language such as Java. Efficiency and precision of such a tool rely partly on low level components which only depend on the syntactic structure of the language and therefore should not be redesigned for each implementation of a new static analysis. This paper describes the Sawja library: a static analysis workshop fully compliant with Java 6 which provides OCaml modules for efficiently manipulating Java bytecode programs. We present the main features of the library, including i) efficient functional data-structures for representing a program with implicit sharing and lazy parsing, ii) an intermediate stack-less representation, and iii) fast computation and manipulation of complete programs. We provide experimental evaluations of the different features with respect to time, memory and precision.

Transnational nursing programs: models, advantages and challenges.

PubMed

Wilson, Michael

2002-07-01

Conducting transnational programs can be a very rewarding activity for a School, Faculty or University. Apart from increasing the profile of the university, the conduct of transnational programs can also provide the university with openings for business opportunities, consultative activities, and collaborative research. It can also be a costly exercise placing an enormous strain on limited resources with little reward for the provider. Transnational ventures can become nonviable entities in a very short period of time due to unanticipated global economic trends. Transnational courses offered by Faculties of Business and Computing are commonplace, however, there is a growing number of health science programs, particularly nursing that are being offered transnational. This paper plans an overview of several models employed for the delivery of transnational nursing courses and discusses several key issues pertaining to conducting courses outside the host university's country.

A parallelization scheme of the periodic signals tracking algorithm for isochronous mass spectrometry on GPUs

NASA Astrophysics Data System (ADS)

Chen, R. J.; Wang, M.; Yan, X. L.; Yang, Q.; Lam, Y. H.; Yang, L.; Zhang, Y. H.

2017-12-01

The periodic signals tracking algorithm has been used to determine the revolution times of ions stored in storage rings in isochronous mass spectrometry (IMS) experiments. It has been a challenge to perform real-time data analysis by using the periodic signals tracking algorithm in the IMS experiments. In this paper, a parallelization scheme of the periodic signals tracking algorithm is introduced and a new program is developed. The computing time of data analysis can be reduced by a factor of ∼71 and of ∼346 by using our new program on Tesla C1060 GPU and Tesla K20c GPU, compared to using old program on Xeon E5540 CPU. We succeed in performing real-time data analysis for the IMS experiments by using the new program on Tesla K20c GPU.

An Investigation of Unified Memory Access Performance in CUDA

PubMed Central

Landaverde, Raphael; Zhang, Tiansheng; Coskun, Ayse K.; Herbordt, Martin

2015-01-01

Managing memory between the CPU and GPU is a major challenge in GPU computing. A programming model, Unified Memory Access (UMA), has been recently introduced by Nvidia to simplify the complexities of memory management while claiming good overall performance. In this paper, we investigate this programming model and evaluate its performance and programming model simplifications based on our experimental results. We find that beyond on-demand data transfers to the CPU, the GPU is also able to request subsets of data it requires on demand. This feature allows UMA to outperform full data transfer methods for certain parallel applications and small data sizes. We also find, however, that for the majority of applications and memory access patterns, the performance overheads associated with UMA are significant, while the simplifications to the programming model restrict flexibility for adding future optimizations. PMID:26594668

Adversarial reasoning: challenges and approaches

NASA Astrophysics Data System (ADS)

Kott, Alexander; Ownby, Michael

2005-05-01

This paper defines adversarial reasoning as computational approaches to inferring and anticipating an enemy's perceptions, intents and actions. It argues that adversarial reasoning transcends the boundaries of game theory and must also leverage such disciplines as cognitive modeling, control theory, AI planning and others. To illustrate the challenges of applying adversarial reasoning to real-world problems, the paper explores the lessons learned in the CADET -- a battle planning system that focuses on brigade-level ground operations and involves adversarial reasoning. From this example of current capabilities, the paper proceeds to describe RAID -- a DARPA program that aims to build capabilities in adversarial reasoning, and how such capabilities would address practical requirements in Defense and other application areas.

Text-based CAPTCHAs over the years

NASA Astrophysics Data System (ADS)

Chow, Y. W.; Susilo, W.

2017-11-01

The notion of CAPTCHAs has been around for more than two decades. Since its introduction, CAPTCHAs have now become a ubiquitous part of the Internet. Over the years, research on various aspects of CAPTCHAs has evolved and different design principles have emerged. This article discusses text-based CAPTCHAs in terms of their fundamental requirements, namely, security and usability. Practicality necessitates that humans must be able to correctly solve CAPTCHA challenges, while at the same time automated computer programs should have difficulty solving the challenges. This article also presents alternative paradigms to text-based CAPTCHA design that have been examined in previous work. With the advances in techniques to defeat CAPTCHAs, the future of auto- mated Turing tests is an open question.

Assessment of Automated Analyses of Cell Migration on Flat and Nanostructured Surfaces

PubMed Central

Grădinaru, Cristian; Łopacińska, Joanna M.; Huth, Johannes; Kestler, Hans A.; Flyvbjerg, Henrik; Mølhave, Kristian

2012-01-01

Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact that the segmentation routines of such programs are often challenged by nanostructured surfaces makes the question more pertinent. Here we illustrate how it is possible to track cells on bright field microscopy images with image analysis routines implemented in an open-source cell tracking program, PACT (Program for Automated Cell Tracking). We compare the automated motility analysis of three cell tracking programs, PACT, Autozell, and TLA, using the same movies as input for all three programs. We find that different programs track overlapping, but different subsets of cells due to different segmentation methods. Unfortunately, population averages based on such different cell populations, differ significantly in some cases. Thus, results obtained with one software package are not necessarily reproducible by other software. PMID:24688640

Artificial Intelligence and Machine Learning in Radiology: Opportunities, Challenges, Pitfalls, and Criteria for Success.

PubMed

Thrall, James H; Li, Xiang; Li, Quanzheng; Cruz, Cinthia; Do, Synho; Dreyer, Keith; Brink, James

2018-03-01

Worldwide interest in artificial intelligence (AI) applications, including imaging, is high and growing rapidly, fueled by availability of large datasets ("big data"), substantial advances in computing power, and new deep-learning algorithms. Apart from developing new AI methods per se, there are many opportunities and challenges for the imaging community, including the development of a common nomenclature, better ways to share image data, and standards for validating AI program use across different imaging platforms and patient populations. AI surveillance programs may help radiologists prioritize work lists by identifying suspicious or positive cases for early review. AI programs can be used to extract "radiomic" information from images not discernible by visual inspection, potentially increasing the diagnostic and prognostic value derived from image datasets. Predictions have been made that suggest AI will put radiologists out of business. This issue has been overstated, and it is much more likely that radiologists will beneficially incorporate AI methods into their practices. Current limitations in availability of technical expertise and even computing power will be resolved over time and can also be addressed by remote access solutions. Success for AI in imaging will be measured by value created: increased diagnostic certainty, faster turnaround, better outcomes for patients, and better quality of work life for radiologists. AI offers a new and promising set of methods for analyzing image data. Radiologists will explore these new pathways and are likely to play a leading role in medical applications of AI. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Knowledge-based computer systems for radiotherapy planning.

PubMed

Kalet, I J; Paluszynski, W

1990-08-01

Radiation therapy is one of the first areas of clinical medicine to utilize computers in support of routine clinical decision making. The role of the computer has evolved from simple dose calculations to elaborate interactive graphic three-dimensional simulations. These simulations can combine external irradiation from megavoltage photons, electrons, and particle beams with interstitial and intracavitary sources. With the flexibility and power of modern radiotherapy equipment and the ability of computer programs that simulate anything the machinery can do, we now face a challenge to utilize this capability to design more effective radiation treatments. How can we manage the increased complexity of sophisticated treatment planning? A promising approach will be to use artificial intelligence techniques to systematize our present knowledge about design of treatment plans, and to provide a framework for developing new treatment strategies. Far from replacing the physician, physicist, or dosimetrist, artificial intelligence-based software tools can assist the treatment planning team in producing more powerful and effective treatment plans. Research in progress using knowledge-based (AI) programming in treatment planning already has indicated the usefulness of such concepts as rule-based reasoning, hierarchical organization of knowledge, and reasoning from prototypes. Problems to be solved include how to handle continuously varying parameters and how to evaluate plans in order to direct improvements.

Data management and analysis for the Earth System Grid

NASA Astrophysics Data System (ADS)

Williams, D. N.; Ananthakrishnan, R.; Bernholdt, D. E.; Bharathi, S.; Brown, D.; Chen, M.; Chervenak, A. L.; Cinquini, L.; Drach, R.; Foster, I. T.; Fox, P.; Hankin, S.; Henson, V. E.; Jones, P.; Middleton, D. E.; Schwidder, J.; Schweitzer, R.; Schuler, R.; Shoshani, A.; Siebenlist, F.; Sim, A.; Strand, W. G.; Wilhelmi, N.; Su, M.

2008-07-01

The international climate community is expected to generate hundreds of petabytes of simulation data within the next five to seven years. This data must be accessed and analyzed by thousands of analysts worldwide in order to provide accurate and timely estimates of the likely impact of climate change on physical, biological, and human systems. Climate change is thus not only a scientific challenge of the first order but also a major technological challenge. In order to address this technological challenge, the Earth System Grid Center for Enabling Technologies (ESG-CET) has been established within the U.S. Department of Energy's Scientific Discovery through Advanced Computing (SciDAC)-2 program, with support from the offices of Advanced Scientific Computing Research and Biological and Environmental Research. ESG-CET's mission is to provide climate researchers worldwide with access to the data, information, models, analysis tools, and computational capabilities required to make sense of enormous climate simulation datasets. Its specific goals are to (1) make data more useful to climate researchers by developing Grid technology that enhances data usability; (2) meet specific distributed database, data access, and data movement needs of national and international climate projects; (3) provide a universal and secure web-based data access portal for broad multi-model data collections; and (4) provide a wide-range of Grid-enabled climate data analysis tools and diagnostic methods to international climate centers and U.S. government agencies. Building on the successes of the previous Earth System Grid (ESG) project, which has enabled thousands of researchers to access tens of terabytes of data from a small number of ESG sites, ESG-CET is working to integrate a far larger number of distributed data providers, high-bandwidth wide-area networks, and remote computers in a highly collaborative problem-solving environment.

Parallel programming of industrial applications

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

Heroux, M; Koniges, A; Simon, H

1998-07-21

In the introductory material, we overview the typical MPP environment for real application computing and the special tools available such as parallel debuggers and performance analyzers. Next, we draw from a series of real applications codes and discuss the specific challenges and problems that are encountered in parallelizing these individual applications. The application areas drawn from include biomedical sciences, materials processing and design, plasma and fluid dynamics, and others. We show how it was possible to get a particular application to run efficiently and what steps were necessary. Finally we end with a summary of the lessons learned from thesemore » applications and predictions for the future of industrial parallel computing. This tutorial is based on material from a forthcoming book entitled: "Industrial Strength Parallel Computing" to be published by Morgan Kaufmann Publishers (ISBN l-55860-54).« less

The Center for Computational Biology: resources, achievements, and challenges

PubMed Central

Dinov, Ivo D; Thompson, Paul M; Woods, Roger P; Van Horn, John D; Shattuck, David W; Parker, D Stott

2011-01-01

The Center for Computational Biology (CCB) is a multidisciplinary program where biomedical scientists, engineers, and clinicians work jointly to combine modern mathematical and computational techniques, to perform phenotypic and genotypic studies of biological structure, function, and physiology in health and disease. CCB has developed a computational framework built around the Manifold Atlas, an integrated biomedical computing environment that enables statistical inference on biological manifolds. These manifolds model biological structures, features, shapes, and flows, and support sophisticated morphometric and statistical analyses. The Manifold Atlas includes tools, workflows, and services for multimodal population-based modeling and analysis of biological manifolds. The broad spectrum of biomedical topics explored by CCB investigators include the study of normal and pathological brain development, maturation and aging, discovery of associations between neuroimaging and genetic biomarkers, and the modeling, analysis, and visualization of biological shape, form, and size. CCB supports a wide range of short-term and long-term collaborations with outside investigators, which drive the center's computational developments and focus the validation and dissemination of CCB resources to new areas and scientific domains. PMID:22081221

The Center for Computational Biology: resources, achievements, and challenges.

PubMed

Toga, Arthur W; Dinov, Ivo D; Thompson, Paul M; Woods, Roger P; Van Horn, John D; Shattuck, David W; Parker, D Stott

2012-01-01

The Center for Computational Biology (CCB) is a multidisciplinary program where biomedical scientists, engineers, and clinicians work jointly to combine modern mathematical and computational techniques, to perform phenotypic and genotypic studies of biological structure, function, and physiology in health and disease. CCB has developed a computational framework built around the Manifold Atlas, an integrated biomedical computing environment that enables statistical inference on biological manifolds. These manifolds model biological structures, features, shapes, and flows, and support sophisticated morphometric and statistical analyses. The Manifold Atlas includes tools, workflows, and services for multimodal population-based modeling and analysis of biological manifolds. The broad spectrum of biomedical topics explored by CCB investigators include the study of normal and pathological brain development, maturation and aging, discovery of associations between neuroimaging and genetic biomarkers, and the modeling, analysis, and visualization of biological shape, form, and size. CCB supports a wide range of short-term and long-term collaborations with outside investigators, which drive the center's computational developments and focus the validation and dissemination of CCB resources to new areas and scientific domains.

Clinical laboratory technician to clinical laboratory scientist articulation and distance learning.

PubMed

Crowley, J R; Laurich, G A; Mobley, R C; Arnette, A H; Shaikh, A H; Martin, S M

1999-01-01

Laboratory workers and educators alike are challenged to support access to education that is current and provides opportunities for career advancement in the work place. The clinical laboratory science (CLS) program at the Medical College of Georgia in Augusta developed a clinical laboratory technician (CLT) to CLS articulation option, expanded it through distance learning, and integrated computer based learning technology into the educational process over a four year period to address technician needs for access to education. Both positive and negative outcomes were realized through these efforts. Twenty-seven students entered the pilot articulation program, graduated, and took a CLS certification examination. Measured in terms of CLS certification, promotions, pay raises, and career advancement, the program described was a success. However, major problems were encountered related to the use of unfamiliar communication technology; administration of the program at distance sites; communication between educational institutions, students, and employers; and competition with CLT programs for internship sites. These problems must be addressed in future efforts to provide a successful distance learning program. Effective methods for meeting educational needs and career ladder expectations of CLTs and their employers are important to the overall quality and appeal of the profession. Educational technology that includes computer-aided instruction, multimedia, and telecommunications can provide powerful tools for education in general and CLT articulation in particular. Careful preparation and vigilant attention to reliable delivery methods as well as students' progress and outcomes is critical for an efficient, economically feasible, and educationally sound program.

Measurement-Based Linear Optics

NASA Astrophysics Data System (ADS)

Alexander, Rafael N.; Gabay, Natasha C.; Rohde, Peter P.; Menicucci, Nicolas C.

2017-03-01

A major challenge in optical quantum processing is implementing large, stable interferometers. We offer a novel approach: virtual, measurement-based interferometers that are programed on the fly solely by the choice of homodyne measurement angles. The effects of finite squeezing are captured as uniform amplitude damping. We compare our proposal to existing (physical) interferometers and consider its performance for BosonSampling, which could demonstrate postclassical computational power in the near future. We prove its efficiency in time and squeezing (energy) in this setting.

Western State Hospital: implementing a MUMPS-based PC network.

PubMed

Russ, D C

1991-06-01

Western State Hospital, a state-administered 1,200-bed mental health institution near Tacoma, Wash., confronted the challenge of automating its large campus through the application of the Healthcare Integrated Information System (HIIS). It is the first adaptation of the Veterans Administration's Decentralized Hospital Computer Program software in a mental health institution of this size, and the first DHCP application to be installed on a PC client/server network in a large U.S. hospital.

Agent 2003 Conference on Challenges in Social Simulation

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

Margaret Clemmons, ed.

Welcome to the Proceedings of the fourth in a series of agent simulation conferences cosponsored by Argonne National Laboratory and The University of Chicago. Agent 2003 is the second conference in which three Special Interest Groups from the North American Association for Computational Social and Organizational Science (NAACSOS) have been involved in planning the program--Computational Social Theory; Simulation Applications; and Methods, Toolkits and Techniques. The theme of Agent 2003, Challenges in Social Simulation, is especially relevant, as there seems to be no shortage of such challenges. Agent simulation has been applied with increasing frequency to social domains for several decades,more » and its promise is clear and increasingly visible. Like any nascent scientific methodology, however, it faces a number of problems or issues that must be addressed in order to progress. These challenges include: (1) Validating models relative to the social settings they are designed to represent; (2) Developing agents and interactions simple enough to understand but sufficiently complex to do justice to the social processes of interest; (3) Bridging the gap between empirically spare artificial societies and naturally occurring social phenomena; (4) Building multi-level models that span processes across domains; (5) Promoting a dialog among theoretical, qualitative, and empirical social scientists and area experts, on the one hand, and mathematical and computational modelers and engineers, on the other; (6) Using that dialog to facilitate substantive progress in the social sciences; and (7) Fulfilling the aspirations of users in business, government, and other application areas, while recognizing and addressing the preceding challenges. Although this list hardly exhausts the challenges the field faces, it does identify topics addressed throughout the presentations of Agent 2003. Agent 2003 is part of a much larger process in which new methods and techniques are applied to difficult social issues. Among the resources that give us the prospect of success is the innovative and transdisciplinary research community being built. We believe that Agent 2003 contributes to further progress in computational modeling of social processes, and we hope that you find these Proceedings to be stimulating and rewarding. As the horizons of this transdiscipline continue to emerge and converge, we hope to provide similar forums that will promote development of agent simulation modeling in the years to come.« less

Management development: a needs analysis for nurse executives and managers.

PubMed

Kirk, R

1987-04-01

Clearly, both the nurse executive and nurse manager roles are becoming more complex. I feel an enthusiasm by the professionals in those positions to pursue development activities that will help them do their jobs better and with less discomfort. Nurse executives obviously know the power of combining knowledge with experience. How do the different leadership and management development needs identified by these NE fit with your organization's needs? What is the content in your leadership and management development programs? Are your programs meeting the real needs of your executive and management-level staff? One way to find out is to do a simple survey. Today, nurse executives are responsible and accountable for challenges we never considered possible, even a few years ago. But along with the new challenges came the flexibility and positive attitudes of NEs to respond to changes and acquire new skills such as cost accounting, computers, or marketing. It's this type of proactive thinking that helps nurse leaders turn problems into opportunities and their situations into success stories.

