A Silent Revolution: From Sketching to Coding--A Case Study on Code-Based Design Tool Learning

ERIC Educational Resources Information Center

Xu, Song; Fan, Kuo-Kuang

2017-01-01

Along with the information technology rising, Computer Aided Design activities are becoming more modern and more complex. But learning how to operation these new design tools has become the main problem lying in front of each designer. This study was purpose on finding problems encountered during code-based design tools learning period of…

Revisiting Mathematical Problem Solving and Posing in the Digital Era: Toward Pedagogically Sound Uses of Modern Technology

ERIC Educational Resources Information Center

Abramovich, S.

2014-01-01

The availability of sophisticated computer programs such as "Wolfram Alpha" has made many problems found in the secondary mathematics curriculum somewhat obsolete for they can be easily solved by the software. Against this background, an interplay between the power of a modern tool of technology and educational constraints it presents is…

The Humanistic Duo: The Park/Recreation Professional and the Computer. (Computer-Can I Use It?).

ERIC Educational Resources Information Center

Weiner, Myron E.

This paper states that there are two fundamental reasons for the comparative absence of computer use for parks and recreation at the present time. These are (1) lack of clear cut cost justification and (2) reluctance on the part of recreation professionals to accept their role as managers and, consequently, to utilize modern management tools. The…

Computers and neurosurgery.

PubMed

Shaikhouni, Ammar; Elder, J Bradley

2012-11-01

At the turn of the twentieth century, the only computational device used in neurosurgical procedures was the brain of the surgeon. Today, most neurosurgical procedures rely at least in part on the use of a computer to help perform surgeries accurately and safely. The techniques that revolutionized neurosurgery were mostly developed after the 1950s. Just before that era, the transistor was invented in the late 1940s, and the integrated circuit was invented in the late 1950s. During this time, the first automated, programmable computational machines were introduced. The rapid progress in the field of neurosurgery not only occurred hand in hand with the development of modern computers, but one also can state that modern neurosurgery would not exist without computers. The focus of this article is the impact modern computers have had on the practice of neurosurgery. Neuroimaging, neuronavigation, and neuromodulation are examples of tools in the armamentarium of the modern neurosurgeon that owe each step in their evolution to progress made in computer technology. Advances in computer technology central to innovations in these fields are highlighted, with particular attention to neuroimaging. Developments over the last 10 years in areas of sensors and robotics that promise to transform the practice of neurosurgery further are discussed. Potential impacts of advances in computers related to neurosurgery in developing countries and underserved regions are also discussed. As this article illustrates, the computer, with its underlying and related technologies, is central to advances in neurosurgery over the last half century. Copyright © 2012 Elsevier Inc. All rights reserved.

The Effectiveness of Screencasts and Cognitive Tools as Scaffolding for Novice Object-Oriented Programmers

ERIC Educational Resources Information Center

Lee, Mark J. W.; Pradhan, Sunam; Dalgarno, Barney

2008-01-01

Modern information technology and computer science curricula employ a variety of graphical tools and development environments to facilitate student learning of introductory programming concepts and techniques. While the provision of interactive features and the use of visualization can enhance students' understanding and assist them in grasping…

Advanced Tools for Smartphone-Based Experiments: Phyphox

ERIC Educational Resources Information Center

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

2018-01-01

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

Educate at Penn State: Preparing Beginning Teachers with Powerful Digital Tools

ERIC Educational Resources Information Center

Murray, Orrin T.; Zembal-Saul, Carla

2008-01-01

University based teacher education programs are slowly beginning to catch up to other professional programs that use modern digital tools to prepare students to enter professional fields. This discussion looks at how one teacher education program reached the conclusion that students and faculty would use notebook computers. Frequently referred to…

Modernizing and transforming medical education at the Kilimanjaro Christian Medical University College.

PubMed

Lisasi, Esther; Kulanga, Ahaz; Muiruri, Charles; Killewo, Lucy; Fadhili, Ndimangwa; Mimano, Lucy; Kapanda, Gibson; Tibyampansha, Dativa; Ibrahim, Glory; Nyindo, Mramba; Mteta, Kien; Kessi, Egbert; Ntabaye, Moshi; Bartlett, John

2014-08-01

The Kilimanjaro Christian Medical University (KCMU) College and the Medical Education Partnership Initiative (MEPI) are addressing the crisis in Tanzanian health care manpower by modernizing the college's medical education with new tools and techniques. With a $10 million MEPI grant and the participation of its partner, Duke University, KCMU is harnessing the power of information technology (IT) to upgrade tools for students and faculty. Initiatives in eLearning have included bringing fiber-optic connectivity to the campus, offering campus-wide wireless access, opening student and faculty computer laboratories, and providing computer tablets to all incoming medical students. Beyond IT, the college is also offering wet laboratory instruction for hands-on diagnostic skills, team-based learning, and clinical skills workshops. In addition, modern teaching tools and techniques address the challenges posed by increasing numbers of students. To provide incentives for instructors, a performance-based compensation plan and teaching awards have been established. Also for faculty, IT tools and training have been made available, and a medical education course management system is now being widely employed. Student and faculty responses have been favorable, and the rapid uptake of these interventions by students, faculty, and the college's administration suggests that the KCMU College MEPI approach has addressed unmet needs. This enabling environment has transformed the culture of learning and teaching at KCMU College, where a path to sustainability is now being pursued.

Modernizing and Transforming Medical Education at the Kilimanjaro Christian Medical University College

PubMed Central

Lisasi, Esther; Kulanga, Ahaz; Muiruri, Charles; Killewo, Lucy; Fadhili, Ndimangwa; Mimano, Lucy; Kapanda, Gibson; Tibyampansha, Dativa; Ibrahim, Glory; Nyindo, Mramba; Mteta, Kien; Kessi, Egbert; Ntabaye, Moshi; Bartlett, John

2014-01-01

The Kilimanjaro Christian Medical University (KCMU) College and the Medical Education Partnership Initiative (MEPI) are addressing the crisis in Tanzanian health care manpower by modernizing the college’s medical education with new tools and techniques. With a $10 million MEPI grant and the participation of its partner, Duke University, KCMU is harnessing the power of information technology (IT) to upgrade tools for students and faculty. Initiatives in eLearning have included bringing fiber-optic connectivity to the campus, offering campus-wide wireless access, opening student and faculty computer laboratories, and providing computer tablets to all incoming medical students. Beyond IT, the college is also offering wet laboratory instruction for hands-on diagnostic skills, team-based learning, and clinical skills workshops. In addition, modern teaching tools and techniques address the challenges posed by increasing numbers of students. To provide incentives for instructors, a performance-based compensation plan and teaching awards have been established. Also for faculty, IT tools and training have been made available, and a medical education course management system is now being widely employed. Student and faculty responses have been favorable, and the rapid uptake of these interventions by students, faculty, and the college’s administration suggests that the KCMU College MEPI approach has addressed unmet needs. This enabling environment has transformed the culture of learning and teaching at KCMU College, where a path to sustainability is now being pursued. PMID:25072581

Living Color Frame System: PC graphics tool for data visualization

NASA Technical Reports Server (NTRS)

Truong, Long V.

1993-01-01

Living Color Frame System (LCFS) is a personal computer software tool for generating real-time graphics applications. It is highly applicable for a wide range of data visualization in virtual environment applications. Engineers often use computer graphics to enhance the interpretation of data under observation. These graphics become more complicated when 'run time' animations are required, such as found in many typical modern artificial intelligence and expert systems. Living Color Frame System solves many of these real-time graphics problems.

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

NASA Astrophysics Data System (ADS)

Alameda, J. C.

2011-12-01

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

TOXCAST, A TOOL FOR CATEGORIZATION AND ...

EPA Pesticide Factsheets

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

Experience in Education Environment Virtualization within the Automated Information System "Platonus" (Kazakhstan)

ERIC Educational Resources Information Center

Abeldina, Zhaidary; Moldumarova, Zhibek; Abeldina, Rauza; Makysh, Gulmira; Moldumarova, Zhuldyz Ilibaevna

2016-01-01

This work reports on the use of virtual tools as means of learning process activation. A good result can be achieved by combining the classical learning with modern computer technology. By creating a virtual learning environment and using multimedia learning tools one can obtain a significant result while facilitating the development of students'…

MEMORE: An Environment for Data Collection and Analysis on the Use of Computers in Education

ERIC Educational Resources Information Center

Goldschmidt, Ronaldo; Fernandes de Souza, Isabel; Norris, Monica; Passos, Claudio; Ferlin, Claudia; Cavalcanti, Maria Claudia; Soares, Jorge

2016-01-01

The use of computers as teaching and learning tools plays a particularly important role in modern society. Within this scenario, Brazil launched its own version of the "One Laptop per Child" (OLPC) program, and this initiative, termed PROUCA, has already distributed hundreds of low-cost laptops for educational purposes in many Brazilian…

Advanced Scientific Computing Research Exascale Requirements Review. An Office of Science review sponsored by Advanced Scientific Computing Research, September 27-29, 2016, Rockville, Maryland

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

Almgren, Ann; DeMar, Phil; Vetter, Jeffrey

The widespread use of computing in the American economy would not be possible without a thoughtful, exploratory research and development (R&D) community pushing the performance edge of operating systems, computer languages, and software libraries. These are the tools and building blocks — the hammers, chisels, bricks, and mortar — of the smartphone, the cloud, and the computing services on which we rely. Engineers and scientists need ever-more specialized computing tools to discover new material properties for manufacturing, make energy generation safer and more efficient, and provide insight into the fundamentals of the universe, for example. The research division of themore » U.S. Department of Energy’s (DOE’s) Office of Advanced Scientific Computing and Research (ASCR Research) ensures that these tools and building blocks are being developed and honed to meet the extreme needs of modern science. See also http://exascaleage.org/ascr/ for additional information.« less

Unified, Cross-Platform, Open-Source Library Package for High-Performance Computing

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

Kozacik, Stephen

Compute power is continually increasing, but this increased performance is largely found in sophisticated computing devices and supercomputer resources that are difficult to use, resulting in under-utilization. We developed a unified set of programming tools that will allow users to take full advantage of the new technology by allowing them to work at a level abstracted away from the platform specifics, encouraging the use of modern computing systems, including government-funded supercomputer facilities.