A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

DOE PAGES

Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; ...

2008-01-01

Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE) has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA) Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also addressmore » interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.« less

The Center for Nanophase Materials Sciences

NASA Astrophysics Data System (ADS)

Lowndes, Douglas

2005-03-01

The Center for Nanophase Materials Sciences (CNMS) located at Oak Ridge National Laboratory (ORNL) will be the first DOE Nanoscale Science Research Center to begin operation, with construction to be completed in April 2005 and initial operations in October 2005. The CNMS' scientific program has been developed through workshops with the national community, with the goal of creating a highly collaborative research environment to accelerate discovery and drive technological advances. Research at the CNMS is organized under seven Scientific Themes selected to address challenges to understanding and to exploit particular ORNL strengths (see http://cnms.ornl.govhttp://cnms.ornl.gov). These include extensive synthesis and characterization capabilities for soft, hard, nanostructured, magnetic and catalytic materials and their composites; neutron scattering at the Spallation Neutron Source and High Flux Isotope Reactor; computational nanoscience in the CNMS' Nanomaterials Theory Institute and utilizing facilities and expertise of the Center for Computational Sciences and the new Leadership Scientific Computing Facility at ORNL; a new CNMS Nanofabrication Research Laboratory; and a suite of unique and state-of-the-art instruments to be made reliably available to the national community for imaging, manipulation, and properties measurements on nanoscale materials in controlled environments. The new research facilities will be described together with the planned operation of the user research program, the latter illustrated by the current ``jump start'' user program that utilizes existing ORNL/CNMS facilities.

New perspectives on the pedagogy of programming in a developing country context

NASA Astrophysics Data System (ADS)

Apiola, Mikko; Tedre, Matti

2012-09-01

Programming education is a widely researched and intensely discussed topic. The literature proposes a broad variety of pedagogical viewpoints, practical approaches, learning theories, motivational vehicles, and other elements of the learning situation. However, little effort has been put on understanding cultural and contextual differences in pedagogy of programming. Pedagogical literature shows that educational design should account for differences in the ways of learning and teaching between industrialized and developing countries. However, the nature and implications of those differences are hitherto unclear. Using group interviews and quantitative surveys, we identified several crucial elements for contextualizing programming education. Our results reveal that students are facing many similar challenges to students in the west: they often lack deep level learning skills and problem-solving skills, which are required for learning computer programming, and, secondly, that from the students' viewpoint the standard learning environment does not offer enough support for gaining the requisite development. With inadequate support students may resort to surface learning and may adopt extrinsic sources of motivation. Learning is also hindered by many contextually unique factors, such as unfamiliar pedagogical approaches, language problems, and cultural differences. Our analysis suggests that challenges can be minimized by increasing the number of practical exercises, by carefully selecting between guided and minimally guided environments, by rigorously monitoring student progress, and by providing students timely help, repetitive exercises, clear guidelines, and emotional support.

The implementation of AI technologies in computer wargames

NASA Astrophysics Data System (ADS)

Tiller, John A.

2004-08-01

Computer wargames involve the most in-depth analysis of general game theory. The enumerated turns of a game like chess are dwarfed by the exponentially larger possibilities of even a simple computer wargame. Implementing challenging AI is computer wargames is an important goal in both the commercial and military environments. In the commercial marketplace, customers demand a challenging AI opponent when they play a computer wargame and are frustrated by a lack of competence on the part of the AI. In the military environment, challenging AI opponents are important for several reasons. A challenging AI opponent will force the military professional to avoid routine or set-piece approaches to situations and cause them to think much deeper about military situations before taking action. A good AI opponent would also include national characteristics of the opponent being simulated, thus providing the military professional with even more of a challenge in planning and approach. Implementing current AI technologies in computer wargames is a technological challenge. The goal is to join the needs of AI in computer wargames with the solutions of current AI technologies. This talk will address several of those issues, possible solutions, and currently unsolved problems.

The DoD's High Performance Computing Modernization Program - Ensuing the National Earth Systems Prediction Capability Becomes Operational

NASA Astrophysics Data System (ADS)

Burnett, W.

2016-12-01

The Department of Defense's (DoD) High Performance Computing Modernization Program (HPCMP) provides high performance computing to address the most significant challenges in computational resources, software application support and nationwide research and engineering networks. Today, the HPCMP has a critical role in ensuring the National Earth System Prediction Capability (N-ESPC) achieves initial operational status in 2019. A 2015 study commissioned by the HPCMP found that N-ESPC computational requirements will exceed interconnect bandwidth capacity due to the additional load from data assimilation and passing connecting data between ensemble codes. Memory bandwidth and I/O bandwidth will continue to be significant bottlenecks for the Navy's Hybrid Coordinate Ocean Model (HYCOM) scalability - by far the major driver of computing resource requirements in the N-ESPC. The study also found that few of the N-ESPC model developers have detailed plans to ensure their respective codes scale through 2024. Three HPCMP initiatives are designed to directly address and support these issues: Productivity Enhancement, Technology, Transfer and Training (PETTT), the HPCMP Applications Software Initiative (HASI), and Frontier Projects. PETTT supports code conversion by providing assistance, expertise and training in scalable and high-end computing architectures. HASI addresses the continuing need for modern application software that executes effectively and efficiently on next-generation high-performance computers. Frontier Projects enable research and development that could not be achieved using typical HPCMP resources by providing multi-disciplinary teams access to exceptional amounts of high performance computing resources. Finally, the Navy's DoD Supercomputing Resource Center (DSRC) currently operates a 6 Petabyte system, of which Naval Oceanography receives 15% of operational computational system use, or approximately 1 Petabyte of the processing capability. The DSRC will provide the DoD with future computing assets to initially operate the N-ESPC in 2019. This talk will further describe how DoD's HPCMP will ensure N-ESPC becomes operational, efficiently and effectively, using next-generation high performance computing.

Preface: SciDAC 2005

NASA Astrophysics Data System (ADS)

Mezzacappa, Anthony

2005-01-01

On 26-30 June 2005 at the Grand Hyatt on Union Square in San Francisco several hundred computational scientists from around the world came together for what can certainly be described as a celebration of computational science. Scientists from the SciDAC Program and scientists from other agencies and nations were joined by applied mathematicians and computer scientists to highlight the many successes in the past year where computation has led to scientific discovery in a variety of fields: lattice quantum chromodynamics, accelerator modeling, chemistry, biology, materials science, Earth and climate science, astrophysics, and combustion and fusion energy science. Also highlighted were the advances in numerical methods and computer science, and the multidisciplinary collaboration cutting across science, mathematics, and computer science that enabled these discoveries. The SciDAC Program was conceived and funded by the US Department of Energy Office of Science. It is the Office of Science's premier computational science program founded on what is arguably the perfect formula: the priority and focus is science and scientific discovery, with the understanding that the full arsenal of `enabling technologies' in applied mathematics and computer science must be brought to bear if we are to have any hope of attacking and ultimately solving today's computational Grand Challenge problems. The SciDAC Program has been in existence for four years, and many of the computational scientists funded by this program will tell you that the program has given them the hope of addressing their scientific problems in full realism for the very first time. Many of these scientists will also tell you that SciDAC has also fundamentally changed the way they do computational science. We begin this volume with one of DOE's great traditions, and core missions: energy research. As we will see, computation has been seminal to the critical advances that have been made in this arena. Of course, to understand our world, whether it is to understand its very nature or to understand it so as to control it for practical application, will require explorations on all of its scales. Computational science has been no less an important tool in this arena than it has been in the arena of energy research. From explorations of quantum chromodynamics, the fundamental theory that describes how quarks make up the protons and neutrons of which we are composed, to explorations of the complex biomolecules that are the building blocks of life, to explorations of some of the most violent phenomena in our universe and of the Universe itself, computation has provided not only significant insight, but often the only means by which we have been able to explore these complex, multicomponent systems and by which we have been able to achieve scientific discovery and understanding. While our ultimate target remains scientific discovery, it certainly can be said that at a fundamental level the world is mathematical. Equations ultimately govern the evolution of the systems of interest to us, be they physical, chemical, or biological systems. The development and choice of discretizations of these underlying equations is often a critical deciding factor in whether or not one is able to model such systems stably, faithfully, and practically, and in turn, the algorithms to solve the resultant discrete equations are the complementary, critical ingredient in the recipe to model the natural world. The use of parallel computing platforms, especially at the TeraScale, and the trend toward even larger numbers of processors, continue to present significant challenges in the development and implementation of these algorithms. Computational scientists often speak of their `workflows'. A workflow, as the name suggests, is the sum total of all complex and interlocking tasks, from simulation set up, execution, and I/O, to visualization and scientific discovery, through which the advancement in our understanding of the natural world is realized. For the computational scientist, enabling such workflows presents myriad, signiflcant challenges, and it is computer scientists that are called upon at such times to address these challenges. Simulations are currently generating data at the staggering rate of tens of TeraBytes per simulation, over the course of days. In the next few years, these data generation rates are expected to climb exponentially to hundreds of TeraBytes per simulation, performed over the course of months. The output, management, movement, analysis, and visualization of these data will be our key to unlocking the scientific discoveries buried within the data. And there is no hope of generating such data to begin with, or of scientific discovery, without stable computing platforms and a sufficiently high and sustained performance of scientific applications codes on them. Thus, scientific discovery in the realm of computational science at the TeraScale and beyond will occur at the intersection of science, applied mathematics, and computer science. The SciDAC Program was constructed to mirror this reality, and the pages that follow are a testament to the efficacy of such an approach. We would like to acknowledge the individuals on whose talents and efforts the success of SciDAC 2005 was based. Special thanks go to Betsy Riley for her work on the SciDAC 2005 Web site and meeting agenda, for lining up our corporate sponsors, for coordinating all media communications, and for her efforts in processing the proceedings contributions, to Sherry Hempfling for coordinating the overall SciDAC 2005 meeting planning, for handling a significant share of its associated communications, and for coordinating with the ORNL Conference Center and Grand Hyatt, to Angela Harris for producing many of the documents and records on which our meeting planning was based and for her efforts in coordinating with ORNL Graphics Services, to Angie Beach of the ORNL Conference Center for her efforts in procurement and setting up and executing the contracts with the hotel, and to John Bui and John Smith for their superb wireless networking and A/V set up and support. We are grateful for the relentless efforts of all of these individuals, their remarkable talents, and for the joy of working with them during this past year. They were the cornerstones of SciDAC 2005. Thanks also go to Kymba A'Hearn and Patty Boyd for on-site registration, Brittany Hagen for administrative support, Bruce Johnston for netcast support, Tim Jones for help with the proceedings and Web site, Sherry Lamb for housing and registration, Cindy Lathum for Web site design, Carolyn Peters for on-site registration, and Dami Rich for graphic design. And we would like to express our appreciation to the Oak Ridge National Laboratory, especially Jeff Nichols, the Argonne National Laboratory, the Lawrence Berkeley National Laboratory, and to our corporate sponsors, Cray, IBM, Intel, and SGI, for their support. We would like to extend special thanks also to our plenary speakers, technical speakers, poster presenters, and panelists for all of their efforts on behalf of SciDAC 2005 and for their remarkable achievements and contributions. We would like to express our deep appreciation to Lali Chatterjee, Graham Douglas and Margaret Smith of Institute of Physics Publishing, who worked tirelessly in order to provide us with this finished volume within two months, which is nothing short of miraculous. Finally, we wish to express our heartfelt thanks to Michael Strayer, SciDAC Director, whose vision it was to focus SciDAC 2005 on scientific discovery, around which all of the excitement we experienced revolved, and to our DOE SciDAC program managers, especially Fred Johnson, for their support, input, and help throughout.

C-Speak Aphasia Alternative Communication Program for People with Severe Aphasia: Importance of Executive Functioning and Semantic Knowledge

PubMed Central

Nicholas, Marjorie; Sinotte, Michele P.; Helm-Estabrooks, Nancy

2011-01-01

Learning how to use a computer-based communication system can be challenging for people with severe aphasia even if the system is not word-based. This study explored cognitive and linguistic factors relative to how they affected individual patients’ ability to communicate expressively using C-Speak Aphasia, (CSA), an alternative communication computer program that is primarily picture-based. Ten individuals with severe non-fluent aphasia received at least six months of training with CSA. To assess carryover of training, untrained functional communication tasks (i.e., answering autobiographical questions, describing pictures, making telephone calls, describing a short video, and two writing tasks) were repeatedly probed in two conditions: 1) using CSA in addition to natural forms of communication, and 2) using only natural forms of communication, e.g., speaking, writing, gesturing, drawing. Four of the ten participants communicated more information on selected probe tasks using CSA than they did without the computer. Response to treatment also was examined in relation to baseline measures of non-linguistic executive function skills, pictorial semantic abilities, and auditory comprehension. Only nonlinguistic executive function skills were significantly correlated with treatment response. PMID:21506045

Discovery of Boolean metabolic networks: integer linear programming based approach.

PubMed

Qiu, Yushan; Jiang, Hao; Ching, Wai-Ki; Cheng, Xiaoqing

2018-04-11

Traditional drug discovery methods focused on the efficacy of drugs rather than their toxicity. However, toxicity and/or lack of efficacy are produced when unintended targets are affected in metabolic networks. Thus, identification of biological targets which can be manipulated to produce the desired effect with minimum side-effects has become an important and challenging topic. Efficient computational methods are required to identify the drug targets while incurring minimal side-effects. In this paper, we propose a graph-based computational damage model that summarizes the impact of enzymes on compounds in metabolic networks. An efficient method based on Integer Linear Programming formalism is then developed to identify the optimal enzyme-combination so as to minimize the side-effects. The identified target enzymes for known successful drugs are then verified by comparing the results with those in the existing literature. Side-effects reduction plays a crucial role in the study of drug development. A graph-based computational damage model is proposed and the theoretical analysis states the captured problem is NP-completeness. The proposed approaches can therefore contribute to the discovery of drug targets. Our developed software is available at " http://hkumath.hku.hk/~wkc/APBC2018-metabolic-network.zip ".

PREMER: a Tool to Infer Biological Networks.

PubMed

Villaverde, Alejandro F; Becker, Kolja; Banga, Julio R

2017-10-04

Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determining the direction of a causal link - requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems. The computational cost of such calculations can be alleviated by the use of compiled programs and parallelization. To this end we have developed PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction), a software toolbox that can run in parallel and sequential environments. It uses information theoretic criteria to recover network topology and determine the strength and causality of interactions, and allows incorporating prior knowledge, imputing missing data, and correcting outliers. PREMER is a free, open source software tool that does not require any commercial software. Its core algorithms are programmed in FORTRAN 90 and implement OpenMP directives. It has user interfaces in Python and MATLAB/Octave, and runs on Windows, Linux and OSX (https://sites.google.com/site/premertoolbox/).

Third Structure Determination by Powder Diffractometery Round Robin (SDPDRR-3)

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

Le Bail, A.; Cranswick, L; Adil, K

2009-01-01

The results from a third structure determination by powder diffractometry (SDPD) round robin are discussed. From the 175 potential participants having downloaded the powder data, nine sent a total of 12 solutions (8 and 4 for samples 1 and 2, respectively, a tetrahydrated calcium tartrate and a lanthanum tungstate). Participants used seven different computer programs for structure solution (ESPOIR, EXPO, FOX, PSSP, SHELXS, SUPERFLIP, and TOPAS), applying Patterson, direct methods, direct space methods, and charge flipping approach. It is concluded that solving a structure from powder data remains a challenge, at least one order of magnitude more difficult than solvingmore » a problem with similar complexity from single-crystal data. Nevertheless, a few more steps in the direction of increasing the SDPD rate of success were accomplished since the two previous round robins: this time, not only the computer program developers were successful but also some users. No result was obtained from crystal structure prediction experts.« less

Teachers and artificial intelligence. The Logo connection.

PubMed

Merbler, J B

1990-12-01

This article describes a three-phase program for training special education teachers to teach Logo and artificial intelligence. Logo is derived from the LISP computer language and is relatively simple to learn and use, and it is argued that these factors make it an ideal tool for classroom experimentation in basic artificial intelligence concepts. The program trains teachers to develop simple demonstrations of artificial intelligence using Logo. The material that the teachers learn to teach is suitable as an advanced level topic for intermediate- through secondary-level students enrolled in computer competency or similar courses. The material emphasizes problem-solving and thinking skills using a nonverbal expressive medium (Logo), thus it is deemed especially appropriate for hearing-impaired children. It is also sufficiently challenging for academically talented children, whether hearing or deaf. Although the notion of teachers as programmers is controversial, Logo is relatively easy to learn, has direct implications for education, and has been found to be an excellent tool for empowerment-for both teachers and children.

Parallelization of NAS Benchmarks for Shared Memory Multiprocessors

NASA Technical Reports Server (NTRS)

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

1998-01-01

This paper presents our experiences of parallelizing the sequential implementation of NAS benchmarks using compiler directives on SGI Origin2000 distributed shared memory (DSM) system. Porting existing applications to new high performance parallel and distributed computing platforms is a challenging task. Ideally, a user develops a sequential version of the application, leaving the task of porting to new generations of high performance computing systems to parallelization tools and compilers. Due to the simplicity of programming shared-memory multiprocessors, compiler developers have provided various facilities to allow the users to exploit parallelism. Native compilers on SGI Origin2000 support multiprocessing directives to allow users to exploit loop-level parallelism in their programs. Additionally, supporting tools can accomplish this process automatically and present the results of parallelization to the users. We experimented with these compiler directives and supporting tools by parallelizing sequential implementation of NAS benchmarks. Results reported in this paper indicate that with minimal effort, the performance gain is comparable with the hand-parallelized, carefully optimized, message-passing implementations of the same benchmarks.

High-Performance Signal Detection for Adverse Drug Events using MapReduce Paradigm.

PubMed

Fan, Kai; Sun, Xingzhi; Tao, Ying; Xu, Linhao; Wang, Chen; Mao, Xianling; Peng, Bo; Pan, Yue

2010-11-13

Post-marketing pharmacovigilance is important for public health, as many Adverse Drug Events (ADEs) are unknown when those drugs were approved for marketing. However, due to the large number of reported drugs and drug combinations, detecting ADE signals by mining these reports is becoming a challenging task in terms of computational complexity. Recently, a parallel programming model, MapReduce has been introduced by Google to support large-scale data intensive applications. In this study, we proposed a MapReduce-based algorithm, for common ADE detection approach, Proportional Reporting Ratio (PRR), and tested it in mining spontaneous ADE reports from FDA. The purpose is to investigate the possibility of using MapReduce principle to speed up biomedical data mining tasks using this pharmacovigilance case as one specific example. The results demonstrated that MapReduce programming model could improve the performance of common signal detection algorithm for pharmacovigilance in a distributed computation environment at approximately liner speedup rates.