Development of Fuel Shuffling Module for PHISICS

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

Allan Mabe; Andrea Alfonsi; Cristian Rabiti

2013-06-01

PHISICS (Parallel and Highly Innovative Simulation for the INL Code System) [4] code toolkit has been in development at the Idaho National Laboratory. This package is intended to provide a modern analysis tool for reactor physics investigation. It is designed with the mindset to maximize accuracy for a given availability of computational resources and to give state of the art tools to the modern nuclear engineer. This is obtained by implementing several different algorithms and meshing approaches among which the user will be able to choose, in order to optimize his computational resources and accuracy needs. The software is completelymore » modular in order to simplify the independent development of modules by different teams and future maintenance. The package is coupled with the thermo-hydraulic code RELAP5-3D [3]. In the following the structure of the different PHISICS modules is briefly recalled, focusing on the new shuffling module (SHUFFLE), object of this paper.« less

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

Systems Engineering Building Advances Power Grid Research

ScienceCinema

Virden, Jud; Huang, Henry; Skare, Paul; Dagle, Jeff; Imhoff, Carl; Stoustrup, Jakob; Melton, Ron; Stiles, Dennis; Pratt, Rob

2018-01-16

Researchers and industry are now better equipped to tackle the nation’s most pressing energy challenges through PNNL’s new Systems Engineering Building – including challenges in grid modernization, buildings efficiency and renewable energy integration. This lab links real-time grid data, software platforms, specialized laboratories and advanced computing resources for the design and demonstration of new tools to modernize the grid and increase buildings energy efficiency.

Component architecture in drug discovery informatics.

PubMed

Smith, Peter M

2002-05-01

This paper reviews the characteristics of a new model of computing that has been spurred on by the Internet, known as Netcentric computing. Developments in this model led to distributed component architectures, which, although not new ideas, are now realizable with modern tools such as Enterprise Java. The application of this approach to scientific computing, particularly in pharmaceutical discovery research, is discussed and highlighted by a particular case involving the management of biological assay data.

Application of evolutionary computation in ECAD problems

NASA Astrophysics Data System (ADS)

Lee, Dae-Hyun; Hwang, Seung H.

1998-10-01

Design of modern electronic system is a complicated task which demands the use of computer- aided design (CAD) tools. Since a lot of problems in ECAD are combinatorial optimization problems, evolutionary computations such as genetic algorithms and evolutionary programming have been widely employed to solve those problems. We have applied evolutionary computation techniques to solve ECAD problems such as technology mapping, microcode-bit optimization, data path ordering and peak power estimation, where their benefits are well observed. This paper presents experiences and discusses issues in those applications.

Overview of the SAMSI year-long program on Statistical, Mathematical and Computational Methods for Astronomy

NASA Astrophysics Data System (ADS)

Jogesh Babu, G.

2017-01-01

A year-long research (Aug 2016- May 2017) program on `Statistical, Mathematical and Computational Methods for Astronomy (ASTRO)’ is well under way at Statistical and Applied Mathematical Sciences Institute (SAMSI), a National Science Foundation research institute in Research Triangle Park, NC. This program has brought together astronomers, computer scientists, applied mathematicians and statisticians. The main aims of this program are: to foster cross-disciplinary activities; to accelerate the adoption of modern statistical and mathematical tools into modern astronomy; and to develop new tools needed for important astronomical research problems. The program provides multiple avenues for cross-disciplinary interactions, including several workshops, long-term visitors, and regular teleconferences, so participants can continue collaborations, even if they can only spend limited time in residence at SAMSI. The main program is organized around five working groups:i) Uncertainty Quantification and Astrophysical Emulationii) Synoptic Time Domain Surveysiii) Multivariate and Irregularly Sampled Time Seriesiv) Astrophysical Populationsv) Statistics, computation, and modeling in cosmology.A brief description of each of the work under way by these groups will be given. Overlaps among various working groups will also be highlighted. How the wider astronomy community can both participate and benefit from the activities, will be briefly mentioned.

Quantum chemical studies of estrogenic compounds

USDA-ARS?s Scientific Manuscript database

Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

The Effects of Mechanical Transparency on Adjustment to a Complex Visuomotor Transformation at Early and Late Working Age

ERIC Educational Resources Information Center

Heuer, Herbert; Hegele, Mathias

2010-01-01

Mechanical tools are transparent in the sense that their input-output relations can be derived from their perceptible characteristics. Modern technology creates more and more tools that lack mechanical transparency, such as in the control of the position of a cursor by means of a computer mouse or some other input device. We inquired whether an…

New Trends in Computer Assisted Language Learning and Teaching.

ERIC Educational Resources Information Center

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

2002-01-01

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

Execution environment for intelligent real-time control systems

NASA Technical Reports Server (NTRS)

Sztipanovits, Janos

1987-01-01

Modern telerobot control technology requires the integration of symbolic and non-symbolic programming techniques, different models of parallel computations, and various programming paradigms. The Multigraph Architecture, which has been developed for the implementation of intelligent real-time control systems is described. The layered architecture includes specific computational models, integrated execution environment and various high-level tools. A special feature of the architecture is the tight coupling between the symbolic and non-symbolic computations. It supports not only a data interface, but also the integration of the control structures in a parallel computing environment.

Internal Flow

NASA Astrophysics Data System (ADS)

Greitzer, E. M.; Tan, C. S.; Graf, M. B.

2004-06-01

Focusing on phenomena important in implementing the performance of a broad range of fluid devices, this work describes the behavior of internal flows encountered in propulsion systems, fluid machinery (compressors, turbines, and pumps) and ducts (diffusers, nozzles and combustion chambers). The book equips students and practicing engineers with a range of new analytical tools. These tools offer enhanced interpretation and application of both experimental measurements and the computational procedures that characterize modern fluids engineering.

The Amber Biomolecular Simulation Programs

PubMed Central

CASE, DAVID A.; CHEATHAM, THOMAS E.; DARDEN, TOM; GOHLKE, HOLGER; LUO, RAY; MERZ, KENNETH M.; ONUFRIEV, ALEXEY; SIMMERLING, CARLOS; WANG, BING; WOODS, ROBERT J.

2006-01-01

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. PMID:16200636

Hands-on Approach to Prepare Specialists in Climate Changes Modeling and Analysis Using an Information-Computational Web-GIS Portal "Climate"

NASA Astrophysics Data System (ADS)

Shulgina, T. M.; Gordova, Y. E.; Martynova, Y. V.

2014-12-01

A problem of making education relevant to the workplace tasks is a key problem of higher education in the professional field of environmental sciences. To answer this challenge several new courses for students of "Climatology" and "Meteorology" specialties were developed and implemented at the Tomsk State University, which comprises theoretical knowledge from up-to-date environmental sciences with computational tasks. To organize the educational process we use an open-source course management system Moodle (www.moodle.org). It gave us an opportunity to combine text and multimedia in a theoretical part of educational courses. The hands-on approach is realized through development of innovative trainings which are performed within the information-computational web GIS platform "Climate" (http://climate.scert.ru/). The platform has a set of tools and data bases allowing a researcher to perform climate changes analysis on the selected territory. The tools are also used for students' trainings, which contain practical tasks on climate modeling and climate changes assessment and analysis. Laboratory exercises are covering three topics: "Analysis of regional climate changes"; "Analysis of climate extreme indices on the regional scale"; and "Analysis of future climate". They designed to consolidate students' knowledge of discipline, to instill in them the skills to work independently with large amounts of geophysical data using modern processing and analysis tools of web-GIS platform "Climate" and to train them to present results obtained on laboratory work as reports with the statement of the problem, the results of calculations and logically justified conclusion. Thus, students are engaged in n the use of modern tools of the geophysical data analysis and it cultivates dynamic of their professional learning. The approach can help us to fill in this gap because it is the only approach that offers experience, increases students involvement, advance the use of modern information and communication tools. Financial support for this research from the RFBR (13-05-12034, 14-05-00502), SB RAS project VIII.80.2.1 and grant of the President of RF (№ 181) is acknowledged.

Teaching Classic Probability Problems With Modern Digital Tools

ERIC Educational Resources Information Center

Abramovich, Sergei; Nikitin, Yakov Yu.

2017-01-01

This article is written to share teaching ideas about using commonly available computer applications--a spreadsheet, "The Geometer's Sketchpad", and "Wolfram Alpha"--to explore three classic and historically significant problems from the probability theory. These ideas stem from the authors' work with prospective economists,…

High Throughput Genotoxicity Profiling of the US EPA ToxCast Chemical Library

EPA Science Inventory

A key aim of the ToxCast project is to investigate modern molecular and genetic high content and high throughput screening (HTS) assays, along with various computational tools to supplement and perhaps replace traditional assays for evaluating chemical toxicity. Genotoxicity is a...

Getting Connected

ERIC Educational Resources Information Center

Stuart, Reginald

2010-01-01

When Alexander Johnson, a college freshman studying for a career in animation, began pondering colleges to attend, the opportunity to use modern computer technology tools in his classes played a major role in his consideration. Today, Johnson considers himself lucky to be among the students at historically Black colleges and universities (HBCUs)…

"Extreme Programming" in a Bioinformatics Class

ERIC Educational Resources Information Center

Kelley, Scott; Alger, Christianna; Deutschman, Douglas

2009-01-01

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

Student Research in Computational Astrophysics

NASA Astrophysics Data System (ADS)

Blondin, J. M.

1999-12-01

Computational physics can shorten the long road from freshman physics major to independent research by providing students with powerful tools to deal with the complexities of modern research problems. At North Carolina State University we have introduced dozens of students to astrophysics research using the tools of computational fluid dynamics. We have used several formats for working with students, including the traditional approach of one-on-one mentoring, a more group-oriented format in which several students work together on one or more related projects, and a novel attempt to involve an entire class in a coordinated semester research project. The advantages and disadvantages of these formats will be discussed at length, but the single most important influence has been peer support. Having students work in teams or learn the tools of research together but tackle different problems has led to more positive experiences than a lone student diving into solo research. This work is supported by an NSF CAREER Award.

Multidisciplinary analysis and design of printed wiring boards

NASA Astrophysics Data System (ADS)

Fulton, Robert E.; Hughes, Joseph L.; Scott, Waymond R., Jr.; Umeagukwu, Charles; Yeh, Chao-Pin

1991-04-01

Modern printed wiring board design depends on electronic prototyping using computer-based simulation and design tools. Existing electrical computer-aided design (ECAD) tools emphasize circuit connectivity with only rudimentary analysis capabilities. This paper describes a prototype integrated PWB design environment denoted Thermal Structural Electromagnetic Testability (TSET) being developed at Georgia Tech in collaboration with companies in the electronics industry. TSET provides design guidance based on enhanced electrical and mechanical CAD capabilities including electromagnetic modeling testability analysis thermal management and solid mechanics analysis. TSET development is based on a strong analytical and theoretical science base and incorporates an integrated information framework and a common database design based on a systematic structured methodology.

Hands-on approach to teaching Earth system sciences using a information-computational web-GIS portal "Climate"

NASA Astrophysics Data System (ADS)

Gordova, Yulia; Gorbatenko, Valentina; Martynova, Yulia; Shulgina, Tamara

2014-05-01

A problem of making education relevant to the workplace tasks is a key problem of higher education because old-school training programs are not keeping pace with the rapidly changing situation in the professional field of environmental sciences. A joint group of specialists from Tomsk State University and Siberian center for Environmental research and Training/IMCES SB RAS developed several new courses for students of "Climatology" and "Meteorology" specialties, which comprises theoretical knowledge from up-to-date environmental sciences with practical tasks. To organize the educational process we use an open-source course management system Moodle (www.moodle.org). It gave us an opportunity to combine text and multimedia in a theoretical part of educational courses. The hands-on approach is realized through development of innovative trainings which are performed within the information-computational platform "Climate" (http://climate.scert.ru/) using web GIS tools. These trainings contain practical tasks on climate modeling and climate changes assessment and analysis and should be performed using typical tools which are usually used by scientists performing such kind of research. Thus, students are engaged in n the use of modern tools of the geophysical data analysis and it cultivates dynamic of their professional learning. The hands-on approach can help us to fill in this gap because it is the only approach that offers experience, increases students involvement, advance the use of modern information and communication tools. The courses are implemented at Tomsk State University and help forming modern curriculum in Earth system science area. This work is partially supported by SB RAS project VIII.80.2.1, RFBR grants numbers 13-05-12034 and 14-05-00502.

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

NASA Astrophysics Data System (ADS)

Brescia, Massimo

2012-11-01

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

Rethinking Technology-Enhanced Physics Teacher Education: From Theory to Practice

ERIC Educational Resources Information Center

Milner-Bolotin, Marina

2016-01-01

This article discusses how modern technology, such as electronic response systems, PeerWise system, data collection and analysis tools, computer simulations, and modeling software can be used in physics methods courses to promote teacher-candidates' professional competencies and their positive attitudes about mathematics and science education. We…

Researching for Public Speaking Classes: Requiring Various Media.

ERIC Educational Resources Information Center

Greenberg, Cindy A.

This paper presents steps for incorporating research into a community college public speaking class curriculum. It outlines, from an historical perspective, the different techniques and tools of research, including face-to-face contact, the printing press, modern machinery, and computers. It suggests discussing research surveys and taking students…

On the Edge: Intelligent CALL in the 1990s.

ERIC Educational Resources Information Center

Underwood, John

1989-01-01

Examines the possibilities of developing computer-assisted language learning (CALL) based on the best of modern technology, arguing that artificial intelligence (AI) strategies will radically improve the kinds of exercises that can be performed. Recommends combining AI technology with other tools for delivering instruction, such as simulation and…

Automation Training Tools of the Future.

ERIC Educational Resources Information Center

Rehg, James

1986-01-01

Manufacturing isn't what it used to be, and the United States must ensure its position in the world trade market by educating factory workers in new automated systems. A computer manufacturing engineer outlines the training requirements of a modern workforce and details robotic training devices suitable for classroom use. (JN)

Robotics for Computer Scientists: What's the Big Idea?

ERIC Educational Resources Information Center

Touretzky, David S.

2013-01-01

Modern robots, like today's smartphones, are complex devices with intricate software systems. Introductory robot programming courses must evolve to reflect this reality, by teaching students to make use of the sophisticated tools their robots provide rather than reimplementing basic algorithms. This paper focuses on teaching with Tekkotsu, an open…

A computer network with scada and case tools for on-line process control in greenhouses

NASA Astrophysics Data System (ADS)

Gieling, Th. H.; van Meurs, W. Th. M.; Janssen, H. J. J.

Climate control computers in greenhouses are used to control heating and ventilation, supply water and dilute and dispense nutrients. They integrate models into optimally controlled systems. This paper describes how information technology, as in use in other sectors of industry, is applied to greenhouse control. The introduction of modern software and hardware concepts in horticulture adds power and extra opportunities to climate control in greenhouses.

Open source tools for large-scale neuroscience.

PubMed

Freeman, Jeremy

2015-06-01

New technologies for monitoring and manipulating the nervous system promise exciting biology but pose challenges for analysis and computation. Solutions can be found in the form of modern approaches to distributed computing, machine learning, and interactive visualization. But embracing these new technologies will require a cultural shift: away from independent efforts and proprietary methods and toward an open source and collaborative neuroscience. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

A computer network with SCADA and case tools for on-line process control in greenhouses.

PubMed

Gieling ThH; van Meurs WTh; Janssen, H J

1996-01-01

Climate control computers in greenhouses are used to control heating and ventilation, supply water and dilute and dispense nutrients. They integrate models into optimally controlled systems. This paper describes how information technology, as in use in other sectors of industry, is applied to greenhouse control. The introduction of modern software and hardware concepts in horticulture adds power and extra oppurtunities to climate contol in greenhouses.

Applications of an architecture design and assessment system (ADAS)

NASA Technical Reports Server (NTRS)

Gray, F. Gail; Debrunner, Linda S.; White, Tennis S.

1988-01-01

A new Architecture Design and Assessment System (ADAS) tool package is introduced, and a range of possible applications is illustrated. ADAS was used to evaluate the performance of an advanced fault-tolerant computer architecture in a modern flight control application. Bottlenecks were identified and possible solutions suggested. The tool was also used to inject faults into the architecture and evaluate the synchronization algorithm, and improvements are suggested. Finally, ADAS was used as a front end research tool to aid in the design of reconfiguration algorithms in a distributed array architecture.