SOFIA pointing history

NASA Astrophysics Data System (ADS)

Kärcher, Hans J.; Kunz, Nans; Temi, Pasquale; Krabbe, Alfred; Wagner, Jörg; Süß, Martin

2014-07-01

The original pointing accuracy requirement of the Stratospheric Observatory for Infrared Astronomy SOFIA was defined at the beginning of the program in the late 1980s as very challenging 0.2 arcsec rms. The early science flights of the observatory started in December 2010 and the observatory has reached in the mean time nearly 0.7 arcsec rms, which is sufficient for most of the SOFIA science instruments. NASA and DLR, the owners of SOFIA, are planning now a future 4 year program to bring the pointing down to the ultimate 0.2 arcsec rms. This may be the right time to recall the history of the pointing requirement and its verification and the possibility of its achievement via early computer models and wind tunnel tests, later computer aided end-to-end simulations up to the first commissioning flights some years ago. The paper recollects the tools used in the different project phases for the verification of the pointing performance, explains the achievements and may give hints for the planning of the upcoming final pointing improvement phase.

Adapting bioinformatics curricula for big data.

PubMed

Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

2016-01-01

Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. © The Author 2015. Published by Oxford University Press.

Adapting bioinformatics curricula for big data

PubMed Central

Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

2016-01-01

Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

dREL: a relational expression language for dictionary methods.

PubMed

Spadaccini, Nick; Castleden, Ian R; du Boulay, Doug; Hall, Sydney R

2012-08-27

The provision of precise metadata is an important but a largely underrated challenge for modern science [Nature 2009, 461, 145]. We describe here a dictionary methods language dREL that has been designed to enable complex data relationships to be expressed as formulaic scripts in data dictionaries written in DDLm [Spadaccini and Hall J. Chem. Inf. Model.2012 doi:10.1021/ci300075z]. dREL describes data relationships in a simple but powerful canonical form that is easy to read and understand and can be executed computationally to evaluate or validate data. The execution of dREL expressions is not a substitute for traditional scientific computation; it is to provide precise data dependency information to domain-specific definitions and a means for cross-validating data. Some scientific fields apply conventional programming languages to methods scripts but these tend to inhibit both dictionary development and accessibility. dREL removes the programming barrier and encourages the production of the metadata needed for seamless data archiving and exchange in science.

ASCR Cybersecurity for Scientific Computing Integrity - Research Pathways and Ideas Workshop

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

Peisert, Sean; Potok, Thomas E.; Jones, Todd

At the request of the U.S. Department of Energy's (DOE) Office of Science (SC) Advanced Scientific Computing Research (ASCR) program office, a workshop was held June 2-3, 2015, in Gaithersburg, MD, to identify potential long term (10 to +20 year) cybersecurity fundamental basic research and development challenges, strategies and roadmap facing future high performance computing (HPC), networks, data centers, and extreme-scale scientific user facilities. This workshop was a follow-on to the workshop held January 7-9, 2015, in Rockville, MD, that examined higher level ideas about scientific computing integrity specific to the mission of the DOE Office of Science. Issues includedmore » research computation and simulation that takes place on ASCR computing facilities and networks, as well as network-connected scientific instruments, such as those run by various DOE Office of Science programs. Workshop participants included researchers and operational staff from DOE national laboratories, as well as academic researchers and industry experts. Participants were selected based on the submission of abstracts relating to the topics discussed in the previous workshop report [1] and also from other ASCR reports, including "Abstract Machine Models and Proxy Architectures for Exascale Computing" [27], the DOE "Preliminary Conceptual Design for an Exascale Computing Initiative" [28], and the January 2015 machine learning workshop [29]. The workshop was also attended by several observers from DOE and other government agencies. The workshop was divided into three topic areas: (1) Trustworthy Supercomputing, (2) Extreme-Scale Data, Knowledge, and Analytics for Understanding and Improving Cybersecurity, and (3) Trust within High-end Networking and Data Centers. Participants were divided into three corresponding teams based on the category of their abstracts. The workshop began with a series of talks from the program manager and workshop chair, followed by the leaders for each of the three topics and a representative of each of the four major DOE Office of Science Advanced Scientific Computing Research Facilities: the Argonne Leadership Computing Facility (ALCF), the Energy Sciences Network (ESnet), the National Energy Research Scientific Computing Center (NERSC), and the Oak Ridge Leadership Computing Facility (OLCF). The rest of the workshop consisted of topical breakout discussions and focused writing periods that produced much of this report.« less

Evolvix BEST Names for semantic reproducibility across code2brain interfaces

PubMed Central

Scheuer, Katherine S.; Keel, Seth A.; Vyas, Vaibhav; Liblit, Ben; Hanlon, Bret; Ferris, Michael C.; Yin, John; Dutra, Inês; Pietsch, Anthony; Javid, Christine G.; Moog, Cecilia L.; Meyer, Jocelyn; Dresel, Jerdon; McLoone, Brian; Loberger, Sonya; Movaghar, Arezoo; Gilchrist‐Scott, Morgaine; Sabri, Yazeed; Sescleifer, Dave; Pereda‐Zorrilla, Ivan; Zietlow, Andrew; Smith, Rodrigo; Pietenpol, Samantha; Goldfinger, Jacob; Atzen, Sarah L.; Freiberg, Erika; Waters, Noah P.; Nusbaum, Claire; Nolan, Erik; Hotz, Alyssa; Kliman, Richard M.; Mentewab, Ayalew; Fregien, Nathan; Loewe, Martha

2016-01-01

Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general‐purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality. To protect learning and coding investments, C2B interfaces require long‐term backward compatibility and semantic reproducibility (accurate reproduction of computational meaning from coder‐brains to reader‐brains by code alone). Semantic reproducibility is often assumed until confusing synonyms degrade modeling in biology to deciphering exercises. We highlight empirical naming priorities from diverse individuals and roles of names in different modes of computing to show how naming easily becomes impossibly difficult. We present the Evolvix BEST (Brief, Explicit, Summarizing, Technical) Names concept for reducing naming priority conflicts, test it on a real challenge by naming subfolders for the Project Organization Stabilizing Tool system, and provide naming questionnaires designed to facilitate C2B debugging by improving names used as keywords in a stabilizing programming language. Our experiences inspired us to develop Evolvix using a flipped programming language design approach with some unexpected features and BEST Names at its core. PMID:27918836

Using the Principles of BIO2010 to Develop an Introductory, Interdisciplinary Course for Biology Students

PubMed Central

Adams, Peter; Goos, Merrilyn

2010-01-01

Modern biological sciences require practitioners to have increasing levels of knowledge, competence, and skills in mathematics and programming. A recent review of the science curriculum at the University of Queensland, a large, research-intensive institution in Australia, resulted in the development of a more quantitatively rigorous undergraduate program. Inspired by the National Research Council's BIO2010 report, a new interdisciplinary first-year course (SCIE1000) was created, incorporating mathematics and computer programming in the context of modern science. In this study, the perceptions of biological science students enrolled in SCIE1000 in 2008 and 2009 are measured. Analysis indicates that, as a result of taking SCIE1000, biological science students gained a positive appreciation of the importance of mathematics in their discipline. However, the data revealed that SCIE1000 did not contribute positively to gains in appreciation for computing and only slightly influenced students' motivation to enroll in upper-level quantitative-based courses. Further comparisons between 2008 and 2009 demonstrated the positive effect of using genuine, real-world contexts to enhance student perceptions toward the relevance of mathematics. The results support the recommendation from BIO2010 that mathematics should be introduced to biology students in first-year courses using real-world examples, while challenging the benefits of introducing programming in first-year courses. PMID:20810961

Accessible Earth: An accessible study abroad capstone for the geoscience curriculum

NASA Astrophysics Data System (ADS)

Bennett, R. A.; Lamb, D. A.

2017-12-01

International capstone field courses offer geoscience-students opportunities to reflect upon their knowledge, develop intercultural competence, appreciate diversity, and recognize themselves as geoscientists on a global scale. Such experiences are often described as pivotal to a geoscientist's education, a right of passage. However, field-based experiences present insurmountable barriers to many students, undermining the goal of inclusive excellence. Nevertheless, there remains a widespread belief that successful geoscientists are those able to traverse inaccessible terrain. One path forward from this apparent dilemma is emerging as we take steps to address a parallel challenge: as we move into the 21st century the geoscience workforce will require an ever increasing range of skills, including analysis, modeling, communication, and computational proficiency. Computer programing, laboratory experimentation, numerical simulation, etc, are inherently more accessible than fieldwork, yet equally valuable. Students interested in pursuing such avenues may be better served by capstone experiences that align more closely with their career goals. Moreover, many of the desirable learning outcomes attributed to field-based education are not unique to immersion in remote inaccessible locations. Affective and cognitive gains may also result from social bonding through extended time with peers and mentors, creative synthesis of knowledge, project-based learning, and intercultural experience. Developing an inclusive course for the geoscience curriculum requires considering all learners, including different genders, ages, physical abilities, familial dynamics, and a multitude of other attributes. The Accessible Earth Study Abroad Program endeavors to provide geoscience students an inclusive capstone experience focusing on modern geophysical observation systems (satellite based observations and permanent networks of ground-based instruments), computational thinking and methods of data science, scientific collaboration, and professional development. In this presentation, we will describe our thought process for creating the Accessible Earth curriculum, our successes to-date, and the anticipated challenges ahead.

Enhancements to TetrUSS for NASA Constellation Program

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Frink, Neal T.; Abdol-Hamid, Khaled S.; Samareh, Jamshid A,; Parlete, Edward B.; Taft, James R.

2011-01-01

The NASA Constellation program is utilizing Computational Fluid Dynamics (CFD) predictions for generating aerodynamic databases and design loads for the Ares I, Ares I-X, and Ares V launch vehicles and for aerodynamic databases for the Orion crew exploration vehicle and its launch abort system configuration. This effort presents several challenges to applied aerodynamicists due to complex geometries and flow physics, as well as from the juxtaposition of short schedule program requirements with high fidelity CFD simulations. NASA TetrUSS codes (GridTool/VGRID/USM3D) have been making extensive contributions in this effort. This paper will provide an overview of several enhancements made to the various elements of TetrUSS suite of codes. Representative TetrUSS solutions for selected Constellation program elements will be shown. Best practices guidelines and scripting developed for generating TetrUSS solutions in a production environment will also be described.

POCA Update: An NSF PAARE Project

NASA Astrophysics Data System (ADS)

Walter, Donald K.; Brittain, S. D.; Cash, J. L.; Hartmann, D. H.; Howell, S. B.; King, J. R.; Leising, M. D.; Mayo, E. A.; Mighell, K. J.; Smith, D. M., Jr.

2011-01-01

We report on the status of "A Partnership in Observational and Computational Astronomy (POCA)” under the NSF's "Partnerships in Astronomy and Astrophysics Research and Education (PAARE)" program. This partnership includes South Carolina State University (a Historically Black College/University), Clemson University (a Ph.D. granting institution) and the National Optical Astronomy Observatory. We have reached the midpoint of this 5-year award and discuss the successes, challenges and obstacles encountered to date. Included is a summary of our summer REU program, the POCA graduate fellowship program, faculty research capacity building, outreach activities, increased use of NSF facilities and shared resources. Additional POCA research presentations by the authors are described elsewhere in these proceedings. Support for this work was provided by the NSF PAARE program to South Carolina State University under award AST-0750814 as well as resources and support provided by Clemson University and the National Optical Astronomy Observatory.

Computational identification of potential multi-drug combinations for reduction of microglial inflammation in Alzheimer disease

PubMed Central

Anastasio, Thomas J.

2015-01-01

Like other neurodegenerative diseases, Alzheimer Disease (AD) has a prominent inflammatory component mediated by brain microglia. Reducing microglial inflammation could potentially halt or at least slow the neurodegenerative process. A major challenge in the development of treatments targeting brain inflammation is the sheer complexity of the molecular mechanisms that determine whether microglia become inflammatory or take on a more neuroprotective phenotype. The process is highly multifactorial, raising the possibility that a multi-target/multi-drug strategy could be more effective than conventional monotherapy. This study takes a computational approach in finding combinations of approved drugs that are potentially more effective than single drugs in reducing microglial inflammation in AD. This novel approach exploits the distinct advantages of two different computer programming languages, one imperative and the other declarative. Existing programs written in both languages implement the same model of microglial behavior, and the input/output relationships of both programs agree with each other and with data on microglia over an extensive test battery. Here the imperative program is used efficiently to screen the model for the most efficacious combinations of 10 drugs, while the declarative program is used to analyze in detail the mechanisms of action of the most efficacious combinations. Of the 1024 possible drug combinations, the simulated screen identifies only 7 that are able to move simulated microglia at least 50% of the way from a neurotoxic to a neuroprotective phenotype. Subsequent analysis shows that of the 7 most efficacious combinations, 2 stand out as superior both in strength and reliability. The model offers many experimentally testable and therapeutically relevant predictions concerning effective drug combinations and their mechanisms of action. PMID:26097457

Pattern-Recognition Algorithm for Locking Laser Frequency

NASA Technical Reports Server (NTRS)

Karayan, Vahag; Klipstein, William; Enzer, Daphna; Yates, Philip; Thompson, Robert; Wells, George

2006-01-01

A computer program serves as part of a feedback control system that locks the frequency of a laser to one of the spectral peaks of cesium atoms in an optical absorption cell. The system analyzes a saturation absorption spectrum to find a target peak and commands a laser-frequency-control circuit to minimize an error signal representing the difference between the laser frequency and the target peak. The program implements an algorithm consisting of the following steps: Acquire a saturation absorption signal while scanning the laser through the frequency range of interest. Condition the signal by use of convolution filtering. Detect peaks. Match the peaks in the signal to a pattern of known spectral peaks by use of a pattern-recognition algorithm. Add missing peaks. Tune the laser to the desired peak and thereafter lock onto this peak. Finding and locking onto the desired peak is a challenging problem, given that the saturation absorption signal includes noise and other spurious signal components; the problem is further complicated by nonlinearity and shifting of the voltage-to-frequency correspondence. The pattern-recognition algorithm, which is based on Hausdorff distance, is what enables the program to meet these challenges.

Brilliant gamma beams for industrial applications: new opportunities, new challenges

NASA Astrophysics Data System (ADS)

Iancu, V.; Suliman, G.; Turturica, G. V.; Iovea, M.; Daito, I.; Ohgaki, H.; Matei, C.; Ur, C. A.; Balabanski, D. L.

2016-10-01

The Nuclear Physics oriented pillar of the pan-European Extreme Light Infrastructure (ELI-NP) will host an ultra-bright, energy tunable, and quasi-monochromatic gamma-ray beam system in the range of 0.2-19.5 MeV produced by laser-Compton backscattering technique. The applied research program envisioned at ELI-NP targets to use nuclear resonance fluorescence (NRF) and computed tomography to provide new opportunities for industry and society. High sensitivity NRF-based investigations can be successfully applied to safeguard applications and management of radioactive wastes as well as to uncharted fields like cultural heritage and medical imaging. Gamma-ray radioscopy and computed tomography performed at ELI-NP has the potential to achieve high resolution in industrial-sized objects provided the detection challenges introduced by the unique characteristics of the gamma beam are overcome. Here we discuss the foreseen industrial applications that will benefit from the high quality and unique characteristics of ELI-NP gamma beam and the challenges they present. We present the experimental setups proposed to be implemented for this goal, discuss their performance based on analytical calculations and numerical Monte-Carlo simulations, and comment about constrains imposed by the limitation of current scintillator detectors. Several gamma-beam monitoring devices based on scintillator detectors will also be discussed.

Online System for Faster Multipoint Linkage Analysis via Parallel Execution on Thousands of Personal Computers

PubMed Central

Silberstein, M.; Tzemach, A.; Dovgolevsky, N.; Fishelson, M.; Schuster, A.; Geiger, D.

2006-01-01

Computation of LOD scores is a valuable tool for mapping disease-susceptibility genes in the study of Mendelian and complex diseases. However, computation of exact multipoint likelihoods of large inbred pedigrees with extensive missing data is often beyond the capabilities of a single computer. We present a distributed system called “SUPERLINK-ONLINE,” for the computation of multipoint LOD scores of large inbred pedigrees. It achieves high performance via the efficient parallelization of the algorithms in SUPERLINK, a state-of-the-art serial program for these tasks, and through the use of the idle cycles of thousands of personal computers. The main algorithmic challenge has been to efficiently split a large task for distributed execution in a highly dynamic, nondedicated running environment. Notably, the system is available online, which allows computationally intensive analyses to be performed with no need for either the installation of software or the maintenance of a complicated distributed environment. As the system was being developed, it was extensively tested by collaborating medical centers worldwide on a variety of real data sets, some of which are presented in this article. PMID:16685644

Multiscale Modeling in Computational Biomechanics: Determining Computational Priorities and Addressing Current Challenges

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

Tawhai, Merryn; Bischoff, Jeff; Einstein, Daniel R.

2009-05-01

Abstract In this article, we describe some current multiscale modeling issues in computational biomechanics from the perspective of the musculoskeletal and respiratory systems and mechanotransduction. First, we outline the necessity of multiscale simulations in these biological systems. Then we summarize challenges inherent to multiscale biomechanics modeling, regardless of the subdiscipline, followed by computational challenges that are system-specific. We discuss some of the current tools that have been utilized to aid research in multiscale mechanics simulations, and the priorities to further the field of multiscale biomechanics computation.

Low-Thrust Many-Revolution Trajectory Optimization via Differential Dynamic Programming and a Sundman Transformation

NASA Astrophysics Data System (ADS)

Aziz, Jonathan D.; Parker, Jeffrey S.; Scheeres, Daniel J.; Englander, Jacob A.

2018-01-01

Low-thrust trajectories about planetary bodies characteristically span a high count of orbital revolutions. Directing the thrust vector over many revolutions presents a challenging optimization problem for any conventional strategy. This paper demonstrates the tractability of low-thrust trajectory optimization about planetary bodies by applying a Sundman transformation to change the independent variable of the spacecraft equations of motion to an orbit angle and performing the optimization with differential dynamic programming. Fuel-optimal geocentric transfers are computed with the transfer duration extended up to 2000 revolutions. The flexibility of the approach to higher fidelity dynamics is shown with Earth's J 2 perturbation and lunar gravity included for a 500 revolution transfer.