Computer Simulation Performed for Columbia Project Cooling System

NASA Technical Reports Server (NTRS)

Ahmad, Jasim

2005-01-01

This demo shows a high-fidelity simulation of the air flow in the main computer room housing the Columbia (10,024 intel titanium processors) system. The simulation asseses the performance of the cooling system and identified deficiencies, and recommended modifications to eliminate them. It used two in house software packages on NAS supercomputers: Chimera Grid tools to generate a geometric model of the computer room, OVERFLOW-2 code for fluid and thermal simulation. This state-of-the-art technology can be easily extended to provide a general capability for air flow analyses on any modern computer room. Columbia_CFD_black.tiff

A Format for Phylogenetic Placements

PubMed Central

Matsen, Frederick A.; Hoffman, Noah G.; Gallagher, Aaron; Stamatakis, Alexandros

2012-01-01

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement. PMID:22383988

A format for phylogenetic placements.

PubMed

Matsen, Frederick A; Hoffman, Noah G; Gallagher, Aaron; Stamatakis, Alexandros

2012-01-01

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.

Introducing the Computer to Family Practice

PubMed Central

Petreman, Mel

1984-01-01

The medical profession has been far more reluctant than the general business community to adopt the computer as a useful business tool. The experience of a group of five family physicians who have been using a computer since 1979 demonstrates that it is possible to achieve significant financial benefits, and to reduce the stress and workload of both physicians and office staff. The computerization of medical records, scheduling, and patient billing is discussed in detail. Physicians have controlled the paper load of the modern medical office by pioneering their own medical software system. PMID:21279036

National Combustion Code, a Multidisciplinary Combustor Design System, Will Be Transferred to the Commercial Sector

NASA Technical Reports Server (NTRS)

Steele, Gynelle C.

1999-01-01

The NASA Lewis Research Center and Flow Parametrics will enter into an agreement to commercialize the National Combustion Code (NCC). This multidisciplinary combustor design system utilizes computer-aided design (CAD) tools for geometry creation, advanced mesh generators for creating solid model representations, a common framework for fluid flow and structural analyses, modern postprocessing tools, and parallel processing. This integrated system can facilitate and enhance various phases of the design and analysis process.

Some Observations on the Current Status of Performing Finite Element Analyses

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.; Knight, Norman F., Jr; Shivakumar, Kunigal N.

2015-01-01

Aerospace structures are complex high-performance structures. Advances in reliable and efficient computing and modeling tools are enabling analysts to consider complex configurations, build complex finite element models, and perform analysis rapidly. Many of the early career engineers of today are very proficient in the usage of modern computers, computing engines, complex software systems, and visualization tools. These young engineers are becoming increasingly efficient in building complex 3D models of complicated aerospace components. However, the current trends demonstrate blind acceptance of the results of the finite element analysis results. This paper is aimed at raising an awareness of this situation. Examples of the common encounters are presented. To overcome the current trends, some guidelines and suggestions for analysts, senior engineers, and educators are offered.

Development of an Automated Modality-Independent Elastographic Image Analysis System for Tumor Screening

DTIC Science & Technology

2008-02-01

journal article. Didactic coursework requirements for the PhD degree have been completed at this time as well as successful presentation of the...Libraries", Modern Software Tools in Scientific Computing. Birkhauser Press, pp. 163-202, 1997. [5] Doyley MM, Weaver JB, Van Houten EEW, Kennedy FE...data from MR, x-ray computed tomography (CT) and digital photography have been used to successfully drive the algorithm in two-dimensional (2D) work

A Conceptual Design Model for CBT Development: A NATO Case Study

ERIC Educational Resources Information Center

Kok, Ayse

2014-01-01

CBT (computer-based training) can benefit from the modern multimedia tools combined with network capabilities to overcame traditional education. The objective of this paper is focused on CBT development to improve strategic decision-making with regard to air command and control system for NATO staff in virtual environment. A conceptual design for…

Automated Formative Assessment as a Tool to Scaffold Student Documentary Writing

ERIC Educational Resources Information Center

Ferster, Bill; Hammond, Thomas C.; Alexander, R. Curby; Lyman, Hunt

2012-01-01

The hurried pace of the modern classroom does not permit formative feedback on writing assignments at the frequency or quality recommended by the research literature. One solution for increasing individual feedback to students is to incorporate some form of computer-generated assessment. This study explores the use of automated assessment of…

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

ERIC Educational Resources Information Center

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

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

Bridging the Gap between Basic and Clinical Sciences: A Description of a Radiological Anatomy Course

ERIC Educational Resources Information Center

Torres, Anna; Staskiewicz, Grzegorz J.; Lisiecka, Justyna; Pietrzyk, Lukasz; Czekajlo, Michael; Arancibia, Carlos U.; Maciejewski, Ryszard; Torres, Kamil

2016-01-01

A wide variety of medical imaging techniques pervade modern medicine, and the changing portability and performance of tools like ultrasound imaging have brought these medical imaging techniques into the everyday practice of many specialties outside of radiology. However, proper interpretation of ultrasonographic and computed tomographic images…

Mobile Educational Features in Authoring Tools for Personalised Tutoring

ERIC Educational Resources Information Center

Virvou, Maria; Alepis, Eythimios

2005-01-01

One important field where mobile technology can make significant contributions is Education. In the fast pace of modern life, students and instructors would appreciate using constructively some spare time that they may have, in order to work on lessons at any place, even when away from offices, classrooms and labs where computers are usually…

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

PubMed Central

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

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

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Rich Language Analysis for Counterterrorism

NASA Astrophysics Data System (ADS)

Guidère, Mathieu; Howard, Newton; Argamon, Shlomo

Accurate and relevant intelligence is critical for effective counterterrorism. Too much irrelevant information is as bad or worse than not enough information. Modern computational tools promise to provide better search and summarization capabilities to help analysts filter and select relevant and key information. However, to do this task effectively, such tools must have access to levels of meaning beyond the literal. Terrorists operating in context-rich cultures like fundamentalist Islam use messages with multiple levels of interpretation, which are easily misunderstood by non-insiders. This chapter discusses several kinds of such “encryption” used by terrorists and insurgents in the Arabic language, and how knowledge of such methods can be used to enhance computational text analysis techniques for use in counterterrorism.

Advanced tools for smartphone-based experiments: phyphox

NASA Astrophysics Data System (ADS)

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

2018-07-01

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

Adjoint-Based Aerodynamic Design of Complex Aerospace Configurations

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.

2016-01-01

An overview of twenty years of adjoint-based aerodynamic design research at NASA Langley Research Center is presented. Adjoint-based algorithms provide a powerful tool for efficient sensitivity analysis of complex large-scale computational fluid dynamics (CFD) simulations. Unlike alternative approaches for which computational expense generally scales with the number of design parameters, adjoint techniques yield sensitivity derivatives of a simulation output with respect to all input parameters at the cost of a single additional simulation. With modern large-scale CFD applications often requiring millions of compute hours for a single analysis, the efficiency afforded by adjoint methods is critical in realizing a computationally tractable design optimization capability for such applications.

Parallel algorithm for computation of second-order sequential best rotations

NASA Astrophysics Data System (ADS)

Redif, Soydan; Kasap, Server

2013-12-01

Algorithms for computing an approximate polynomial matrix eigenvalue decomposition of para-Hermitian systems have emerged as a powerful, generic signal processing tool. A technique that has shown much success in this regard is the sequential best rotation (SBR2) algorithm. Proposed is a scheme for parallelising SBR2 with a view to exploiting the modern architectural features and inherent parallelism of field-programmable gate array (FPGA) technology. Experiments show that the proposed scheme can achieve low execution times while requiring minimal FPGA resources.

Visualization and Interaction in Research, Teaching, and Scientific Communication

NASA Astrophysics Data System (ADS)

Ammon, C. J.

2017-12-01

Modern computing provides many tools for exploring observations, numerical calculations, and theoretical relationships. The number of options is, in fact, almost overwhelming. But the choices provide those with modest programming skills opportunities to create unique views of scientific information and to develop deeper insights into their data, their computations, and the underlying theoretical data-model relationships. I present simple examples of using animation and human-computer interaction to explore scientific data and scientific-analysis approaches. I illustrate how valuable a little programming ability can free scientists from the constraints of existing tools and can facilitate the development of deeper appreciation data and models. I present examples from a suite of programming languages ranging from C to JavaScript including the Wolfram Language. JavaScript is valuable for sharing tools and insight (hopefully) with others because it is integrated into one of the most powerful communication tools in human history, the web browser. Although too much of that power is often spent on distracting advertisements, the underlying computation and graphics engines are efficient, flexible, and almost universally available in desktop and mobile computing platforms. Many are working to fulfill the browser's potential to become the most effective tool for interactive study. Open-source frameworks for visualizing everything from algorithms to data are available, but advance rapidly. One strategy for dealing with swiftly changing tools is to adopt common, open data formats that are easily adapted (often by framework or tool developers). I illustrate the use of animation and interaction in research and teaching with examples from earthquake seismology.

Leveraging Social Computing for Personalized Crisis Communication using Social Media.