Low-Thrust Many-Revolution Trajectory Optimization via Differential Dynamic Programming and a Sundman Transformation

NASA Astrophysics Data System (ADS)

Aziz, Jonathan D.; Parker, Jeffrey S.; Scheeres, Daniel J.; Englander, Jacob A.

2018-06-01

Low-thrust trajectories about planetary bodies characteristically span a high count of orbital revolutions. Directing the thrust vector over many revolutions presents a challenging optimization problem for any conventional strategy. This paper demonstrates the tractability of low-thrust trajectory optimization about planetary bodies by applying a Sundman transformation to change the independent variable of the spacecraft equations of motion to an orbit angle and performing the optimization with differential dynamic programming. Fuel-optimal geocentric transfers are computed with the transfer duration extended up to 2000 revolutions. The flexibility of the approach to higher fidelity dynamics is shown with Earth's J 2 perturbation and lunar gravity included for a 500 revolution transfer.

OpenARC: Extensible OpenACC Compiler Framework for Directive-Based Accelerator Programming Study

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

Lee, Seyong; Vetter, Jeffrey S

2014-01-01

Directive-based, accelerator programming models such as OpenACC have arisen as an alternative solution to program emerging Scalable Heterogeneous Computing (SHC) platforms. However, the increased complexity in the SHC systems incurs several challenges in terms of portability and productivity. This paper presents an open-sourced OpenACC compiler, called OpenARC, which serves as an extensible research framework to address those issues in the directive-based accelerator programming. This paper explains important design strategies and key compiler transformation techniques needed to implement the reference OpenACC compiler. Moreover, this paper demonstrates the efficacy of OpenARC as a research framework for directive-based programming study, by proposing andmore » implementing OpenACC extensions in the OpenARC framework to 1) support hybrid programming of the unified memory and separate memory and 2) exploit architecture-specific features in an abstract manner. Porting thirteen standard OpenACC programs and three extended OpenACC programs to CUDA GPUs shows that OpenARC performs similarly to a commercial OpenACC compiler, while it serves as a high-level research framework.« less

Adding question answering to an e-tutor for programming languages

NASA Astrophysics Data System (ADS)

Taylor, Kate; Moore, Simon

Control over a closed domain of textual material removes many question answering issues, as does an ontology that is closely intertwined with its sources. This pragmatic, shallow approach to many challenging areas of research in adaptive hypermedia, question answering, intelligent tutoring and humancomputer interaction has been put into practice at Cambridge in the Computer Science undergraduate course to teach the hardware description language Veri/og. This language itself poses many challenges as it crosses the interdisciplinary boundary between hardware and software engineers, giving rise to severalhuman ontologies as well as theprogramming language itself We present further results from ourformal and informal surveys. We look at further work to increase the dialogue between studentand tutor and export our knowledge to the Semantic Web.

A Case Study in Flight Computer Software Redesign

NASA Astrophysics Data System (ADS)

Shimoni, R.; Ben-Zur, Y.

2004-06-01

Historically many real-time systems were developed using technologies that are now obsolete. There is a need for upgrading these systems. A good development process is essential to achieve a well-designed software product. We, at MLM, a subsidary of Israel Aircraft Industries, faced a similar situation in the Flight Mission Computer (Main Airborne Computer-MAC) of the SHAVIT launcher. It was necessary to upgrade the computer hardware and we decided to update the software as well. During the last two years, we have designed and implemented and new version of the MAC software, to be run on a new and stronger target platform. We undertook to create a new version of the MAC program using modern software development techniques. The process included Object-Oriented design using a CASE tool suitable for embedded real-time systems. We have partially implemented the ROPES development process. In this article we present the difficulties and challenges we faced in the software development process.

Heterogeneous scalable framework for multiphase flows

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

Morris, Karla Vanessa

2013-09-01

Two categories of challenges confront the developer of computational spray models: those related to the computation and those related to the physics. Regarding the computation, the trend towards heterogeneous, multi- and many-core platforms will require considerable re-engineering of codes written for the current supercomputing platforms. Regarding the physics, accurate methods for transferring mass, momentum and energy from the dispersed phase onto the carrier fluid grid have so far eluded modelers. Significant challenges also lie at the intersection between these two categories. To be competitive, any physics model must be expressible in a parallel algorithm that performs well on evolving computermore » platforms. This work created an application based on a software architecture where the physics and software concerns are separated in a way that adds flexibility to both. The develop spray-tracking package includes an application programming interface (API) that abstracts away the platform-dependent parallelization concerns, enabling the scientific programmer to write serial code that the API resolves into parallel processes and threads of execution. The project also developed the infrastructure required to provide similar APIs to other application. The API allow object-oriented Fortran applications direct interaction with Trilinos to support memory management of distributed objects in central processing units (CPU) and graphic processing units (GPU) nodes for applications using C++.« less

Mobile Computing and Ubiquitous Networking: Concepts, Technologies and Challenges.

ERIC Educational Resources Information Center

Pierre, Samuel

2001-01-01

Analyzes concepts, technologies and challenges related to mobile computing and networking. Defines basic concepts of cellular systems. Describes the evolution of wireless technologies that constitute the foundations of mobile computing and ubiquitous networking. Presents characterization and issues of mobile computing. Analyzes economical and…

REDItools: high-throughput RNA editing detection made easy.

PubMed

Picardi, Ernesto; Pesole, Graziano

2013-07-15

The reliable detection of RNA editing sites from massive sequencing data remains challenging and, although several methodologies have been proposed, no computational tools have been released to date. Here, we introduce REDItools a suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. REDItools are in python programming language and freely available at http://code.google.com/p/reditools/. ernesto.picardi@uniba.it or graziano.pesole@uniba.it Supplementary data are available at Bioinformatics online.

NASA's Role in Aeronautics: A Workshop. Volume 6: Aeronautical research

NASA Technical Reports Server (NTRS)

1981-01-01

While each aspect of its aeronautical technology program is important to the current preeminence of the United States in aeronautics, the most essential contributions of NASA derive from its research. Successes and challenges in NASA's efforts to improve civil and military aviation are discussed for the following areas: turbulence, noise, supercritical aerodynamics, computational aerodynamics, fuels, high temperature materials, composite materials, single crystal components, powder metallurgy, and flight controls. Spin offs to engineering and other sciences explored include NASTRAN, lubricants, and composites.

The difficult legacy of Turing's wager.

PubMed

Thwaites, Andrew; Soltan, Andrew; Wieser, Eric; Nimmo-Smith, Ian

2017-08-01

Describing the human brain in mathematical terms is an important ambition of neuroscience research, yet the challenges remain considerable. It was Alan Turing, writing in 1950, who first sought to demonstrate how time-consuming such an undertaking would be. Through analogy to the computer program, Turing argued that arriving at a complete mathematical description of the mind would take well over a thousand years. In this opinion piece, we argue that - despite seventy years of progress in the field - his arguments remain both prescient and persuasive.

Managing computer-controlled operations

NASA Technical Reports Server (NTRS)

Plowden, J. B.

1985-01-01

A detailed discussion of Launch Processing System Ground Software Production is presented to establish the interrelationships of firing room resource utilization, configuration control, system build operations, and Shuttle data bank management. The production of a test configuration identifier is traced from requirement generation to program development. The challenge of the operational era is to implement fully automated utilities to interface with a resident system build requirements document to eliminate all manual intervention in the system build operations. Automatic update/processing of Shuttle data tapes will enhance operations during multi-flow processing.

DoD HPC Insights Fall 2016A publication of the Department of Defense High Performance Computing Modernization Program

DTIC Science & Technology

2016-09-01

HPCMP will continue to be a key resource in solving challenging problems for the Department of Defense . 1 Fall 2016 High-F idel i ty Simulat ions of...laser interactions. The group had studied plasma expansion experimentally, but this wasn’t sufficient to understand the problem . Feister adapted and...focused on increasing the efficiency of jet turbine engines and extending aircraft flight ranges by changing the shape (articulation) of the turbine

High-speed inlet research program and supporting analysis

NASA Technical Reports Server (NTRS)

Coltrin, Robert E.

1990-01-01

The technology challenges faced by the high speed inlet designer are discussed by describing the considerations that went into the design of the Mach 5 research inlet. It is shown that the emerging three dimensional viscous computational fluid dynamics (CFD) flow codes, together with small scale experiments, can be used to guide larger scale full inlet systems research. Then, in turn, the results of the large scale research, if properly instrumented, can be used to validate or at least to calibrate the CFD codes.

Time-Reversal Based Range Extension Technique for Ultra-wideband (UWB) Sensors and Applications in Tactical Communications and Networking

DTIC Science & Technology

2008-04-16

Zhen (Edward) Hu Peng (Peter) Zhang Yu Song Amanpreet Singh Saini Corey Cooke April 16, 2006 Department of Electrical and Computer Engineering Center...and RF frequency agility is the most challenging issue for spectrum sensing. The radio under development is an ultra-wideband software -defined radio...PC USB programming cable and accom- panying PC software as well as download test vectors to the waveform memory module, as shown in Figure 3.25,3I

Development of an imaging-planning program for screen/film and computed radiography mammography for breasts with short chest wall to nipple distance.

PubMed

Dong, S L; Su, J L; Yeh, Y H; Chu, T C; Lin, Y C; Chuang, K S

2011-04-01

Imaging breasts with a short chest wall to nipple distance (CWND) using a traditional mammographic X-ray unit is a technical challenge for mammographers. The purpose of this study is the development of an imaging-planning program to assist in determination of imaging parameters of screen/film (SF) and computed radiography (CR) mammography for short CWND breasts. A traditional mammographic X-ray unit (Mammomat 3000, Siemens, Munich, Germany) was employed. The imaging-planning program was developed by combining the compressed breast thickness correction, the equivalent polymethylmethacrylate thickness assessment for breasts and the tube loading (mAs) measurement. Both phantom exposures and a total of 597 exposures were used for examining the imaging-planning program. Results of the phantom study show that the tube loading rapidly decreased with the CWND when the automatic exposure control (AEC) detector was not fully covered by the phantom. For patient exposures with the AEC fully covered by breast tissue, the average fractional tube loadings, defined as the ratio of the predicted mAs using the imaging-planning program and mAs of the mammogram, were 1.10 and 1.07 for SF and CR mammograms, respectively. The predicted mAs values were comparable to the mAs values, as determined by the AEC. By applying the imaging-planning program in clinical practice, the experiential dependence of the mammographer for determination of the imaging parameters for short CWND breasts is minimised.

Nonlinear Boltzmann equation for the homogeneous isotropic case: Minimal deterministic Matlab program

NASA Astrophysics Data System (ADS)

Asinari, Pietro

2010-10-01

The homogeneous isotropic Boltzmann equation (HIBE) is a fundamental dynamic model for many applications in thermodynamics, econophysics and sociodynamics. Despite recent hardware improvements, the solution of the Boltzmann equation remains extremely challenging from the computational point of view, in particular by deterministic methods (free of stochastic noise). This work aims to improve a deterministic direct method recently proposed [V.V. Aristov, Kluwer Academic Publishers, 2001] for solving the HIBE with a generic collisional kernel and, in particular, for taking care of the late dynamics of the relaxation towards the equilibrium. Essentially (a) the original problem is reformulated in terms of particle kinetic energy (exact particle number and energy conservation during microscopic collisions) and (b) the computation of the relaxation rates is improved by the DVM-like correction, where DVM stands for Discrete Velocity Model (ensuring that the macroscopic conservation laws are exactly satisfied). Both these corrections make possible to derive very accurate reference solutions for this test case. Moreover this work aims to distribute an open-source program (called HOMISBOLTZ), which can be redistributed and/or modified for dealing with different applications, under the terms of the GNU General Public License. The program has been purposely designed in order to be minimal, not only with regards to the reduced number of lines (less than 1000), but also with regards to the coding style (as simple as possible). Program summaryProgram title: HOMISBOLTZ Catalogue identifier: AEGN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 23 340 No. of bytes in distributed program, including test data, etc.: 7 635 236 Distribution format: tar.gz Programming language: Tested with Matlab version ⩽6.5. However, in principle, any recent version of Matlab or Octave should work Computer: All supporting Matlab or Octave Operating system: All supporting Matlab or Octave RAM: 300 MBytes Classification: 23 Nature of problem: The problem consists in integrating the homogeneous Boltzmann equation for a generic collisional kernel in case of isotropic symmetry, by a deterministic direct method. Difficulties arise from the multi-dimensionality of the collisional operator and from satisfying the conservation of particle number and energy (momentum is trivial for this test case) as accurately as possible, in order to preserve the late dynamics. Solution method: The solution is based on the method proposed by Aristov (2001) [1], but with two substantial improvements: (a) the original problem is reformulated in terms of particle kinetic energy (this allows one to ensure exact particle number and energy conservation during microscopic collisions) and (b) a DVM-like correction (where DVM stands for Discrete Velocity Model) is adopted for improving the relaxation rates (this allows one to satisfy exactly the conservation laws at macroscopic level, which is particularly important for describing the late dynamics in the relaxation towards the equilibrium). Both these corrections make possible to derive very accurate reference solutions for this test case. Restrictions: The nonlinear Boltzmann equation is extremely challenging from the computational point of view, in particular for deterministic methods, despite the increased computational power of recent hardware. In this work, only the homogeneous isotropic case is considered, for making possible the development of a minimal program (by a simple scripting language) and allowing the user to check the advantages of the proposed improvements beyond Aristov's (2001) method [1]. The initial conditions are supposed parameterized according to a fixed analytical expression, but this can be easily modified. Running time: From minutes to hours (depending on the adopted discretization of the kinetic energy space). For example, on a 64 bit workstation with Intel CoreTM i7-820Q Quad Core CPU at 1.73 GHz and 8 MBytes of RAM, the provided test run (with the corresponding binary data file storing the pre-computed relaxation rates) requires 154 seconds. References:V.V. Aristov, Direct Methods for Solving the Boltzmann Equation and Study of Nonequilibrium Flows, Kluwer Academic Publishers, 2001.

WaterBotics: Pooling Students to STEM

NASA Astrophysics Data System (ADS)

Stambaugh, Beverly

2015-04-01

The STEM workforce of the future is sitting in today's K-12 classrooms, attending summer camps, and participating in after-school programs. How do we attract more youth -- particularly those currently underrepresented in STEM fields such as girls and minorities -- to explore the marvels of engineering and science? How do we entice them to become active participants - not merely witnesses - in the creation of solutions for our global neighborhood's greatest challenges, from environmental cleanup, to safe and efficient energy production, to improvements in healthcare? The WaterBotics program is one vehicle that has demonstrated success in engaging young learners. This underwater robotics program is designed to provide hands-on experiences for middle and high school age youth to engineering design, information technology tools, and science concepts, and to increase awareness and interest in engineering and IT careers. Middle and high school participants demonstrate increased enjoyment in studying science and engineering and interest in STEM careers as a result of WaterBotics. Such results can be seen from a statewide initiative that reached more than 2,600 middle and high school students in New Jersey in 2006-09 where student learning of science concepts and programming increased (McGrath et al, 2009, 2008). These findings provide the impetus to expand the WaterBotics program nationally. The curriculum can be used either in traditional classroom settings or in after-school and summer-camp settings. This problem-based program requires teams of students to work together to design, build, test, and redesign underwater robots, or "bots" made of LEGO® and other components. Students use the NXT and LEGO Mindstorms® software to program their robots to maneuver in the water, thereby gaining valuable experience with computer programming, as well as 21st Century skills. Teams must complete a series of increasingly sophisticated challenges which culminates with a final challenge that integrates learning from the prior challenges. The nature of these challenges allows for easy adaptation to various real-world scenarios for students to engage in, such as developing a submarine for ocean floor study or designing a vehicle to explore and mine the ocean for mineral resources. First-hand experience with WaterBotics curriculum has shown the increased engagement and excitement for STEM. Starting with a peanut butter and jelly sandwich leads to amazing discovery as students work through the engineering design process, sketching and building their LEGO robots and learning the steps to simple programs that allow their robotic creations to complete various tasks. With LEGOs being so easy to use, students can easily revise their design over and over again until it looks and works as it should. Once the students have the opportunity to test their design in the water for the first time, they are hooked. They can see that something they designed and built actually completes the task, even if it takes multiple tries, and they want to try the next challenge.

Opening Remarks: SciDAC 2007

NASA Astrophysics Data System (ADS)

Strayer, Michael

2007-09-01

Good morning. Welcome to Boston, the home of the Red Sox, Celtics and Bruins, baked beans, tea parties, Robert Parker, and SciDAC 2007. A year ago I stood before you to share the legacy of the first SciDAC program and identify the challenges that we must address on the road to petascale computing—a road E E Cummins described as `. . . never traveled, gladly beyond any experience.' Today, I want to explore the preparations for the rapidly approaching extreme scale (X-scale) generation. These preparations are the first step propelling us along the road of burgeoning scientific discovery enabled by the application of X- scale computing. We look to petascale computing and beyond to open up a world of discovery that cuts across scientific fields and leads us to a greater understanding of not only our world, but our universe. As part of the President's America Competitiveness Initiative, the ASCR Office has been preparing a ten year vision for computing. As part of this planning the LBNL together with ORNL and ANL hosted three town hall meetings on Simulation and Modeling at the Exascale for Energy, Ecological Sustainability and Global Security (E3). The proposed E3 initiative is organized around four programmatic themes: Engaging our top scientists, engineers, computer scientists and applied mathematicians; investing in pioneering large-scale science; developing scalable analysis algorithms, and storage architectures to accelerate discovery; and accelerating the build-out and future development of the DOE open computing facilities. It is clear that we have only just started down the path to extreme scale computing. Plan to attend Thursday's session on the out-briefing and discussion of these meetings. The road to the petascale has been at best rocky. In FY07, the continuing resolution provided 12% less money for Advanced Scientific Computing than either the President, the Senate, or the House. As a consequence, many of you had to absorb a no cost extension for your SciDAC work. I am pleased that the President's FY08 budget restores the funding for SciDAC. Quoting from Advanced Scientific Computing Research description in the House Energy and Water Development Appropriations Bill for FY08, "Perhaps no other area of research at the Department is so critical to sustaining U.S. leadership in science and technology, revolutionizing the way science is done and improving research productivity." As a society we need to revolutionize our approaches to energy, environmental and global security challenges. As we go forward along the road to the X-scale generation, the use of computation will continue to be a critical tool along with theory and experiment in understanding the behavior of the fundamental components of nature as well as for fundamental discovery and exploration of the behavior of complex systems. The foundation to overcome these societal challenges will build from the experiences and knowledge gained as you, members of our SciDAC research teams, work together to attack problems at the tera- and peta- scale. If SciDAC is viewed as an experiment for revolutionizing scientific methodology, then a strategic goal of ASCR program must be to broaden the intellectual base prepared to address the challenges of the new X-scale generation of computing. We must focus our computational science experiences gained over the past five years on the opportunities introduced with extreme scale computing. Our facilities are on a path to provide the resources needed to undertake the first part of our journey. Using the newly upgraded 119 teraflop Cray XT system at the Leadership Computing Facility, SciDAC research teams have in three days performed a 100-year study of the time evolution of the atmospheric CO2 concentration originating from the land surface. The simulation of the El Nino/Southern Oscillation which was part of this study has been characterized as `the most impressive new result in ten years' gained new insight into the behavior of superheated ionic gas in the ITER reactor as a result of an AORSA run on 22,500 processors that achieved over 87 trillion calculations per second (87 teraflops) which is 74% of the system's theoretical peak. Tomorrow, Argonne and IBM will announce that the first IBM Blue Gene/P, a 100 teraflop system, will be shipped to the Argonne Leadership Computing Facility later this fiscal year. By the end of FY2007 ASCR high performance and leadership computing resources will include the 114 teraflop IBM Blue Gene/P; a 102 teraflop Cray XT4 at NERSC and a 119 teraflop Cray XT system at Oak Ridge. Before ringing in the New Year, Oak Ridge will upgrade to 250 teraflops with the replacement of the dual core processors with quad core processors and Argonne will upgrade to between 250-500 teraflops, and next year, a petascale Cray Baker system is scheduled for delivery at Oak Ridge. The multidisciplinary teams in our SciDAC Centers for Enabling Technologies and our SciDAC Institutes must continue to work with our Scientific Application teams to overcome the barriers that prevent effective use of these new systems. These challenges include: the need for new algorithms as well as operating system and runtime software and tools which scale to parallel systems composed of hundreds of thousands processors; program development environments and tools which scale effectively and provide ease of use for developers and scientific end users; and visualization and data management systems that support moving, storing, analyzing, manipulating and visualizing multi-petabytes of scientific data and objects. The SciDAC Centers, located primarily at our DOE national laboratories will take the lead in ensuring that critical computer science and applied mathematics issues are addressed in a timely and comprehensive fashion and to address issues associated with research software lifecycle. In contrast, the SciDAC Institutes, which are university-led centers of excellence, will have more flexibility to pursue new research topics through a range of research collaborations. The Institutes will also work to broaden the intellectual and researcher base—conducting short courses and summer schools to take advantage of new high performance computing capabilities. The SciDAC Outreach Center at Lawrence Berkeley National Laboratory complements the outreach efforts of the SciDAC Institutes. The Outreach Center is our clearinghouse for SciDAC activities and resources and will communicate with the high performance computing community in part to understand their needs for workshops, summer schools and institutes. SciDAC is not ASCR's only effort to broaden the computational science community needed to meet the challenges of the new X-scale generation. I hope that you were able to attend the Computational Science Graduate Fellowship poster session last night. ASCR developed the fellowship in 1991 to meet the nation's growing need for scientists and technology professionals with advanced computer skills. CSGF, now jointly funded between ASCR and NNSA, is more than a traditional academic fellowship. It has provided more than 200 of the best and brightest graduate students with guidance, support and community in preparing them as computational scientists. Today CSGF alumni are bringing their diverse top-level skills and knowledge to research teams at DOE laboratories and in industries such as Proctor and Gamble, Lockheed Martin and Intel. At universities they are working to train the next generation of computational scientists. To build on this success, we intend to develop a wholly new Early Career Principal Investigator's (ECPI) program. Our objective is to stimulate academic research in scientific areas within ASCR's purview especially among faculty in early stages of their academic careers. Last February, we lost Ken Kennedy, one of the leading lights of our community. As we move forward into the extreme computing generation, his vision and insight will be greatly missed. In memorial to Ken Kennedy, we shall designate the ECPI grants to beginning faculty in Computer Science as the Ken Kennedy Fellowship. Watch the ASCR website for more information about ECPI and other early career programs in the computational sciences. We look to you, our scientists, researchers, and visionaries to take X-scale computing and use it to explode scientific discovery in your fields. We at SciDAC will work to ensure that this tool is the sharpest and most precise and efficient instrument to carve away the unknown and reveal the most exciting secrets and stimulating scientific discoveries of our time. The partnership between research and computing is the marriage that will spur greater discovery, and as Spencer said to Susan in Robert Parker's novel, `Sudden Mischief', `We stick together long enough, and we may get as smart as hell'. Michael Strayer

Computational biology of RNA interactions.

PubMed

Dieterich, Christoph; Stadler, Peter F

2013-01-01

The biodiversity of the RNA world has been underestimated for decades. RNA molecules are key building blocks, sensors, and regulators of modern cells. The biological function of RNA molecules cannot be separated from their ability to bind to and interact with a wide space of chemical species, including small molecules, nucleic acids, and proteins. Computational chemists, physicists, and biologists have developed a rich tool set for modeling and predicting RNA interactions. These interactions are to some extent determined by the binding conformation of the RNA molecule. RNA binding conformations are approximated with often acceptable accuracy by sequence and secondary structure motifs. Secondary structure ensembles of a given RNA molecule can be efficiently computed in many relevant situations by employing a standard energy model for base pair interactions and dynamic programming techniques. The case of bi-molecular RNA-RNA interactions can be seen as an extension of this approach. However, unbiased transcriptome-wide scans for local RNA-RNA interactions are computationally challenging yet become efficient if the binding motif/mode is known and other external information can be used to confine the search space. Computational methods are less developed for proteins and small molecules, which bind to RNA with very high specificity. Binding descriptors of proteins are usually determined by in vitro high-throughput assays (e.g., microarrays or sequencing). Intriguingly, recent experimental advances, which are mostly based on light-induced cross-linking of binding partners, render in vivo binding patterns accessible yet require new computational methods for careful data interpretation. The grand challenge is to model the in vivo situation where a complex interplay of RNA binders competes for the same target RNA molecule. Evidently, bioinformaticians are just catching up with the impressive pace of these developments. Copyright © 2012 John Wiley & Sons, Ltd.

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.

Non-standard analysis and embedded software

NASA Technical Reports Server (NTRS)

Platek, Richard

1995-01-01

One model for computing in the future is ubiquitous, embedded computational devices analogous to embedded electrical motors. Many of these computers will control physical objects and processes. Such hidden computerized environments introduce new safety and correctness concerns whose treatment go beyond present Formal Methods. In particular, one has to begin to speak about Real Space software in analogy with Real Time software. By this we mean, computerized systems which have to meet requirements expressed in the real geometry of space. How to translate such requirements into ordinary software specifications and how to carry out proofs is a major challenge. In this talk we propose a research program based on the use of no-standard analysis. Much detail remains to be carried out. The purpose of the talk is to inform the Formal Methods community that Non-Standard Analysis provides a possible avenue to attack which we believe will be fruitful.

Mississippi Curriculum Framework for Computer Information Systems Technology. Computer Information Systems Technology (Program CIP: 52.1201--Management Information Systems & Business Data). Computer Programming (Program CIP: 52.1201). Network Support (Program CIP: 52.1290--Computer Network Support Technology). Postsecondary Programs.

ERIC Educational Resources Information Center

Mississippi Research and Curriculum Unit for Vocational and Technical Education, State College.

This document, which is intended for use by community and junior colleges throughout Mississippi, contains curriculum frameworks for two programs in the state's postsecondary-level computer information systems technology cluster: computer programming and network support. Presented in the introduction are program descriptions and suggested course…

Parallel programming of gradient-based iterative image reconstruction schemes for optical tomography.

PubMed

Hielscher, Andreas H; Bartel, Sebastian

2004-02-01

Optical tomography (OT) is a fast developing novel imaging modality that uses near-infrared (NIR) light to obtain cross-sectional views of optical properties inside the human body. A major challenge remains the time-consuming, computational-intensive image reconstruction problem that converts NIR transmission measurements into cross-sectional images. To increase the speed of iterative image reconstruction schemes that are commonly applied for OT, we have developed and implemented several parallel algorithms on a cluster of workstations. Static process distribution as well as dynamic load balancing schemes suitable for heterogeneous clusters and varying machine performances are introduced and tested. The resulting algorithms are shown to accelerate the reconstruction process to various degrees, substantially reducing the computation times for clinically relevant problems.

Remote control missile model test

NASA Technical Reports Server (NTRS)

Allen, Jerry M.; Shaw, David S.; Sawyer, Wallace C.

1989-01-01

An extremely large, systematic, axisymmetric body/tail fin data base was gathered through tests of an innovative missile model design which is described herein. These data were originally obtained for incorporation into a missile aerodynamics code based on engineering methods (Program MISSILE3), but can also be used as diagnostic test cases for developing computational methods because of the individual-fin data included in the data base. Detailed analysis of four sample cases from these data are presented to illustrate interesting individual-fin force and moment trends. These samples quantitatively show how bow shock, fin orientation, fin deflection, and body vortices can produce strong, unusual, and computationally challenging effects on individual fin loads. Comparisons between these data and calculations from the SWINT Euler code are also presented.

CFD Vision 2030 Study: A Path to Revolutionary Computational Aerosciences

NASA Technical Reports Server (NTRS)

Slotnick, Jeffrey; Khodadoust, Abdollah; Alonso, Juan; Darmofal, David; Gropp, William; Lurie, Elizabeth; Mavriplis, Dimitri

2014-01-01

This report documents the results of a study to address the long range, strategic planning required by NASA's Revolutionary Computational Aerosciences (RCA) program in the area of computational fluid dynamics (CFD), including future software and hardware requirements for High Performance Computing (HPC). Specifically, the "Vision 2030" CFD study is to provide a knowledge-based forecast of the future computational capabilities required for turbulent, transitional, and reacting flow simulations across a broad Mach number regime, and to lay the foundation for the development of a future framework and/or environment where physics-based, accurate predictions of complex turbulent flows, including flow separation, can be accomplished routinely and efficiently in cooperation with other physics-based simulations to enable multi-physics analysis and design. Specific technical requirements from the aerospace industrial and scientific communities were obtained to determine critical capability gaps, anticipated technical challenges, and impediments to achieving the target CFD capability in 2030. A preliminary development plan and roadmap were created to help focus investments in technology development to help achieve the CFD vision in 2030.

Memristor-Based Analog Computation and Neural Network Classification with a Dot Product Engine.

PubMed

Hu, Miao; Graves, Catherine E; Li, Can; Li, Yunning; Ge, Ning; Montgomery, Eric; Davila, Noraica; Jiang, Hao; Williams, R Stanley; Yang, J Joshua; Xia, Qiangfei; Strachan, John Paul

2018-03-01

Using memristor crossbar arrays to accelerate computations is a promising approach to efficiently implement algorithms in deep neural networks. Early demonstrations, however, are limited to simulations or small-scale problems primarily due to materials and device challenges that limit the size of the memristor crossbar arrays that can be reliably programmed to stable and analog values, which is the focus of the current work. High-precision analog tuning and control of memristor cells across a 128 × 64 array is demonstrated, and the resulting vector matrix multiplication (VMM) computing precision is evaluated. Single-layer neural network inference is performed in these arrays, and the performance compared to a digital approach is assessed. Memristor computing system used here reaches a VMM accuracy equivalent of 6 bits, and an 89.9% recognition accuracy is achieved for the 10k MNIST handwritten digit test set. Forecasts show that with integrated (on chip) and scaled memristors, a computational efficiency greater than 100 trillion operations per second per Watt is possible. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Semantic Web Services Challenge, Results from the First Year. Series: Semantic Web And Beyond, Volume 8.

NASA Astrophysics Data System (ADS)

Petrie, C.; Margaria, T.; Lausen, H.; Zaremba, M.

Explores trade-offs among existing approaches. Reveals strengths and weaknesses of proposed approaches, as well as which aspects of the problem are not yet covered. Introduces software engineering approach to evaluating semantic web services. Service-Oriented Computing is one of the most promising software engineering trends because of the potential to reduce the programming effort for future distributed industrial systems. However, only a small part of this potential rests on the standardization of tools offered by the web services stack. The larger part of this potential rests upon the development of sufficient semantics to automate service orchestration. Currently there are many different approaches to semantic web service descriptions and many frameworks built around them. A common understanding, evaluation scheme, and test bed to compare and classify these frameworks in terms of their capabilities and shortcomings, is necessary to make progress in developing the full potential of Service-Oriented Computing. The Semantic Web Services Challenge is an open source initiative that provides a public evaluation and certification of multiple frameworks on common industrially-relevant problem sets. This edited volume reports on the first results in developing common understanding of the various technologies intended to facilitate the automation of mediation, choreography and discovery for Web Services using semantic annotations. Semantic Web Services Challenge: Results from the First Year is designed for a professional audience composed of practitioners and researchers in industry. Professionals can use this book to evaluate SWS technology for their potential practical use. The book is also suitable for advanced-level students in computer science.

Towards Large-area Field-scale Operational Evapotranspiration for Water Use Mapping

NASA Astrophysics Data System (ADS)

Senay, G. B.; Friedrichs, M.; Morton, C.; Huntington, J. L.; Verdin, J.

2017-12-01

Field-scale evapotranspiration (ET) estimates are needed for improving surface and groundwater use and water budget studies. Ideally, field-scale ET estimates would be at regional to national levels and cover long time periods. As a result of large data storage and computational requirements associated with processing field-scale satellite imagery such as Landsat, numerous challenges remain to develop operational ET estimates over large areas for detailed water use and availability studies. However, the combination of new science, data availability, and cloud computing technology is enabling unprecedented capabilities for ET mapping. To demonstrate this capability, we used Google's Earth Engine cloud computing platform to create nationwide annual ET estimates with 30-meter resolution Landsat ( 16,000 images) and gridded weather data using the Operational Simplified Surface Energy Balance (SSEBop) model in support of the National Water Census, a USGS research program designed to build decision support capacity for water management agencies and other natural resource managers. By leveraging Google's Earth Engine Application Programming Interface (API) and developing software in a collaborative, open-platform environment, we rapidly advance from research towards applications for large-area field-scale ET mapping. Cloud computing of the Landsat image archive combined with other satellite, climate, and weather data, is creating never imagined opportunities for assessing ET model behavior and uncertainty, and ultimately providing the ability for more robust operational monitoring and assessment of water use at field-scales.

Challenges and considerations for the design and production of a purpose-optimized body-worn wrist-watch computer

NASA Astrophysics Data System (ADS)

Narayanaswami, Chandra; Raghunath, Mandayam T.

2004-09-01

We outline a collection of technological challenges in the design of wearable computers with a focus on one of the most desirable form-factors, the wrist watch. We describe our experience with building three generations of wrist watch computers. We built these research prototypes as platforms to investigate the fundamental limitations of wearable computing. Results of our investigations are presented in the form of challenges that have been overcome and those that still remain.

MO-E-18A-01: Imaging: Best Practices In Pediatric Imaging

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

Willis, C; Strauss, K; MacDougall, R

This imaging educational program will focus on solutions to common pediatric imaging challenges. The speakers will present collective knowledge on best practices in pediatric imaging from their experience at dedicated children's hospitals. Areas of focus will include general radiography, the use of manual and automatic dose management in computed tomography, and enterprise-wide radiation dose management in the pediatric practice. The educational program will begin with a discussion of the complexities of exposure factor control in pediatric projection radiography. Following this introduction will be two lectures addressing the challenges of computed tomography (CT) protocol optimization in the pediatric population. The firstmore » will address manual CT protocol design in order to establish a managed radiation dose for any pediatric exam on any CT scanner. The second CT lecture will focus on the intricacies of automatic dose modulation in pediatric imaging with an emphasis on getting reliable results in algorithmbased technique selection. The fourth and final lecture will address the key elements needed to developing a comprehensive radiation dose management program for the pediatric environment with particular attention paid to new regulations and obligations of practicing medical physicists. Learning Objectives: To understand how general radiographic techniques can be optimized using exposure indices in order to improve pediatric radiography. To learn how to establish diagnostic dose reference levels for pediatric patients as a function of the type of examination, patient size, and individual design characteristics of the CT scanner. To learn how to predict the patient's radiation dose prior to the exam and manually adjust technique factors if necessary to match the patient's dose to the department's established dose reference levels. To learn how to utilize manufacturer-provided automatic dose modulation technology to consistently achieve patient doses within the department's established size-based diagnostic reference range. To understand the key components of an enterprise-wide pediatric dose management program that integrates the expanding responsibilities of medial physicists in the new era of dose monitoring.« less

Flexible Description Language for HPC based Processing of Remote Sense Data

NASA Astrophysics Data System (ADS)

Nandra, Constantin; Gorgan, Dorian; Bacu, Victor

2016-04-01

When talking about Big Data, the most challenging aspect lays in processing them in order to gain new insight, find new patterns and gain knowledge from them. This problem is likely most apparent in the case of Earth Observation (EO) data. With ever higher numbers of data sources and increasing data acquisition rates, dealing with EO data is indeed a challenge [1]. Geoscientists should address this challenge by using flexible and efficient tools and platforms. To answer this trend, the BigEarth project [2] aims to combine the advantages of high performance computing solutions with flexible processing description methodologies in order to reduce both task execution times and task definition time and effort. As a component of the BigEarth platform, WorDeL (Workflow Description Language) [3] is intended to offer a flexible, compact and modular approach to the task definition process. WorDeL, unlike other description alternatives such as Python or shell scripts, is oriented towards the description topologies, using them as abstractions for the processing programs. This feature is intended to make it an attractive alternative for users lacking in programming experience. By promoting modular designs, WorDeL not only makes the processing descriptions more user-readable and intuitive, but also helps organizing the processing tasks into independent sub-tasks, which can be executed in parallel on multi-processor platforms in order to improve execution times. As a BigEarth platform [4] component, WorDeL represents the means by which the user interacts with the system, describing processing algorithms in terms of existing operators and workflows [5], which are ultimately translated into sets of executable commands. The WorDeL language has been designed to help in the definition of compute-intensive, batch tasks which can be distributed and executed on high-performance, cloud or grid-based architectures in order to improve the processing time. Main references for further information: [1] Gorgan, D., "Flexible and Adaptive Processing of Earth Observation Data over High Performance Computation Architectures", International Conference and Exhibition Satellite 2015, August 17-19, Houston, Texas, USA. [2] Bigearth project - flexible processing of big earth data over high performance computing architectures. http://cgis.utcluj.ro/bigearth, (2014) [3] Nandra, C., Gorgan, D., "Workflow Description Language for Defining Big Earth Data Processing Tasks", Proceedings of the Intelligent Computer Communication and Processing (ICCP), IEEE-Press, pp. 461-468, (2015). [4] Bacu, V., Stefan, T., Gorgan, D., "Adaptive Processing of Earth Observation Data on Cloud Infrastructures Based on Workflow Description", Proceedings of the Intelligent Computer Communication and Processing (ICCP), IEEE-Press, pp.444-454, (2015). [5] Mihon, D., Bacu, V., Colceriu, V., Gorgan, D., "Modeling of Earth Observation Use Cases through the KEOPS System", Proceedings of the Intelligent Computer Communication and Processing (ICCP), IEEE-Press, pp. 455-460, (2015).