PubMed

Leykin, Dmitry; Aharonson-Daniel, Limor; Lahad, Mooli

2016-03-24

The extensive use of social media in modern life redefines social interaction and communication. Communication plays an important role in mitigating, or exacerbating, the psychological and behavioral responses to critical incidents and disasters. As recent disasters demonstrated, people tend to converge to social media during and following emergencies. Authorities can then use this media and other computational methods to gain insights from the public, mainly to enhance situational awareness, but also to improve their communication with the public and public adherence to instructions. The current review presents a conceptual framework for studying psychological aspects of crisis and risk communication using the social media through social computing. Advanced analytical tools can be integrated in the processes and objectives of crisis communication. The availability of the computational techniques can improve communication with the public by a process of Hyper-Targeted Crisis Communication. The review suggests that using advanced computational tools for target-audience profiling and linguistic matching in social media, can facilitate more sensitive and personalized emergency communication.

Dynamic Analyses of Result Quality in Energy-Aware Approximate Programs

NASA Astrophysics Data System (ADS)

RIngenburg, Michael F.

Energy efficiency is a key concern in the design of modern computer systems. One promising approach to energy-efficient computation, approximate computing, trades off output precision for energy efficiency. However, this tradeoff can have unexpected effects on computation quality. This thesis presents dynamic analysis tools to study, debug, and monitor the quality and energy efficiency of approximate computations. We propose three styles of tools: prototyping tools that allow developers to experiment with approximation in their applications, online tools that instrument code to determine the key sources of error, and online tools that monitor the quality of deployed applications in real time. Our prototyping tool is based on an extension to the functional language OCaml. We add approximation constructs to the language, an approximation simulator to the runtime, and profiling and auto-tuning tools for studying and experimenting with energy-quality tradeoffs. We also present two online debugging tools and three online monitoring tools. The first online tool identifies correlations between output quality and the total number of executions of, and errors in, individual approximate operations. The second tracks the number of approximate operations that flow into a particular value. Our online tools comprise three low-cost approaches to dynamic quality monitoring. They are designed to monitor quality in deployed applications without spending more energy than is saved by approximation. Online monitors can be used to perform real time adjustments to energy usage in order to meet specific quality goals. We present prototype implementations of all of these tools and describe their usage with several applications. Our prototyping, profiling, and autotuning tools allow us to experiment with approximation strategies and identify new strategies, our online tools succeed in providing new insights into the effects of approximation on output quality, and our monitors succeed in controlling output quality while still maintaining significant energy efficiency gains.

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

NASA Astrophysics Data System (ADS)

Grapenthin, Ronni

2011-12-01

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

Screen Capture Technology: A Digital Window into Students' Writing Processes

ERIC Educational Resources Information Center

Seror, Jeremie

2013-01-01

Technological innovations and the prevalence of the computer as a means of producing and engaging with texts have dramatically transformed how literacy is defined and developed in modern society. This rise in digital writing practices has led to a growing number of tools and methods that can be used to explore second language (L2) writing…

Modern Theories of Pelvic Floor Support : A Topical Review of Modern Studies on Structural and Functional Pelvic Floor Support from Medical Imaging, Computational Modeling, and Electromyographic Perspectives.

PubMed

Peng, Yun; Miller, Brandi D; Boone, Timothy B; Zhang, Yingchun

2018-02-12

Weakened pelvic floor support is believed to be the main cause of various pelvic floor disorders. Modern theories of pelvic floor support stress on the structural and functional integrity of multiple structures and their interplay to maintain normal pelvic floor functions. Connective tissues provide passive pelvic floor support while pelvic floor muscles provide active support through voluntary contraction. Advanced modern medical technologies allow us to comprehensively and thoroughly evaluate the interaction of supporting structures and assess both active and passive support functions. The pathophysiology of various pelvic floor disorders associated with pelvic floor weakness is now under scrutiny from the combination of (1) morphological, (2) dynamic (through computational modeling), and (3) neurophysiological perspectives. This topical review aims to update newly emerged studies assessing pelvic floor support function among these three categories. A literature search was performed with emphasis on (1) medical imaging studies that assess pelvic floor muscle architecture, (2) subject-specific computational modeling studies that address new topics such as modeling muscle contractions, and (3) pelvic floor neurophysiology studies that report novel devices or findings such as high-density surface electromyography techniques. We found that recent computational modeling studies are featured with more realistic soft tissue constitutive models (e.g., active muscle contraction) as well as an increasing interest in simulating surgical interventions (e.g., artificial sphincter). Diffusion tensor imaging provides a useful non-invasive tool to characterize pelvic floor muscles at the microstructural level, which can be potentially used to improve the accuracy of the simulation of muscle contraction. Studies using high-density surface electromyography anal and vaginal probes on large patient cohorts have been recently reported. Influences of vaginal delivery on the distribution of innervation zones of pelvic floor muscles are clarified, providing useful guidance for a better protection of women during delivery. We are now in a period of transition to advanced diagnostic and predictive pelvic floor medicine. Our findings highlight the application of diffusion tensor imaging, computational models with consideration of active pelvic floor muscle contraction, high-density surface electromyography, and their potential integration, as tools to push the boundary of our knowledge in pelvic floor support and better shape current clinical practice.

The environment power system analysis tool development program

NASA Technical Reports Server (NTRS)

Jongeward, Gary A.; Kuharski, Robert A.; Kennedy, Eric M.; Stevens, N. John; Putnam, Rand M.; Roche, James C.; Wilcox, Katherine G.

1990-01-01

The Environment Power System Analysis Tool (EPSAT) is being developed to provide space power system design engineers with an analysis tool for determining system performance of power systems in both naturally occurring and self-induced environments. The program is producing an easy to use computer aided engineering (CAE) tool general enough to provide a vehicle for technology transfer from space scientists and engineers to power system design engineers. The results of the project after two years of a three year development program are given. The EPSAT approach separates the CAE tool into three distinct functional units: a modern user interface to present information, a data dictionary interpreter to coordinate analysis; and a data base for storing system designs and results of analysis.

Computational protein design-the next generation tool to expand synthetic biology applications.

PubMed

Gainza-Cirauqui, Pablo; Correia, Bruno Emanuel

2018-05-02

One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells. Copyright © 2018. Published by Elsevier Ltd.

Computer assisted screening, correction, and analysis of historical weather measurements

NASA Astrophysics Data System (ADS)

Burnette, Dorian J.; Stahle, David W.

2013-04-01

A computer program, Historical Observation Tools (HOB Tools), has been developed to facilitate many of the calculations used by historical climatologists to develop instrumental and documentary temperature and precipitation datasets and makes them readily accessible to other researchers. The primitive methodology used by the early weather observers makes the application of standard techniques difficult. HOB Tools provides a step-by-step framework to visually and statistically assess, adjust, and reconstruct historical temperature and precipitation datasets. These routines include the ability to check for undocumented discontinuities, adjust temperature data for poor thermometer exposures and diurnal averaging, and assess and adjust daily precipitation data for undercount. This paper provides an overview of the Visual Basic.NET program and a demonstration of how it can assist in the development of extended temperature and precipitation datasets using modern and early instrumental measurements from the United States.

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

NASA Astrophysics Data System (ADS)

Dogan, Firat; Atilgan, Yasemin

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

Leveraging e-Science infrastructure for electrochemical research.

PubMed

Peachey, Tom; Mashkina, Elena; Lee, Chong-Yong; Enticott, Colin; Abramson, David; Bond, Alan M; Elton, Darrell; Gavaghan, David J; Stevenson, Gareth P; Kennedy, Gareth F

2011-08-28

As in many scientific disciplines, modern chemistry involves a mix of experimentation and computer-supported theory. Historically, these skills have been provided by different groups, and range from traditional 'wet' laboratory science to advanced numerical simulation. Increasingly, progress is made by global collaborations, in which new theory may be developed in one part of the world and applied and tested in the laboratory elsewhere. e-Science, or cyber-infrastructure, underpins such collaborations by providing a unified platform for accessing scientific instruments, computers and data archives, and collaboration tools. In this paper we discuss the application of advanced e-Science software tools to electrochemistry research performed in three different laboratories--two at Monash University in Australia and one at the University of Oxford in the UK. We show that software tools that were originally developed for a range of application domains can be applied to electrochemical problems, in particular Fourier voltammetry. Moreover, we show that, by replacing ad-hoc manual processes with e-Science tools, we obtain more accurate solutions automatically.

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

NASA Astrophysics Data System (ADS)

Friedrich, J.; Karslioglu, M. O.

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

State of the art of sonic boom modeling

NASA Astrophysics Data System (ADS)

Plotkin, Kenneth J.

2002-01-01

Based on fundamental theory developed through the 1950s and 1960s, sonic boom modeling has evolved into practical tools. Over the past decade, there have been requirements for design tools for an advanced supersonic transport, and for tools for environmental assessment of various military and aerospace activities. This has resulted in a number of advances in the understanding of the physics of sonic booms, including shock wave rise times, propagation through turbulence, and blending sonic boom theory with modern computational fluid dynamics (CFD) aerodynamic design methods. This article reviews the early fundamental theory, recent advances in theory, and the application of these advances to practical models.

State of the art of sonic boom modeling.