Virtualizing access to scientific applications with the Application Hosting Environment

NASA Astrophysics Data System (ADS)

Zasada, S. J.; Coveney, P. V.

2009-12-01

The growing power and number of high performance computing resources made available through computational grids present major opportunities as well as a number of challenges to the user. At issue is how these resources can be accessed and how their power can be effectively exploited. In this paper we first present our views on the usability of contemporary high-performance computational resources. We introduce the concept of grid application virtualization as a solution to some of the problems with grid-based HPC usability. We then describe a middleware tool that we have developed to realize the virtualization of grid applications, the Application Hosting Environment (AHE), and describe the features of the new release, AHE 2.0, which provides access to a common platform of federated computational grid resources in standard and non-standard ways. Finally, we describe a case study showing how AHE supports clinical use of whole brain blood flow modelling in a routine and automated fashion. Program summaryProgram title: Application Hosting Environment 2.0 Catalogue identifier: AEEJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public Licence, Version 2 No. of lines in distributed program, including test data, etc.: not applicable No. of bytes in distributed program, including test data, etc.: 1 685 603 766 Distribution format: tar.gz Programming language: Perl (server), Java (Client) Computer: x86 Operating system: Linux (Server), Linux/Windows/MacOS (Client) RAM: 134 217 728 (server), 67 108 864 (client) bytes Classification: 6.5 External routines: VirtualBox (server), Java (client) Nature of problem: The middleware that makes grid computing possible has been found by many users to be too unwieldy, and presents an obstacle to use rather than providing assistance [1,2]. Such problems are compounded when one attempts to harness the power of a grid, or a federation of different grids, rather than just a single resource on the grid. Solution method: To address the above problem, we have developed AHE, a lightweight interface, designed to simplify the process of running scientific codes on a grid of HPC and local resources. AHE does this by introducing a layer of middleware between the user and the grid, which encapsulates much of the complexity associated with launching grid applications. Unusual features: The server is distributed as a VirtualBox virtual machine. VirtualBox ( http://www.virtualbox.org) must be downloaded and installed in order to run the AHE server virtual machine. Details of how to do this are given in the AHE 2.0 Quick Start Guide. Running time: Not applicable References:J. Chin, P.V. Coveney, Towards tractable toolkits for the grid: A plea for lightweight, useable middleware, NeSC Technical Report, 2004, http://nesc.ac.uk/technical_papers/UKeS-2004-01.pdf. P.V. Coveney, R.S. Saksena, S.J. Zasada, M. McKeown, S. Pickles, The Application Hosting Environment: Lightweight middleware for grid-based computational science, Computer Physics Communications 176 (2007) 406-418.

78 FR 73195 - Privacy Act of 1974: CMS Computer Matching Program Match No. 2013-01; HHS Computer Matching...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-05

.... Description of the Matching Program A. General The Computer Matching and Privacy Protection Act of 1988 (Pub... 1974: CMS Computer Matching Program Match No. 2013-01; HHS Computer Matching Program Match No. 1312...). ACTION: Notice of Computer Matching Program (CMP). SUMMARY: In accordance with the requirements of the...

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Handheld Computer Use in U.S. Family Practice Residency Programs

PubMed Central

Criswell, Dan F.; Parchman, Michael L.

2002-01-01

Objective: The purpose of the study was to evaluate the uses of handheld computers (also called personal digital assistants, or PDAs) in family practice residency programs in the United States. Study Design: In November 2000, the authors mailed a questionnaire to the program directors of all American Academy of Family Physicians (AAFP) and American College of Osteopathic Family Practice (ACOFP) residency programs in the United States. Measurements: Data and patterns of the use and non-use of handheld computers were identified. Results: Approximately 50 percent (306 of 610) of the programs responded to the survey. Two thirds of the programs reported that handheld computers were used in their residencies, and an additional 14 percent had plans for implementation within 24 months. Both the Palm and the Windows CE operating systems were used, with the Palm operating system the most common. Military programs had the highest rate of use (8 of 10 programs, 80 percent), and osteopathic programs had the lowest (23 of 55 programs, 42 percent). Of programs that reported handheld computer use, 45 percent had required handheld computer applications that are used uniformly by all users. Funding for handheld computers and related applications was non-budgeted in 76percent of the programs in which handheld computers were used. In programs providing a budget for handheld computers, the average annual budget per user was $461.58. Interested faculty or residents, rather than computer information services personnel, performed upkeep and maintenance of handheld computers in 72 percent of the programs in which the computers are used. In addition to the installed calendar, memo pad, and address book, the most common clinical uses of handheld computers in the programs were as medication reference tools, electronic textbooks, and clinical computational or calculator-type programs. Conclusions: Handheld computers are widely used in family practice residency programs in the United States. Although handheld computers were designed as electronic organizers, in family practice residencies they are used as medication reference tools, electronic textbooks, and clinical computational programs and to track activities that were previously associated with desktop database applications. PMID:11751806

Handheld computer use in U.S. family practice residency programs.

PubMed

Criswell, Dan F; Parchman, Michael L

2002-01-01

The purpose of the study was to evaluate the uses of handheld computers (also called personal digital assistants, or PDAs) in family practice residency programs in the United States. In November 2000, the authors mailed a questionnaire to the program directors of all American Academy of Family Physicians (AAFP) and American College of Osteopathic Family Practice (ACOFP) residency programs in the United States. Data and patterns of the use and non-use of handheld computers were identified. Approximately 50 percent (306 of 610) of the programs responded to the survey. Two thirds of the programs reported that handheld computers were used in their residencies, and an additional 14 percent had plans for implementation within 24 months. Both the Palm and the Windows CE operating systems were used, with the Palm operating system the most common. Military programs had the highest rate of use (8 of 10 programs, 80 percent), and osteopathic programs had the lowest (23 of 55 programs, 42 percent). Of programs that reported handheld computer use, 45 percent had required handheld computer applications that are used uniformly by all users. Funding for handheld computers and related applications was non-budgeted in 76percent of the programs in which handheld computers were used. In programs providing a budget for handheld computers, the average annual budget per user was 461.58 dollars. Interested faculty or residents, rather than computer information services personnel, performed upkeep and maintenance of handheld computers in 72 percent of the programs in which the computers are used. In addition to the installed calendar, memo pad, and address book, the most common clinical uses of handheld computers in the programs were as medication reference tools, electronic textbooks, and clinical computational or calculator-type programs. Handheld computers are widely used in family practice residency programs in the United States. Although handheld computers were designed as electronic organizers, in family practice residencies they are used as medication reference tools, electronic textbooks, and clinical computational programs and to track activities that were previously associated with desktop database applications.

The RANDOM computer program: A linear congruential random number generator

NASA Technical Reports Server (NTRS)

Miles, R. F., Jr.

1986-01-01

The RANDOM Computer Program is a FORTRAN program for generating random number sequences and testing linear congruential random number generators (LCGs). The linear congruential form of random number generator is discussed, and the selection of parameters of an LCG for a microcomputer described. This document describes the following: (1) The RANDOM Computer Program; (2) RANDOM.MOD, the computer code needed to implement an LCG in a FORTRAN program; and (3) The RANCYCLE and the ARITH Computer Programs that provide computational assistance in the selection of parameters for an LCG. The RANDOM, RANCYCLE, and ARITH Computer Programs are written in Microsoft FORTRAN for the IBM PC microcomputer and its compatibles. With only minor modifications, the RANDOM Computer Program and its LCG can be run on most micromputers or mainframe computers.

Fluid-Structure Interaction Modeling of Parachutes with Disreefing and Modified Geometric Porosity and Separation Aerodynamics of a Cover Jettisoned to the Spacecraft Wake

NASA Astrophysics Data System (ADS)

Fritze, Matthew D.

Fluid-structure interaction (FSI) modeling of spacecraft parachutes involves a number of computational challenges. The canopy complexity created by the hundreds of gaps and slits and design-related modification of that geometric porosity by removal of some of the sails and panels are among the formidable challenges. Disreefing from one stage to another when the parachute is used in multiple stages is another formidable challenge. This thesis addresses the computational challenges involved in disreefing of spacecraft parachutes and fully-open and reefed stages of the parachutes with modified geometric porosity. The special techniques developed to address these challenges are described and the FSI computations are be reported. The thesis also addresses the modeling and computation challenges involved in very early stages, where the sudden separation of a cover jettisoned to the spacecraft wake needs to be modeled. Higher-order temporal representations used in modeling the separation motion are described, and the computed separation and wake-induced forces acting on the cover are reported.

DIALOG: An executive computer program for linking independent programs

NASA Technical Reports Server (NTRS)

Glatt, C. R.; Hague, D. S.; Watson, D. A.

1973-01-01

A very large scale computer programming procedure called the DIALOG executive system was developed for the CDC 6000 series computers. The executive computer program, DIALOG, controls the sequence of execution and data management function for a library of independent computer programs. Communication of common information is accomplished by DIALOG through a dynamically constructed and maintained data base of common information. Each computer program maintains its individual identity and is unaware of its contribution to the large scale program. This feature makes any computer program a candidate for use with the DIALOG executive system. The installation and uses of the DIALOG executive system are described.

Separation of ion types in tandem mass spectrometry data interpretation -- a graph-theoretic approach.

PubMed

Yan, Bo; Pan, Chongle; Olman, Victor N; Hettich, Robert L; Xu, Ying

2004-01-01

Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein through identifying its unique mass spectral pattern. While the problem is theoretically solvable, it remains a challenging problem computationally. One of the key challenges comes from the difficulty in distinguishing the N- and C-terminus ions, mostly b- and y-ions respectively. In this paper, we present a graph algorithm for solving the problem of separating bfrom y-ions in a set of mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types, predicted based on local information. The ion-separation problem is then formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, namely b-, y-ions and others respectively, so to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. We have tested PRIME on 18 data sets of high accurate FT-ICR tandem mass spectra and found that it achieved ~90% accuracy for separation of b- and y- ions.

Leadership behaviors of athletic training leaders compared with leaders in other fields.

PubMed

Laurent, Timothy G; Bradney, Debbie A

2007-01-01

Athletic trainers are in positions of leadership. To determine self-reported leadership practices of head athletic trainers (HATCs) and program directors (PDs). Cross-sectional study. Respondents' academic institutions. A total of 238 athletic training leaders completed the Leadership Practices Inventory. Of these, 50.4% (n = 120) were HATCs and 49.6% (n = 118) were PDs; 69.3% (n = 165) were men and 30.7% (n = 73) were women; almost all respondents (97.1%, n = 231) were white. Respondents typically reported having 11 to 15 years of experience as an athletic trainer (n = 57, 23.9%) and being between the ages of 30 and 39 years (n = 109, 45.8%). Categories of leadership behaviors (ie, Model, Inspire, Challenge, Encourage, and Enable) were scored from 1 (almost never) to 10 (almost always). Item scores were summed to compute mean category scores. We analyzed demographic information; used t ratios to compare the data from athletic training leaders (PDs and HATCs) with normative data; compared sex, age, position, ethnicity, and years of experience with leadership practices; and computed mean scores. Athletic training leaders reported using leadership behaviors similar to those of other leaders. The PDs reported using inspiring, challenging, enabling, and encouraging leadership behaviors more often than did the HATCs. No differences were found by ethnicity, age, years of experience, or leadership practices. Athletic training leaders are transformational leaders. Athletic training education program accreditation requirements likely account for the difference in leadership practices between PDs and HATCs.

A CAD (Classroom Assessment Design) of a Computer Programming Course

ERIC Educational Resources Information Center

Hawi, Nazir S.

2012-01-01

This paper presents a CAD (classroom assessment design) of an entry-level undergraduate computer programming course "Computer Programming I". CAD has been the product of a long experience in teaching computer programming courses including teaching "Computer Programming I" 22 times. Each semester, CAD is evaluated and modified…

A reduced successive quadratic programming strategy for errors-in-variables estimation.

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

Tjoa, I.-B.; Biegler, L. T.; Carnegie-Mellon Univ.

Parameter estimation problems in process engineering represent a special class of nonlinear optimization problems, because the maximum likelihood structure of the objective function can be exploited. Within this class, the errors in variables method (EVM) is particularly interesting. Here we seek a weighted least-squares fit to the measurements with an underdetermined process model. Thus, both the number of variables and degrees of freedom available for optimization increase linearly with the number of data sets. Large optimization problems of this type can be particularly challenging and expensive to solve because, for general-purpose nonlinear programming (NLP) algorithms, the computational effort increases atmore » least quadratically with problem size. In this study we develop a tailored NLP strategy for EVM problems. The method is based on a reduced Hessian approach to successive quadratic programming (SQP), but with the decomposition performed separately for each data set. This leads to the elimination of all variables but the model parameters, which are determined by a QP coordination step. In this way the computational effort remains linear in the number of data sets. Moreover, unlike previous approaches to the EVM problem, global and superlinear properties of the SQP algorithm apply naturally. Also, the method directly incorporates inequality constraints on the model parameters (although not on the fitted variables). This approach is demonstrated on five example problems with up to 102 degrees of freedom. Compared to general-purpose NLP algorithms, large improvements in computational performance are observed.« less

Computing in Hydraulic Engineering Education

NASA Astrophysics Data System (ADS)

Duan, J. G.

2011-12-01

Civil engineers, pioneers of our civilization, are rarely perceived as leaders and innovators in modern society because of retardations in technology innovation. This crisis has resulted in the decline of the prestige of civil engineering profession, reduction of federal funding on deteriorating infrastructures, and problems with attracting the most talented high-school students. Infusion of cutting-edge computer technology and stimulating creativity and innovation therefore are the critical challenge to civil engineering education. To better prepare our graduates to innovate, this paper discussed the adaption of problem-based collaborative learning technique and integration of civil engineering computing into a traditional civil engineering curriculum. Three interconnected courses: Open Channel Flow, Computational Hydraulics, and Sedimentation Engineering, were developed with emphasis on computational simulations. In Open Channel flow, the focuses are principles of free surface flow and the application of computational models. This prepares students to the 2nd course, Computational Hydraulics, that introduce the fundamental principles of computational hydraulics, including finite difference and finite element methods. This course complements the Open Channel Flow class to provide students with in-depth understandings of computational methods. The 3rd course, Sedimentation Engineering, covers the fundamentals of sediment transport and river engineering, so students can apply the knowledge and programming skills gained from previous courses to develop computational models for simulating sediment transport. These courses effectively equipped students with important skills and knowledge to complete thesis and dissertation research.

Comparison of two computer programs by predicting turbulent mixing of helium in a ducted supersonic airstream

NASA Technical Reports Server (NTRS)

Pan, Y. S.; Drummond, J. P.; Mcclinton, C. R.

1978-01-01

Two parabolic flow computer programs, SHIP (a finite-difference program) and COMOC (a finite-element program), are used for predicting three-dimensional turbulent reacting flow fields in supersonic combustors. The theoretical foundation of the two computer programs are described, and then the programs are applied to a three-dimensional turbulent mixing experiment. The cold (nonreacting) flow experiment was performed to study the mixing of helium jets with a supersonic airstream in a rectangular duct. Surveys of the flow field at an upstream were used as the initial data by programs; surveys at a downstream station provided comparison to assess program accuracy. Both computer programs predicted the experimental results and data trends reasonably well. However, the comparison between the computations from the two programs indicated that SHIP was more accurate in computation and more efficient in both computer storage and computing time than COMOC.

The Future of Electronic Device Design: Device and Process Simulation Find Intelligence on the World Wide Web

NASA Technical Reports Server (NTRS)

Biegel, Bryan A.

1999-01-01

We are on the path to meet the major challenges ahead for TCAD (technology computer aided design). The emerging computational grid will ultimately solve the challenge of limited computational power. The Modular TCAD Framework will solve the TCAD software challenge once TCAD software developers realize that there is no other way to meet industry's needs. The modular TCAD framework (MTF) also provides the ideal platform for solving the TCAD model challenge by rapid implementation of models in a partial differential solver.

Computer program CDCID: an automated quality control program using CDC update

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

Singer, G.L.; Aguilar, F.

1984-04-01

A computer program, CDCID, has been developed in coordination with a quality control program to provide a highly automated method of documenting changes to computer codes at EG and G Idaho, Inc. The method uses the standard CDC UPDATE program in such a manner that updates and their associated documentation are easily made and retrieved in various formats. The method allows each card image of a source program to point to the document which describes it, who created the card, and when it was created. The method described is applicable to the quality control of computer programs in general. Themore » computer program described is executable only on CDC computing systems, but the program could be modified and applied to any computing system with an adequate updating program.« less

Testing New Programming Paradigms with NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Schultz, M.; Yan, J.

2000-01-01

Over the past decade, high performance computing has evolved rapidly, not only in hardware architectures but also with increasing complexity of real applications. Technologies have been developing to aim at scaling up to thousands of processors on both distributed and shared memory systems. Development of parallel programs on these computers is always a challenging task. Today, writing parallel programs with message passing (e.g. MPI) is the most popular way of achieving scalability and high performance. However, writing message passing programs is difficult and error prone. Recent years new effort has been made in defining new parallel programming paradigms. The best examples are: HPF (based on data parallelism) and OpenMP (based on shared memory parallelism). Both provide simple and clear extensions to sequential programs, thus greatly simplify the tedious tasks encountered in writing message passing programs. HPF is independent of memory hierarchy, however, due to the immaturity of compiler technology its performance is still questionable. Although use of parallel compiler directives is not new, OpenMP offers a portable solution in the shared-memory domain. Another important development involves the tremendous progress in the internet and its associated technology. Although still in its infancy, Java promisses portability in a heterogeneous environment and offers possibility to "compile once and run anywhere." In light of testing these new technologies, we implemented new parallel versions of the NAS Parallel Benchmarks (NPBs) with HPF and OpenMP directives, and extended the work with Java and Java-threads. The purpose of this study is to examine the effectiveness of alternative programming paradigms. NPBs consist of five kernels and three simulated applications that mimic the computation and data movement of large scale computational fluid dynamics (CFD) applications. We started with the serial version included in NPB2.3. Optimization of memory and cache usage was applied to several benchmarks, noticeably BT and SP, resulting in better sequential performance. In order to overcome the lack of an HPF performance model and guide the development of the HPF codes, we employed an empirical performance model for several primitives found in the benchmarks. We encountered a few limitations of HPF, such as lack of supporting the "REDISTRIBUTION" directive and no easy way to handle irregular computation. The parallelization with OpenMP directives was done at the outer-most loop level to achieve the largest granularity. The performance of six HPF and OpenMP benchmarks is compared with their MPI counterparts for the Class-A problem size in the figure in next page. These results were obtained on an SGI Origin2000 (195MHz) with MIPSpro-f77 compiler 7.2.1 for OpenMP and MPI codes and PGI pghpf-2.4.3 compiler with MPI interface for HPF programs.

shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics.

PubMed

Khomtchouk, Bohdan B; Hennessy, James R; Wahlestedt, Claes

2017-01-01

Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps. We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Also, shinyheatmap features a built-in high performance web plug-in, fastheatmap, for rapidly plotting interactive heatmaps of datasets as large as 105-107 rows within seconds, effectively shattering previous performance benchmarks of heatmap rendering speed. shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap. Users can access fastheatmap directly from within the shinyheatmap web interface, and all source code has been made publicly available on Github: https://github.com/Bohdan-Khomtchouk/fastheatmap.

Major Management Challenges and Program Risks. Department of Education

DTIC Science & Technology

2001-01-01

GAO United States General Accounting Office Performance and Accountability SeriesJanuary 2001 Major Management Challenges and Program Risks ...34) Title and Subtitle Major Management Challenges and Program Risks Department of Education Contract or Grant Number Program Element Number Authors...Accountability Series: Major Management Challenges and Program Risks . In that series, GAO advised the Congress that it planned to reassess the

Exploring the challenges faced by polytechnic students

NASA Astrophysics Data System (ADS)

Matore, Mohd Effendi @ Ewan Mohd; Khairani, Ahmad Zamri

2015-02-01

This study aims to identify other challenges besides those already faced by students, in seven polytechnics in Malaysia as a continuation to the previous research that had identified 52 main challenges faced by students using the Rasch Model. The explorative study focuses on the challenges that are not included in the Mooney Problem Checklist (MPCL). A total of 121 polytechnic students submitted 183 written responses through the open questions provided. Two hundred fifty two students had responded from a students' perspective on the dichotomous questions regarding their view on the challenges faced. The data was analysed qualitatively using the NVivo 8.0. The findings showed that students from Politeknik Seberang Perai (PSP) gave the highest response, which was 56 (30.6%) and Politeknik Metro Kuala Lumpur (PMKL) had the lowest response of 2 (1.09%). Five dominant challenges were identified, which were the English language (32, 17.5%), learning (14, 7.7%), vehicles (13, 7.1%), information technology and communication (ICT) (13, 7.1%), and peers (11, 6.0%). This article, however, focus on three apparent challenges, namely, English language, vehicles, as well as computer and ICT, as the challenges of learning and peers had been analysed in the previous MPCL. The challenge of English language that had been raised was regarding the weakness in commanding the aspects of speech and fluency. The computer and ICT challenge covered the weakness in mastering ICT and computers, as well as computer breakdowns and low-performance computers. The challenge of vehicles emphasized the unavailability of vehicles to attend lectures and go elsewhere, lack of transportation service in the polytechnic and not having a valid driving license. These challenges are very relevant and need to be discussed in an effort to prepare polytechnics in facing the transformational process of polytechnics.

The Effect of Problem-Solving Instruction on the Programming Self-efficacy and Achievement of Introductory Computer Science Students

NASA Astrophysics Data System (ADS)

Maddrey, Elizabeth

Research in academia and industry continues to identify a decline in enrollment in computer science. One major component of this decline in enrollment is a shortage of female students. The primary reasons for the gender gap presented in the research include lack of computer experience prior to their first year in college, misconceptions about the field, negative cultural stereotypes, lack of female mentors and role models, subtle discriminations in the classroom, and lack of self-confidence (Pollock, McCoy, Carberry, Hundigopal, & You, 2004). Male students are also leaving the field due to misconceptions about the field, negative cultural stereotypes, and a lack of self-confidence. Analysis of first year attrition revealed that one of the major challenges faced by students of both genders is a lack of problem-solving skills (Beaubouef, Lucas & Howatt, 2001; Olsen, 2005; Paxton & Mumey, 2001). The purpose of this study was to investigate whether specific, non-mathematical problem-solving instruction as part of introductory programming courses significantly increased computer programming self-efficacy and achievement of students. The results of this study showed that students in the experimental group had significantly higher achievement than students in the control group. While this shows statistical significance, due to the effect size and disordinal nature of the data between groups, care has to be taken in its interpretation. The study did not show significantly higher programming self-efficacy among the experimental students. There was not enough data collected to statistically analyze the effect of the treatment on self-efficacy and achievement by gender. However, differences in means were observed between the gender groups, with females in the experimental group demonstrating a higher than average degree of self-efficacy when compared with males in the experimental group and both genders in the control group. These results suggest that the treatment from this study may provide a gender-based increase in self-efficacy and future research should focus on exploring this possibility.

Teaching and learning experiences in a collaborative distance-education environment.

PubMed

Martin, Peter; Scheetz, Laura Temple

2011-01-01

The Great Plains Distance Education Alliance (Great Plains IDEA) emphasizes the importance of a collaborative environment for instructors and students in distance education. The authors highlight a number of important principles for distance-education programs and point out similarities and differences when compared to traditional face-face-to classes such as communication, classroom management, connectivity, and technical challenges. They summarize general topics concerning the faculty, the syllabus, office hours, the calendar, and announcements. Three essential lesson components are noted: an overview, the lesson itself, and supplemanetary material. The authors also take the student perspective, emphasizing the diversity of students, the importance of computer proficiency, and student interactions. Finally, they summarize a first round of course evaluations in the Great Plains IDEA gerontology master's program.

Bonsai: an event-based framework for processing and controlling data streams

PubMed Central

Lopes, Gonçalo; Bonacchi, Niccolò; Frazão, João; Neto, Joana P.; Atallah, Bassam V.; Soares, Sofia; Moreira, Luís; Matias, Sara; Itskov, Pavel M.; Correia, Patrícia A.; Medina, Roberto E.; Calcaterra, Lorenza; Dreosti, Elena; Paton, Joseph J.; Kampff, Adam R.

2015-01-01

The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation. PMID:25904861

Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs.

PubMed

Bekiaris, Pavlos Stephanos; Tekath, Tobias; Staiger, Dorothee; Danisman, Selahattin

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, "CRM Network Generator" (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression.

Computational exploration of cis-regulatory modules in rhythmic expression data using the “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG) programs

PubMed Central

Staiger, Dorothee

2018-01-01

Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, “Exploration of Distinctive CREs and CRMs” (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, “CRM Network Generator” (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression. PMID:29298348

How to get students to love (or not hate) MATLAB and programming

NASA Astrophysics Data System (ADS)

Reckinger, Shanon; Reckinger, Scott

2014-11-01

An effective programming course geared toward engineering students requires the utilization of modern teaching philosophies. A newly designed course that focuses on programming in MATLAB involves flipping the classroom and integrating various active teaching techniques. Vital aspects of the new course design include: lengthening in-class contact hours, Process-Oriented Guided Inquiry Learning (POGIL) method worksheets (self-guided instruction), student created video content posted on YouTube, clicker questions (used in class to practice reading and debugging code), programming exams that don't require computers, integrating oral exams into the classroom, fostering an environment for formal and informal peer learning, and designing in a broader theme to tie together assignments. However, possibly the most important piece to this programming course puzzle: the instructor needs to be able to find programming mistakes very fast and then lead individuals and groups through the steps to find their mistakes themselves. The effectiveness of the new course design is demonstrated through pre- and post- concept exam results and student evaluation feedback. Students reported that the course was challenging and required a lot of effort, but left largely positive feedback.

An Algorithm and R Program for Fitting and Simulation of Pharmacokinetic and Pharmacodynamic Data.

PubMed

Li, Jijie; Yan, Kewei; Hou, Lisha; Du, Xudong; Zhu, Ping; Zheng, Li; Zhu, Cairong

2017-06-01

Pharmacokinetic/pharmacodynamic link models are widely used in dose-finding studies. By applying such models, the results of initial pharmacokinetic/pharmacodynamic studies can be used to predict the potential therapeutic dose range. This knowledge can improve the design of later comparative large-scale clinical trials by reducing the number of participants and saving time and resources. However, the modeling process can be challenging, time consuming, and costly, even when using cutting-edge, powerful pharmacological software. Here, we provide a freely available R program for expediently analyzing pharmacokinetic/pharmacodynamic data, including data importation, parameter estimation, simulation, and model diagnostics. First, we explain the theory related to the establishment of the pharmacokinetic/pharmacodynamic link model. Subsequently, we present the algorithms used for parameter estimation and potential therapeutic dose computation. The implementation of the R program is illustrated by a clinical example. The software package is then validated by comparing the model parameters and the goodness-of-fit statistics generated by our R package with those generated by the widely used pharmacological software WinNonlin. The pharmacokinetic and pharmacodynamic parameters as well as the potential recommended therapeutic dose can be acquired with the R package. The validation process shows that the parameters estimated using our package are satisfactory. The R program developed and presented here provides pharmacokinetic researchers with a simple and easy-to-access tool for pharmacokinetic/pharmacodynamic analysis on personal computers.

Application Portable Parallel Library

NASA Technical Reports Server (NTRS)

Cole, Gary L.; Blech, Richard A.; Quealy, Angela; Townsend, Scott

1995-01-01

Application Portable Parallel Library (APPL) computer program is subroutine-based message-passing software library intended to provide consistent interface to variety of multiprocessor computers on market today. Minimizes effort needed to move application program from one computer to another. User develops application program once and then easily moves application program from parallel computer on which created to another parallel computer. ("Parallel computer" also include heterogeneous collection of networked computers). Written in C language with one FORTRAN 77 subroutine for UNIX-based computers and callable from application programs written in C language or FORTRAN 77.

New Developments in Modeling MHD Systems on High Performance Computing Architectures

NASA Astrophysics Data System (ADS)

Germaschewski, K.; Raeder, J.; Larson, D. J.; Bhattacharjee, A.

2009-04-01

Modeling the wide range of time and length scales present even in fluid models of plasmas like MHD and X-MHD (Extended MHD including two fluid effects like Hall term, electron inertia, electron pressure gradient) is challenging even on state-of-the-art supercomputers. In the last years, HPC capacity has continued to grow exponentially, but at the expense of making the computer systems more and more difficult to program in order to get maximum performance. In this paper, we will present a new approach to managing the complexity caused by the need to write efficient codes: Separating the numerical description of the problem, in our case a discretized right hand side (r.h.s.), from the actual implementation of efficiently evaluating it. An automatic code generator is used to describe the r.h.s. in a quasi-symbolic form while leaving the translation into efficient and parallelized code to a computer program itself. We implemented this approach for OpenGGCM (Open General Geospace Circulation Model), a model of the Earth's magnetosphere, which was accelerated by a factor of three on regular x86 architecture and a factor of 25 on the Cell BE architecture (commonly known for its deployment in Sony's PlayStation 3).

Seismic signal processing on heterogeneous supercomputers

NASA Astrophysics Data System (ADS)

Gokhberg, Alexey; Ermert, Laura; Fichtner, Andreas

2015-04-01

The processing of seismic signals - including the correlation of massive ambient noise data sets - represents an important part of a wide range of seismological applications. It is characterized by large data volumes as well as high computational input/output intensity. Development of efficient approaches towards seismic signal processing on emerging high performance computing systems is therefore essential. Heterogeneous supercomputing systems introduced in the recent years provide numerous computing nodes interconnected via high throughput networks, every node containing a mix of processing elements of different architectures, like several sequential processor cores and one or a few graphical processing units (GPU) serving as accelerators. A typical representative of such computing systems is "Piz Daint", a supercomputer of the Cray XC 30 family operated by the Swiss National Supercomputing Center (CSCS), which we used in this research. Heterogeneous supercomputers provide an opportunity for manifold application performance increase and are more energy-efficient, however they have much higher hardware complexity and are therefore much more difficult to program. The programming effort may be substantially reduced by the introduction of modular libraries of software components that can be reused for a wide class of seismology applications. The ultimate goal of this research is design of a prototype for such library suitable for implementing various seismic signal processing applications on heterogeneous systems. As a representative use case we have chosen an ambient noise correlation application. Ambient noise interferometry has developed into one of the most powerful tools to image and monitor the Earth's interior. Future applications will require the extraction of increasingly small details from noise recordings. To meet this demand, more advanced correlation techniques combined with very large data volumes are needed. This poses new computational problems that require dedicated HPC solutions. The chosen application is using a wide range of common signal processing methods, which include various IIR filter designs, amplitude and phase correlation, computing the analytic signal, and discrete Fourier transforms. Furthermore, various processing methods specific for seismology, like rotation of seismic traces, are used. Efficient implementation of all these methods on the GPU-accelerated systems represents several challenges. In particular, it requires a careful distribution of work between the sequential processors and accelerators. Furthermore, since the application is designed to process very large volumes of data, special attention had to be paid to the efficient use of the available memory and networking hardware resources in order to reduce intensity of data input and output. In our contribution we will explain the software architecture as well as principal engineering decisions used to address these challenges. We will also describe the programming model based on C++ and CUDA that we used to develop the software. Finally, we will demonstrate performance improvements achieved by using the heterogeneous computing architecture. This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under project ID d26.

Addressing the challenges of standalone multi-core simulations in molecular dynamics

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-07-01

Computational modelling in material science involves mathematical abstractions of force fields between particles with the aim to postulate, develop and understand materials by simulation. The aggregated pairwise interactions of the material's particles lead to a deduction of its macroscopic behaviours. For practically meaningful macroscopic scales, a large amount of data are generated, leading to vast execution times. Simulation times of hours, days or weeks for moderately sized problems are not uncommon. The reduction of simulation times, improved result accuracy and the associated software and hardware engineering challenges are the main motivations for many of the ongoing researches in the computational sciences. This contribution is concerned mainly with simulations that can be done on a "standalone" computer based on Message Passing Interfaces (MPI), parallel code running on hardware platforms with wide specifications, such as single/multi- processor, multi-core machines with minimal reconfiguration for upward scaling of computational power. The widely available, documented and standardized MPI library provides this functionality through the MPI_Comm_size (), MPI_Comm_rank () and MPI_Reduce () functions. A survey of the literature shows that relatively little is written with respect to the efficient extraction of the inherent computational power in a cluster. In this work, we discuss the main avenues available to tap into this extra power without compromising computational accuracy. We also present methods to overcome the high inertia encountered in single-node-based computational molecular dynamics. We begin by surveying the current state of the art and discuss what it takes to achieve parallelism, efficiency and enhanced computational accuracy through program threads and message passing interfaces. Several code illustrations are given. The pros and cons of writing raw code as opposed to using heuristic, third-party code are also discussed. The growing trend towards graphical processor units and virtual computing clouds for high-performance computing is also discussed. Finally, we present the comparative results of vacancy formation energy calculations using our own parallelized standalone code called Verlet-Stormer velocity (VSV) operating on 30,000 copper atoms. The code is based on the Sutton-Chen implementation of the Finnis-Sinclair pairwise embedded atom potential. A link to the code is also given.

2014 Runtime Systems Summit. Runtime Systems Report

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

Sarkar, Vivek; Budimlic, Zoran; Kulkani, Milind

2016-09-19

This report summarizes runtime system challenges for exascale computing, that follow from the fundamental challenges for exascale systems that have been well studied in past reports, e.g., [6, 33, 34, 32, 24]. Some of the key exascale challenges that pertain to runtime systems include parallelism, energy efficiency, memory hierarchies, data movement, heterogeneous processors and memories, resilience, performance variability, dynamic resource allocation, performance portability, and interoperability with legacy code. In addition to summarizing these challenges, the report also outlines different approaches to addressing these significant challenges that have been pursued by research projects in the DOE-sponsored X-Stack and OS/R programs. Sincemore » there is often confusion as to what exactly the term “runtime system” refers to in the software stack, we include a section on taxonomy to clarify the terminology used by participants in these research projects. In addition, we include a section on deployment opportunities for vendors and government labs to build on the research results from these projects. Finally, this report is also intended to provide a framework for discussing future research and development investments for exascale runtime systems, and for clarifying the role of runtime systems in exascale software.« less

DIALOG: An executive computer program for linking independent programs

NASA Technical Reports Server (NTRS)

Glatt, C. R.; Hague, D. S.; Watson, D. A.

1973-01-01

A very large scale computer programming procedure called the DIALOG Executive System has been developed for the Univac 1100 series computers. The executive computer program, DIALOG, controls the sequence of execution and data management function for a library of independent computer programs. Communication of common information is accomplished by DIALOG through a dynamically constructed and maintained data base of common information. The unique feature of the DIALOG Executive System is the manner in which computer programs are linked. Each program maintains its individual identity and as such is unaware of its contribution to the large scale program. This feature makes any computer program a candidate for use with the DIALOG Executive System. The installation and use of the DIALOG Executive System are described at Johnson Space Center.

Educational NASA Computational and Scientific Studies (enCOMPASS)

NASA Technical Reports Server (NTRS)

Memarsadeghi, Nargess

2013-01-01

Educational NASA Computational and Scientific Studies (enCOMPASS) is an educational project of NASA Goddard Space Flight Center aimed at bridging the gap between computational objectives and needs of NASA's scientific research, missions, and projects, and academia's latest advances in applied mathematics and computer science. enCOMPASS achieves this goal via bidirectional collaboration and communication between NASA and academia. Using developed NASA Computational Case Studies in university computer science/engineering and applied mathematics classes is a way of addressing NASA's goals of contributing to the Science, Technology, Education, and Math (STEM) National Objective. The enCOMPASS Web site at http://encompass.gsfc.nasa.gov provides additional information. There are currently nine enCOMPASS case studies developed in areas of earth sciences, planetary sciences, and astrophysics. Some of these case studies have been published in AIP and IEEE's Computing in Science and Engineering magazines. A few university professors have used enCOMPASS case studies in their computational classes and contributed their findings to NASA scientists. In these case studies, after introducing the science area, the specific problem, and related NASA missions, students are first asked to solve a known problem using NASA data and past approaches used and often published in a scientific/research paper. Then, after learning about the NASA application and related computational tools and approaches for solving the proposed problem, students are given a harder problem as a challenge for them to research and develop solutions for. This project provides a model for NASA scientists and engineers on one side, and university students, faculty, and researchers in computer science and applied mathematics on the other side, to learn from each other's areas of work, computational needs and solutions, and the latest advances in research and development. This innovation takes NASA science and engineering applications to computer science and applied mathematics university classes, and makes NASA objectives part of the university curricula. There is great potential for growth and return on investment of this program to the point where every major university in the U.S. would use at least one of these case studies in one of their computational courses, and where every NASA scientist and engineer facing a computational challenge (without having resources or expertise to solve it) would use enCOMPASS to formulate the problem as a case study, provide it to a university, and get back their solutions and ideas.