PubMed

Plotkin, Kenneth J

2002-01-01

Based on fundamental theory developed through the 1950s and 1960s, sonic boom modeling has evolved into practical tools. Over the past decade, there have been requirements for design tools for an advanced supersonic transport, and for tools for environmental assessment of various military and aerospace activities. This has resulted in a number of advances in the understanding of the physics of sonic booms, including shock wave rise times, propagation through turbulence, and blending sonic boom theory with modern computational fluid dynamics (CFD) aerodynamic design methods. This article reviews the early fundamental theory, recent advances in theory, and the application of these advances to practical models.

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

DOE PAGES

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

2015-01-01

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

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

PubMed Central

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

2014-01-01

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

Building a Data Science capability for USGS water research and communication

NASA Astrophysics Data System (ADS)

Appling, A.; Read, E. K.

2015-12-01

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

Pattern Discovery in Biomolecular Data – Tools, Techniques, and Applications | Center for Cancer Research

Cancer.gov

Finding patterns in biomolecular data, particularly in DNA and RNA, is at the center of modern biological research. These data are complex and growing rapidly, so the search for patterns requires increasingly sophisticated computer methods. This book provides a summary of principal techniques. Each chapter describes techniques that are drawn from many fields, including graph

Egas Moniz: 90 Years (1927-2017) from Cerebral Angiography.

PubMed

Artico, Marco; Spoletini, Marialuisa; Fumagalli, Lorenzo; Biagioni, Francesca; Ryskalin, Larisa; Fornai, Francesco; Salvati, Maurizio; Frati, Alessandro; Pastore, Francesco Saverio; Taurone, Samanta

2017-01-01

In June 2017 we celebrate the 90th anniversary of the pioneer discovery of cerebral angiography, the seminal imaging technique used for visualizing cerebral blood vessels and vascular alterations as well as other intracranial disorders. Egas Moniz (1874-1955) was the first to describe the use of this revolutionary technique which, until 1975 (when computed tomography, CT, scan was introduced in the clinical practice), was the sole diagnostic tool to provide an imaging of cerebral vessels and therefore alterations due to intracranial pathology. Moniz introduced in the clinical practice this fundamental and important diagnostic tool. The present contribution wishes to pay a tribute to the Portuguese neurosurgeon, who was also a distinguished neurologist and statesman. Despite his tremendous contribution in modern brain imaging, Egas Moniz was awarded the Nobel Prize in Physiology or Medicine in 1949 for prefrontal leucotomy, the neurosurgical intervention nowadays unacceptable, but should rather be remembered for his key contribution to modern brain imaging.

Interactive Voice/Web Response System in clinical research

PubMed Central

Ruikar, Vrishabhsagar

2016-01-01

Emerging technologies in computer and telecommunication industry has eased the access to computer through telephone. An Interactive Voice/Web Response System (IxRS) is one of the user friendly systems for end users, with complex and tailored programs at its backend. The backend programs are specially tailored for easy understanding of users. Clinical research industry has experienced revolution in methodologies of data capture with time. Different systems have evolved toward emerging modern technologies and tools in couple of decades from past, for example, Electronic Data Capture, IxRS, electronic patient reported outcomes, etc. PMID:26952178

Interactive Voice/Web Response System in clinical research.

PubMed

Ruikar, Vrishabhsagar

2016-01-01

Emerging technologies in computer and telecommunication industry has eased the access to computer through telephone. An Interactive Voice/Web Response System (IxRS) is one of the user friendly systems for end users, with complex and tailored programs at its backend. The backend programs are specially tailored for easy understanding of users. Clinical research industry has experienced revolution in methodologies of data capture with time. Different systems have evolved toward emerging modern technologies and tools in couple of decades from past, for example, Electronic Data Capture, IxRS, electronic patient reported outcomes, etc.

Access and visualization using clusters and other parallel computers

NASA Technical Reports Server (NTRS)

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

Analysis of lead twist in modern high-performance grinding methods

NASA Astrophysics Data System (ADS)

Kundrák, J.; Gyáni, K.; Felhő, C.; Markopoulos, AP; Deszpoth, I.

2016-11-01

According to quality requirements of road vehicles shafts, which bear dynamic seals, twisted-pattern micro-geometrical topography is not allowed. It is a question whether newer modern grinding methods - such as quick-point grinding and peel grinding - could provide twist- free topography. According to industrial experience, twist-free surfaces can be made, however with certain settings, same twist occurs. In this paper it is proved by detailed chip-geometrical analysis that the topography generated by the new procedures is theoretically twist-patterned because of the feeding motion of the CBN tool. The presented investigation was carried out by a single-grain wheel model and computer simulation.

Mathematical support for automated geometry analysis of lathe machining of oblique peakless round-nose tools

NASA Astrophysics Data System (ADS)

Filippov, A. V.; Tarasov, S. Yu; Podgornyh, O. A.; Shamarin, N. N.; Filippova, E. O.

2017-01-01

Automatization of engineering processes requires developing relevant mathematical support and a computer software. Analysis of metal cutting kinematics and tool geometry is a necessary key task at the preproduction stage. This paper is focused on developing a procedure for determining the geometry of oblique peakless round-nose tool lathe machining with the use of vector/matrix transformations. Such an approach allows integration into modern mathematical software packages in distinction to the traditional analytic description. Such an advantage is very promising for developing automated control of the preproduction process. A kinematic criterion for the applicable tool geometry has been developed from the results of this study. The effect of tool blade inclination and curvature on the geometry-dependent process parameters was evaluated.

ParCAT: A Parallel Climate Analysis Toolkit

NASA Astrophysics Data System (ADS)

Haugen, B.; Smith, B.; Steed, C.; Ricciuto, D. M.; Thornton, P. E.; Shipman, G.

2012-12-01

Climate science has employed increasingly complex models and simulations to analyze the past and predict the future of our climate. The size and dimensionality of climate simulation data has been growing with the complexity of the models. This growth in data is creating a widening gap between the data being produced and the tools necessary to analyze large, high dimensional data sets. With single run data sets increasing into 10's, 100's and even 1000's of gigabytes, parallel computing tools are becoming a necessity in order to analyze and compare climate simulation data. The Parallel Climate Analysis Toolkit (ParCAT) provides basic tools that efficiently use parallel computing techniques to narrow the gap between data set size and analysis tools. ParCAT was created as a collaborative effort between climate scientists and computer scientists in order to provide efficient parallel implementations of the computing tools that are of use to climate scientists. Some of the basic functionalities included in the toolkit are the ability to compute spatio-temporal means and variances, differences between two runs and histograms of the values in a data set. ParCAT is designed to facilitate the "heavy lifting" that is required for large, multidimensional data sets. The toolkit does not focus on performing the final visualizations and presentation of results but rather, reducing large data sets to smaller, more manageable summaries. The output from ParCAT is provided in commonly used file formats (NetCDF, CSV, ASCII) to allow for simple integration with other tools. The toolkit is currently implemented as a command line utility, but will likely also provide a C library for developers interested in tighter software integration. Elements of the toolkit are already being incorporated into projects such as UV-CDAT and CMDX. There is also an effort underway to implement portions of the CCSM Land Model Diagnostics package using ParCAT in conjunction with Python and gnuplot. ParCAT is implemented in C to provide efficient file IO. The file IO operations in the toolkit use the parallel-netcdf library; this enables the code to use the parallel IO capabilities of modern HPC systems. Analysis that currently requires an estimated 12+ hours with the traditional CCSM Land Model Diagnostics Package can now be performed in as little as 30 minutes on a single desktop workstation and a few minutes for relatively small jobs completed on modern HPC systems such as ORNL's Jaguar.

Methods and Research for Multi-Component Cutting Force Sensing Devices and Approaches in Machining

PubMed Central

Liang, Qiaokang; Zhang, Dan; Wu, Wanneng; Zou, Kunlin

2016-01-01

Multi-component cutting force sensing systems in manufacturing processes applied to cutting tools are gradually becoming the most significant monitoring indicator. Their signals have been extensively applied to evaluate the machinability of workpiece materials, predict cutter breakage, estimate cutting tool wear, control machine tool chatter, determine stable machining parameters, and improve surface finish. Robust and effective sensing systems with capability of monitoring the cutting force in machine operations in real time are crucial for realizing the full potential of cutting capabilities of computer numerically controlled (CNC) tools. The main objective of this paper is to present a brief review of the existing achievements in the field of multi-component cutting force sensing systems in modern manufacturing. PMID:27854322

Methods and Research for Multi-Component Cutting Force Sensing Devices and Approaches in Machining.

PubMed

Liang, Qiaokang; Zhang, Dan; Wu, Wanneng; Zou, Kunlin

2016-11-16

Multi-component cutting force sensing systems in manufacturing processes applied to cutting tools are gradually becoming the most significant monitoring indicator. Their signals have been extensively applied to evaluate the machinability of workpiece materials, predict cutter breakage, estimate cutting tool wear, control machine tool chatter, determine stable machining parameters, and improve surface finish. Robust and effective sensing systems with capability of monitoring the cutting force in machine operations in real time are crucial for realizing the full potential of cutting capabilities of computer numerically controlled (CNC) tools. The main objective of this paper is to present a brief review of the existing achievements in the field of multi-component cutting force sensing systems in modern manufacturing.