Demo of three ways to use a computer to assist in lab

NASA Technical Reports Server (NTRS)

Neville, J. P.

1990-01-01

The objective is to help the slow learner and students with a language problem, or to challenge the advanced student. Technology has advanced to the point where images generated on a computer can easily be recorded on a VCR and used as a video tutorial. This transfer can be as simple as pointing a video camera at the screen and recording the image. For more clarity and professional results, a board may be inserted into a computer which will convert the signals directly to the TV standard. Using a computer program that generates movies one can animate various principles which would normally be impossible to show or would require time-lapse photography. For example, you might show the change in shape of grains as a piece of metal is cold worked and then show the recrystallization and grain growth as heat is applied. More imaginative titles and graphics are also possible using this technique. Remedial help may also be offered via computer to those who find a specific concept difficult. A printout of specific data, details of the theory or equipment set-up can be offered. Programs are now available that will help as well as test the student in specific areas so that a Keller type approach can be used with each student to insure each knows the subject before going on to the next topic. A computer can serve as an information source and contain the microstructures, physical data and availability of each material tested in the lab. With this source present unknowns can be evaluated and various tests simulated to create a simple or complex case study lab assignment.

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

Analysis of selected data from the triservice missile data base

NASA Technical Reports Server (NTRS)

Allen, Jerry M.; Shaw, David S.; Sawyer, Wallace C.

1989-01-01

An extremely large, systematic, axisymmetric-body/tail-fin data base has been gathered through tests of an innovative missile model design which is described herein. These data were originally obtained for incorporation into a missile aerodynamics code based on engineering methods (Program MISSILE3), but these data are also valuable as diagnostic test cases for developing computational methods because of the individual-fin data included in the data base. Detailed analyses of four sample cases from these data are presented to illustrate interesting individual-fin force and moment trends. These samples quantitatively show how bow shock, fin orientation, fin deflection, and body vortices can produce strong, unusual, and computationally challenging effects on individual fin loads. Flow-visualization photographs are examined to provide physical insight into the cause of these effects.

The personal computer and GP-B management. [Gravity Probe experiment

NASA Technical Reports Server (NTRS)

Neighbors, A. K.

1986-01-01

The Gravity Probe-B (GP-B) experiment is one of the most sophisticated and challenging developments to be undertaken by NASA. Its objective is to measure the relativistic drift of gyroscopes in orbit about the earth. In this paper, the experiment is described, and the strategy of phased procurements for accomplishing the engineering development of the hardware is discussed. The microcomputer is a very convenient and powerful tool in the management of GP-B. It is used in creating and monitoring such project data as schedules, budgets, hardware procurements and technical and interface requirements. Commercially available software in word processing, database management, communications, spreadsheet, graphics and program management are used. Examples are described of the efficacy of the application of the computer by the management team.

Feasibility of Computer-Based Videogame Therapy for Children with Cerebral Palsy

PubMed Central

Radtka, Sandra; Hone, Robert; Brown, Charles; Mastick, Judy; Melnick, Marsha E.

2013-01-01

Abstract Objectives Standing and gait balance problems are common in children with cerebral palsy (CP), resulting in falls and injuries. Task-oriented exercises to strengthen and stretch muscles that shift the center of mass and change the base of support are effective in improving balance. Gaming environments can be challenging and fun, encouraging children to engage in exercises at home. The aims of this project were to demonstrate the technical feasibility, ease of use, appeal, and safety of a computer-based videogame program designed to improve balance in children with CP. Materials and Methods This study represents a close collaboration between computer design and clinical team members. The first two phases were performed in the laboratory, and the final phase was done in subjects' homes. The prototype balance game was developed using computer-based real-time three-dimensional programming that enabled the team to capture engineering data necessary to tune the system. Videogame modifications, including identifying compensatory movements, were made in an iterative fashion based on feedback from subjects and observations of clinical and software team members. Results Subjects (n=14) scored the game 21.5 out of 30 for ease of use and appeal, 4.0 out of 5 for enjoyment, and 3.5 on comprehension. There were no safety issues, and the games performed without technical flaws in final testing. Conclusions A computer-based videogame incorporating therapeutic movements to improve gait and balance in children with CP was appealing and feasible for home use. A follow-up study examining its effectiveness in improving balance in children with CP is recommended. PMID:24761324

Feasibility of Computer-Based Videogame Therapy for Children with Cerebral Palsy.

PubMed

Radtka, Sandra; Hone, Robert; Brown, Charles; Mastick, Judy; Melnick, Marsha E; Dowling, Glenna A

2013-08-01

Standing and gait balance problems are common in children with cerebral palsy (CP), resulting in falls and injuries. Task-oriented exercises to strengthen and stretch muscles that shift the center of mass and change the base of support are effective in improving balance. Gaming environments can be challenging and fun, encouraging children to engage in exercises at home. The aims of this project were to demonstrate the technical feasibility, ease of use, appeal, and safety of a computer-based videogame program designed to improve balance in children with CP. This study represents a close collaboration between computer design and clinical team members. The first two phases were performed in the laboratory, and the final phase was done in subjects' homes. The prototype balance game was developed using computer-based real-time three-dimensional programming that enabled the team to capture engineering data necessary to tune the system. Videogame modifications, including identifying compensatory movements, were made in an iterative fashion based on feedback from subjects and observations of clinical and software team members. Subjects ( n =14) scored the game 21.5 out of 30 for ease of use and appeal, 4.0 out of 5 for enjoyment, and 3.5 on comprehension. There were no safety issues, and the games performed without technical flaws in final testing. A computer-based videogame incorporating therapeutic movements to improve gait and balance in children with CP was appealing and feasible for home use. A follow-up study examining its effectiveness in improving balance in children with CP is recommended.

Gender Differences in the Use of Computers, Programming, and Peer Interactions in Computer Science Classrooms

ERIC Educational Resources Information Center

Stoilescu, Dorian; Egodawatte, Gunawardena

2010-01-01

Research shows that female and male students in undergraduate computer science programs view computer culture differently. Female students are interested more in the use of computers than in doing programming, whereas male students see computer science mainly as a programming activity. The overall purpose of our research was not to find new…

SnowCloud - a Framework to Predict Streamflow in Snowmelt-dominated Watersheds Using Cloud-based Computing

NASA Astrophysics Data System (ADS)

Sproles, E. A.; Crumley, R. L.; Nolin, A. W.; Mar, E.; Lopez-Moreno, J. J.

2017-12-01

Streamflow in snowy mountain regions is extraordinarily challenging to forecast, and prediction efforts are hampered by the lack of timely snow data—particularly in data sparse regions. SnowCloud is a prototype web-based framework that integrates remote sensing, cloud computing, interactive mapping tools, and a hydrologic model to offer a new paradigm for delivering key data to water resource managers. We tested the skill of SnowCloud to forecast monthly streamflow with one month lead time in three snow-dominated headwaters. These watersheds represent a range of precipitation/runoff schemes: the Río Elqui in northern Chile (200 mm/yr, entirely snowmelt); the John Day River, Oregon, USA (635 mm/yr, primarily snowmelt); and the Río Aragon in the northern Spain (850 mm/yr, snowmelt dominated). Model skill corresponded to snowpack contribution with Nash-Sutcliffe Efficiencies of 0.86, 0.52, and 0.21 respectively. SnowCloud does not require the user to possess advanced programming skills or proprietary software. We access NASA's MOD10A1 snow cover product to calculate the snow metrics globally using Google Earth Engine's geospatial analysis and cloud computing service. The analytics and forecast tools are provided through a web-based portal that requires only internet access and minimal training. To test the efficacy of SnowCloud we provided the tools and a series of tutorials in English and Spanish to water resource managers in Chile, Spain, and the United States. Participants assessed their user experience and provided feedback, and the results of our multi-cultural assessment are also presented. While our results focus on SnowCloud, they outline methods to develop cloud-based tools that function effectively across cultures and languages. Our approach also addresses the primary challenges of science-based computing; human resource limitations, infrastructure costs, and expensive proprietary software. These challenges are particularly problematic in developing countries.

Statistics, Computation, and Modeling in Cosmology

NASA Astrophysics Data System (ADS)

Jewell, Jeff; Guiness, Joe; SAMSI 2016 Working Group in Cosmology

2017-01-01

Current and future ground and space based missions are designed to not only detect, but map out with increasing precision, details of the universe in its infancy to the present-day. As a result we are faced with the challenge of analyzing and interpreting observations from a wide variety of instruments to form a coherent view of the universe. Finding solutions to a broad range of challenging inference problems in cosmology is one of the goals of the “Statistics, Computation, and Modeling in Cosmology” workings groups, formed as part of the year long program on ‘Statistical, Mathematical, and Computational Methods for Astronomy’, hosted by the Statistical and Applied Mathematical Sciences Institute (SAMSI), a National Science Foundation funded institute. Two application areas have emerged for focused development in the cosmology working group involving advanced algorithmic implementations of exact Bayesian inference for the Cosmic Microwave Background, and statistical modeling of galaxy formation. The former includes study and development of advanced Markov Chain Monte Carlo algorithms designed to confront challenging inference problems including inference for spatial Gaussian random fields in the presence of sources of galactic emission (an example of a source separation problem). Extending these methods to future redshift survey data probing the nonlinear regime of large scale structure formation is also included in the working group activities. In addition, the working group is also focused on the study of ‘Galacticus’, a galaxy formation model applied to dark matter-only cosmological N-body simulations operating on time-dependent halo merger trees. The working group is interested in calibrating the Galacticus model to match statistics of galaxy survey observations; specifically stellar mass functions, luminosity functions, and color-color diagrams. The group will use subsampling approaches and fractional factorial designs to statistically and computationally efficiently explore the Galacticus parameter space. The group will also use the Galacticus simulations to study the relationship between the topological and physical structure of the halo merger trees and the properties of the resulting galaxies.

The Awareness and Challenges of Cloud Computing Adoption on Tertiary Education in Malaysia

NASA Astrophysics Data System (ADS)

Hazreeni Hamzah, Nor; Mahmud, Maziah; Zukri, Shamsunarnie Mohamed; Yaacob, Wan Fairos Wan; Yacob, Jusoh

2017-09-01

This preliminary study aims to investigate the awareness of the adoption of cloud computing among the academicians in tertiary education in Malaysia. Besides, this study also want to explore the possible challenges faced by the academician while adopting this new technology. The pilot study was done on 40 lecturers in Universiti Teknologi MARA Kampus Kota Bharu (UiTMKB) by using self administered questionnaire. The results found that almost half (40 percent) were not aware on the existing of cloud computing in teaching and learning (T&L) process. The challenges confronting the adoption of cloud computing are data insecurity, data insecurity, unsolicited advertisement, lock-in, reluctance to eliminate staff positions, privacy concerns, reliability challenge, regulatory compliance concerns/user control and institutional culture/resistance to change in technology. This possible challenges can be factorized in two major factors which were security and dependency factor and user control and mentality factor.

DEGAS: Dynamic Exascale Global Address Space Programming Environments

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

Demmel, James

The Dynamic, Exascale Global Address Space programming environment (DEGAS) project will develop the next generation of programming models and runtime systems to meet the challenges of Exascale computing. The Berkeley part of the project concentrated on communication-optimal code generation to optimize speed and energy efficiency by reducing data movement. Our work developed communication lower bounds, and/or communication avoiding algorithms (that either meet the lower bound, or do much less communication than their conventional counterparts) for a variety of algorithms, including linear algebra, machine learning and genomics. The Berkeley part of the project concentrated on communication-optimal code generation to optimize speedmore » and energy efficiency by reducing data movement. Our work developed communication lower bounds, and/or communication avoiding algorithms (that either meet the lower bound, or do much less communication than their conventional counterparts) for a variety of algorithms, including linear algebra, machine learning and genomics.« less

Real Talk: Developing a Computer-Delivered Sexual Health Program for Black Men Who Have Sex With Men.

PubMed

Klein, Charles; Lomonaco, Carmela

2016-12-01

HIV disproportionately affects Black men who have sex with men (MSM), yet there are few evidence-based programs that respond to the diverse realities of Black MSM communities. This article examines the development of Real Talk, a new harm reduction-based, sexual health intervention for Black MSM. We first analyze the key themes from our formative research: (1) stigma, discrimination, and intersectionalities in the lives of Black MSM, (2) the importance of safe spaces and community provided by health promotion programs, and (3) moving beyond condoms in sexual health messaging. We then describe our agile design product development process and present an overview of the intervention's components and how they respond to the issues identified in the formative research. In conclusion, we discuss dissemination opportunities and challenges in an age of decreased prevention funding, pre-exposure prophylaxis (PrEP), and the increased use of e-health promotion modalities.

The Effect of a Formal Mentoring Program on Career Satisfaction and Intent to Stay in the Faculty Role for Novice Nurse Faculty.

PubMed

Jeffers, Stephanie; Mariani, Bette

The purpose of this mixed-method study was to explore the influence of a formal mentoring program on career satisfaction of novice full-time nurse faculty in academia. The transition from the role of clinician to faculty in an academic setting can be challenging for novice nurse faculty. A link to an electronic survey with open-ended questions was emailed to 1435 participants. The response rate was 17.6 percent (N = 124). Mean scores were obtained, and independent t-test were computed to compare scores of faculty who had participated in a mentoring program with scores of nonparticipants. Content analysis of the open-ended answers was conducted, and common themes were identified. By examining characteristics that contribute to the success of novice nursing faculty, recruitment and retention of faculty may improve, which is essential due to the worsening nursing faculty shortage.

The use of computers to teach human anatomy and physiology to allied health and nursing students

NASA Astrophysics Data System (ADS)

Bergeron, Valerie J.

Educational institutions are under tremendous pressure to adopt the newest technologies in order to prepare their students to meet the challenges of the twenty-first century. For the last twenty years huge amounts of money have been spent on computers, printers, software, multimedia projection equipment, and so forth. A reasonable question is, "Has it worked?" Has this infusion of resources, financial as well as human, resulted in improved learning? Are the students meeting the intended learning goals? Any attempt to develop answers to these questions should include examining the intended goals and exploring the effects of the changes on students and faculty. This project investigated the impact of a specific application of a computer program in a community college setting on students' attitudes and understanding of human anatomy and physiology. In this investigation two sites of the same community college with seemingly similar students populations, seven miles apart, used different laboratory activities to teach human anatomy and physiology. At one site nursing students were taught using traditional dissections and laboratory activities; at the other site two of the dissections, specifically cat and sheep pluck, were replaced with the A.D.A.M.RTM (Animated Dissection of Anatomy for Medicine) computer program. Analysis of the attitude data indicated that students at both sites were extremely positive about their laboratory experiences. Analysis of the content data indicated a statistically significant difference in performance between the two sites in two of the eight content areas that were studied. For both topics the students using the computer program scored higher. A detailed analysis of the surveys, interviews with faculty and students, examination of laboratory materials, and observations of laboratory facilities in both sites, and cost-benefit analysis led to the development of seven recommendations. The recommendations call for action at the level of the institution requiring investment in additional resources, and at the level of the faculty requiring a commitment to exploration and reflective practice.

EnergyPlus Run Time Analysis

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

Hong, Tianzhen; Buhl, Fred; Haves, Philip

2008-09-20

EnergyPlus is a new generation building performance simulation program offering many new modeling capabilities and more accurate performance calculations integrating building components in sub-hourly time steps. However, EnergyPlus runs much slower than the current generation simulation programs. This has become a major barrier to its widespread adoption by the industry. This paper analyzed EnergyPlus run time from comprehensive perspectives to identify key issues and challenges of speeding up EnergyPlus: studying the historical trends of EnergyPlus run time based on the advancement of computers and code improvements to EnergyPlus, comparing EnergyPlus with DOE-2 to understand and quantify the run time differences,more » identifying key simulation settings and model features that have significant impacts on run time, and performing code profiling to identify which EnergyPlus subroutines consume the most amount of run time. This paper provides recommendations to improve EnergyPlus run time from the modeler?s perspective and adequate computing platforms. Suggestions of software code and architecture changes to improve EnergyPlus run time based on the code profiling results are also discussed.« less

Degree counting and Shadow system for Toda system of rank two: One bubbling

NASA Astrophysics Data System (ADS)

Lee, Youngae; Lin, Chang-Shou; Wei, Juncheng; Yang, Wen

2018-04-01

We initiate the program for computing the Leray-Schauder topological degree for Toda systems of rank two. This program still contains a lot of challenging problems for analysts. As the first step, we prove that if a sequence of solutions (u1k ,u2k) blows up, then one of hje ujk/∫Mhje ujk dvg, j = 1 , 2 tends to a sum of Dirac measures. This is so-called the phenomena of weak concentration. Our purposes in this article are (i) to introduce the shadow system due to the bubbling phenomena when one of parameters ρi crosses 4π and ρj ∉ 4 πN where 1 ≤ i ≠ j ≤ 2; (ii) to show how to calculate the topological degree of Toda systems by computing the topological degree of the general shadow systems; (iii) to calculate the topological degree of the shadow system for one point blow up. We believe that the degree counting formula for the shadow system would be useful in other problems.

Impact of a Computer System and the Encoding Staff Organization on the Encoding Stays and on Health Institution Financial Production in France.

PubMed

Sarazin, Marianne; El Merini, Amine; Staccini, Pascal

2016-01-01

In France, medicalization of information systems program (PMSI) is an essential tool for the management planning and funding of health. The performance of encoding data inherent to hospital stays has become a major challenge for health institutions. Some studies have highlighted the impact of organizations set up on encoding quality and financial production. The aim of this study is to evaluate a computerized information system and new staff organization impact for treatment of the encoded information.