Leveraging Social Computing for Personalized Crisis Communication using Social Media

PubMed Central

Leykin, Dmitry; Aharonson-Daniel, Limor; Lahad, Mooli

2016-01-01

Introduction: The extensive use of social media in modern life redefines social interaction and communication. Communication plays an important role in mitigating, or exacerbating, the psychological and behavioral responses to critical incidents and disasters. As recent disasters demonstrated, people tend to converge to social media during and following emergencies. Authorities can then use this media and other computational methods to gain insights from the public, mainly to enhance situational awareness, but also to improve their communication with the public and public adherence to instructions. Methods: The current review presents a conceptual framework for studying psychological aspects of crisis and risk communication using the social media through social computing. Results: Advanced analytical tools can be integrated in the processes and objectives of crisis communication. The availability of the computational techniques can improve communication with the public by a process of Hyper-Targeted Crisis Communication. Discussion: The review suggests that using advanced computational tools for target-audience profiling and linguistic matching in social media, can facilitate more sensitive and personalized emergency communication. PMID:27092290

ParBiBit: Parallel tool for binary biclustering on modern distributed-memory systems

PubMed Central

Expósito, Roberto R.

2018-01-01

Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, a parallel tool to accelerate the search of interesting biclusters on binary datasets, which are very popular on different fields such as genetics, marketing or text mining. It is based on the state-of-the-art sequential Java tool BiBit, which has been proved accurate by several studies, especially on scenarios that result on many large biclusters. ParBiBit uses the same methodology as BiBit (grouping the binary information into patterns) and provides the same results. Nevertheless, our tool significantly improves performance thanks to an efficient implementation based on C++11 that includes support for threads and MPI processes in order to exploit the compute capabilities of modern distributed-memory systems, which provide several multicore CPU nodes interconnected through a network. Our performance evaluation with 18 representative input datasets on two different eight-node systems shows that our tool is significantly faster than the original BiBit. Source code in C++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/parbibit/. PMID:29608567

ParBiBit: Parallel tool for binary biclustering on modern distributed-memory systems.

PubMed

González-Domínguez, Jorge; Expósito, Roberto R

2018-01-01

Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, a parallel tool to accelerate the search of interesting biclusters on binary datasets, which are very popular on different fields such as genetics, marketing or text mining. It is based on the state-of-the-art sequential Java tool BiBit, which has been proved accurate by several studies, especially on scenarios that result on many large biclusters. ParBiBit uses the same methodology as BiBit (grouping the binary information into patterns) and provides the same results. Nevertheless, our tool significantly improves performance thanks to an efficient implementation based on C++11 that includes support for threads and MPI processes in order to exploit the compute capabilities of modern distributed-memory systems, which provide several multicore CPU nodes interconnected through a network. Our performance evaluation with 18 representative input datasets on two different eight-node systems shows that our tool is significantly faster than the original BiBit. Source code in C++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/parbibit/.

Neandertals made the first specialized bone tools in Europe

PubMed Central

Soressi, Marie; McPherron, Shannon P.; Lenoir, Michel; Dogandžić, Tamara; Goldberg, Paul; Jacobs, Zenobia; Maigrot, Yolaine; Martisius, Naomi L.; Miller, Christopher E.; Rendu, William; Richards, Michael; Skinner, Matthew M.; Steele, Teresa E.; Talamo, Sahra; Texier, Jean-Pierre

2013-01-01

Modern humans replaced Neandertals ∼40,000 y ago. Close to the time of replacement, Neandertals show behaviors similar to those of the modern humans arriving into Europe, including the use of specialized bone tools, body ornaments, and small blades. It is highly debated whether these modern behaviors developed before or as a result of contact with modern humans. Here we report the identification of a type of specialized bone tool, lissoir, previously only associated with modern humans. The microwear preserved on one of these lissoir is consistent with the use of lissoir in modern times to obtain supple, lustrous, and more impermeable hides. These tools are from a Neandertal context proceeding the replacement period and are the oldest specialized bone tools in Europe. As such, they are either a demonstration of independent invention by Neandertals or an indication that modern humans started influencing European Neandertals much earlier than previously believed. Because these finds clearly predate the oldest known age for the use of similar objects in Europe by anatomically modern humans, they could also be evidence for cultural diffusion from Neandertals to modern humans. PMID:23940333

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

PubMed Central

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C.

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction. PMID:24904400

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research.

PubMed

Sherif, Tarek; Rioux, Pierre; Rousseau, Marc-Etienne; Kassis, Nicolas; Beck, Natacha; Adalat, Reza; Das, Samir; Glatard, Tristan; Evans, Alan C

2014-01-01

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses. CBRAIN's flexible meta-scheduling has allowed the incorporation of a wide range of heterogeneous computing sites, currently including nine national research High Performance Computing (HPC) centers in Canada, one in Korea, one in Germany, and several local research servers. CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user. Compared with typical grid solutions available, our architecture was designed to be easily extendable and deployed on existing remote computing sites with no tool modification, administrative intervention, or special software/hardware configuration. As October 2013, CBRAIN serves over 200 users spread across 53 cities in 17 countries. The platform is built as a generic framework that can accept data and analysis tools from any discipline. However, its current focus is primarily on neuroimaging research and studies of neurological diseases such as Autism, Parkinson's and Alzheimer's diseases, Multiple Sclerosis as well as on normal brain structure and development. This technical report presents the CBRAIN Platform, its current deployment and usage and future direction.

An Educational Exercise Examining the Role of Model Attributes on the Creation and Alteration of CAD Models

ERIC Educational Resources Information Center

Johnson, Michael D.; Diwakaran, Ram Prasad

2011-01-01

Computer-aided design (CAD) is a ubiquitous tool that today's students will be expected to use proficiently for numerous engineering purposes. Taking full advantage of the features available in modern CAD programs requires that models are created in a manner that allows others to easily understand how they are organized and alter them in an…

Language-Agnostic Reproducible Data Analysis Using Literate Programming.

PubMed

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.

Language-Agnostic Reproducible Data Analysis Using Literate Programming

PubMed Central

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir. PMID:27711123

Development of modern human subadult age and sex estimation standards using multi-slice computed tomography images from medical examiner's offices

NASA Astrophysics Data System (ADS)

Stock, Michala K.; Stull, Kyra E.; Garvin, Heather M.; Klales, Alexandra R.

2016-10-01

Forensic anthropologists are routinely asked to estimate a biological profile (i.e., age, sex, ancestry and stature) from a set of unidentified remains. In contrast to the abundance of collections and techniques associated with adult skeletons, there is a paucity of modern, documented subadult skeletal material, which limits the creation and validation of appropriate forensic standards. Many are forced to use antiquated methods derived from small sample sizes, which given documented secular changes in the growth and development of children, are not appropriate for application in the medico-legal setting. Therefore, the aim of this project is to use multi-slice computed tomography (MSCT) data from a large, diverse sample of modern subadults to develop new methods to estimate subadult age and sex for practical forensic applications. The research sample will consist of over 1,500 full-body MSCT scans of modern subadult individuals (aged birth to 20 years) obtained from two U.S. medical examiner's offices. Statistical analysis of epiphyseal union scores, long bone osteometrics, and os coxae landmark data will be used to develop modern subadult age and sex estimation standards. This project will result in a database of information gathered from the MSCT scans, as well as the creation of modern, statistically rigorous standards for skeletal age and sex estimation in subadults. Furthermore, the research and methods developed in this project will be applicable to dry bone specimens, MSCT scans, and radiographic images, thus providing both tools and continued access to data for forensic practitioners in a variety of settings.

Business continuity strategies for cyber defence: battling time and information overload.

PubMed

Streufert, John

2010-11-01

Can the same numbers and letters which are the life blood of modern business and government computer systems be harnessed to protect computers from attack against known information security risks? For the past seven years, Foreign Service officers and technicians of the US Government have sought to maintain diplomatic operations in the face of rising cyber attacks and test the hypothesis that an ounce of prevention is worth a pound of cure. As eight out of ten attacks leverage known computer security vulnerabilities or configuration setting weaknesses, a pound of cure would seem to be easy to come by. Yet modern security tools present an unusually consequential threat to business continuity - too much rather than too little information on cyber problems is presented, harking back to a phenomenon cited by social scientists in the 1960s called 'information overload'. Experience indicates that the longer the most serious cyber problems go untreated, the wider the attack surface adversaries can find. One technique used at the Department of State, called 'risk scoring', resulted in an 89 per cent overall reduction in measured risk over 12 months for the Department of State's servers and personal computers. Later refinements of risk scoring enabled technicians to correct unique security threats with unprecedented speed. This paper explores how the use of metrics, special care in presenting information to technicians and executives alike, as well as tactical use of organisational incentives can result in stronger cyber defences protecting modern organisations.

Towards quantum chemistry on a quantum computer.

PubMed

Lanyon, B P; Whitfield, J D; Gillett, G G; Goggin, M E; Almeida, M P; Kassal, I; Biamonte, J D; Mohseni, M; Powell, B J; Barbieri, M; Aspuru-Guzik, A; White, A G

2010-02-01

Exact first-principles calculations of molecular properties are currently intractable because their computational cost grows exponentially with both the number of atoms and basis set size. A solution is to move to a radically different model of computing by building a quantum computer, which is a device that uses quantum systems themselves to store and process data. Here we report the application of the latest photonic quantum computer technology to calculate properties of the smallest molecular system: the hydrogen molecule in a minimal basis. We calculate the complete energy spectrum to 20 bits of precision and discuss how the technique can be expanded to solve large-scale chemical problems that lie beyond the reach of modern supercomputers. These results represent an early practical step toward a powerful tool with a broad range of quantum-chemical applications.

Fast Acceleration of 2D Wave Propagation Simulations Using Modern Computational Accelerators

PubMed Central

Wang, Wei; Xu, Lifan; Cavazos, John; Huang, Howie H.; Kay, Matthew

2014-01-01

Recent developments in modern computational accelerators like Graphics Processing Units (GPUs) and coprocessors provide great opportunities for making scientific applications run faster than ever before. However, efficient parallelization of scientific code using new programming tools like CUDA requires a high level of expertise that is not available to many scientists. This, plus the fact that parallelized code is usually not portable to different architectures, creates major challenges for exploiting the full capabilities of modern computational accelerators. In this work, we sought to overcome these challenges by studying how to achieve both automated parallelization using OpenACC and enhanced portability using OpenCL. We applied our parallelization schemes using GPUs as well as Intel Many Integrated Core (MIC) coprocessor to reduce the run time of wave propagation simulations. We used a well-established 2D cardiac action potential model as a specific case-study. To the best of our knowledge, we are the first to study auto-parallelization of 2D cardiac wave propagation simulations using OpenACC. Our results identify several approaches that provide substantial speedups. The OpenACC-generated GPU code achieved more than speedup above the sequential implementation and required the addition of only a few OpenACC pragmas to the code. An OpenCL implementation provided speedups on GPUs of at least faster than the sequential implementation and faster than a parallelized OpenMP implementation. An implementation of OpenMP on Intel MIC coprocessor provided speedups of with only a few code changes to the sequential implementation. We highlight that OpenACC provides an automatic, efficient, and portable approach to achieve parallelization of 2D cardiac wave simulations on GPUs. Our approach of using OpenACC, OpenCL, and OpenMP to parallelize this particular model on modern computational accelerators should be applicable to other computational models of wave propagation in multi-dimensional media. PMID:24497950

Structural biology computing: Lessons for the biomedical research sciences.

PubMed

Morin, Andrew; Sliz, Piotr

2013-11-01

The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields. Copyright © 2013 Wiley Periodicals, Inc.

Advances in electron kinetics and theory of gas discharges

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

Kolobov, Vladimir I.; The University of Alabama in Huntsville, Huntsville, Alabama 35899

2013-10-15

“Electrons, like people, are fertile and infertile: high-energy electrons are fertile and able to reproduce.”—Lev TsendinModern physics of gas discharges increasingly uses physical kinetics for analysis of non-equilibrium plasmas. The description of underlying physics at the kinetic level appears to be important for plasma applications in modern technologies. In this paper, we attempt to grasp the legacy of Professor Lev Tsendin, who advocated the use of the kinetic approach for understanding fundamental problems of gas discharges. We outline the fundamentals of electron kinetics in low-temperature plasmas, describe elements of the modern kinetic theory of gas discharges, and show examples ofmore » the theoretical approach to gas discharge problems used by Lev Tsendin. Important connections between electron kinetics in gas discharges and semiconductors are also discussed. Using several examples, we illustrate how Tsendin's ideas and methods are currently being developed for the implementation of next generation computational tools for adaptive kinetic-fluid simulations of gas discharges used in modern technologies.« less

Optimizing high performance computing workflow for protein functional annotation.

PubMed

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

2014-09-10

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

Optimizing high performance computing workflow for protein functional annotation

PubMed Central

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

2014-01-01

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

Methods for transition toward computer assisted cognitive examination.

PubMed

Jurica, P; Valenzi, S; Struzik, Z R; Cichocki, A

2015-01-01

We present a software framework which enables the extension of current methods for the assessment of cognitive fitness using recent technological advances. Screening for cognitive impairment is becoming more important as the world's population grows older. Current methods could be enhanced by use of computers. Introduction of new methods to clinics requires basic tools for collection and communication of collected data. To develop tools that, with minimal interference, offer new opportunities for the enhancement of the current interview based cognitive examinations. We suggest methods and discuss process by which established cognitive tests can be adapted for data collection through digitization by pen enabled tablets. We discuss a number of methods for evaluation of collected data, which promise to increase the resolution and objectivity of the common scoring strategy based on visual inspection. By involving computers in the roles of both instructing and scoring, we aim to increase the precision and reproducibility of cognitive examination. The tools provided in Python framework CogExTools available at http://bsp. brain.riken.jp/cogextools/ enable the design, application and evaluation of screening tests for assessment of cognitive impairment. The toolbox is a research platform; it represents a foundation for further collaborative development by the wider research community and enthusiasts. It is free to download and use, and open-source. We introduce a set of open-source tools that facilitate the design and development of new cognitive tests for modern technology. We provide these tools in order to enable the adaptation of technology for cognitive examination in clinical settings. The tools provide the first step in a possible transition toward standardized mental state examination using computers.

Ganalyzer: A tool for automatic galaxy image analysis

NASA Astrophysics Data System (ADS)

Shamir, Lior

2011-05-01

Ganalyzer is a model-based tool that automatically analyzes and classifies galaxy images. Ganalyzer works by separating the galaxy pixels from the background pixels, finding the center and radius of the galaxy, generating the radial intensity plot, and then computing the slopes of the peaks detected in the radial intensity plot to measure the spirality of the galaxy and determine its morphological class. Unlike algorithms that are based on machine learning, Ganalyzer is based on measuring the spirality of the galaxy, a task that is difficult to perform manually, and in many cases can provide a more accurate analysis compared to manual observation. Ganalyzer is simple to use, and can be easily embedded into other image analysis applications. Another advantage is its speed, which allows it to analyze ~10,000,000 galaxy images in five days using a standard modern desktop computer. These capabilities can make Ganalyzer a useful tool in analyzing large datasets of galaxy images collected by autonomous sky surveys such as SDSS, LSST or DES.

National Combustion Code: A Multidisciplinary Combustor Design System

NASA Technical Reports Server (NTRS)

Stubbs, Robert M.; Liu, Nan-Suey

1997-01-01

The Internal Fluid Mechanics Division conducts both basic research and technology, and system technology research for aerospace propulsion systems components. The research within the division, which is both computational and experimental, is aimed at improving fundamental understanding of flow physics in inlets, ducts, nozzles, turbomachinery, and combustors. This article and the following three articles highlight some of the work accomplished in 1996. A multidisciplinary combustor design system is critical for optimizing the combustor design process. Such a system should include sophisticated computer-aided design (CAD) tools for geometry creation, advanced mesh generators for creating solid model representations, a common framework for fluid flow and structural analyses, modern postprocessing tools, and parallel processing. The goal of the present effort is to develop some of the enabling technologies and to demonstrate their overall performance in an integrated system called the National Combustion Code.

Conversion of HSPF Legacy Model to a Platform-Independent, Open-Source Language

NASA Astrophysics Data System (ADS)

Heaphy, R. T.; Burke, M. P.; Love, J. T.

2015-12-01

Since its initial development over 30 years ago, the Hydrologic Simulation Program - FORTAN (HSPF) model has been used worldwide to support water quality planning and management. In the United States, HSPF receives widespread endorsement as a regulatory tool at all levels of government and is a core component of the EPA's Better Assessment Science Integrating Point and Nonpoint Sources (BASINS) system, which was developed to support nationwide Total Maximum Daily Load (TMDL) analysis. However, the model's legacy code and data management systems have limitations in their ability to integrate with modern software, hardware, and leverage parallel computing, which have left voids in optimization, pre-, and post-processing tools. Advances in technology and our scientific understanding of environmental processes that have occurred over the last 30 years mandate that upgrades be made to HSPF to allow it to evolve and continue to be a premiere tool for water resource planners. This work aims to mitigate the challenges currently facing HSPF through two primary tasks: (1) convert code to a modern widely accepted, open-source, high-performance computing (hpc) code; and (2) convert model input and output files to modern widely accepted, open-source, data model, library, and binary file format. Python was chosen as the new language for the code conversion. It is an interpreted, object-oriented, hpc code with dynamic semantics that has become one of the most popular open-source languages. While python code execution can be slow compared to compiled, statically typed programming languages, such as C and FORTRAN, the integration of Numba (a just-in-time specializing compiler) has allowed this challenge to be overcome. For the legacy model data management conversion, HDF5 was chosen to store the model input and output. The code conversion for HSPF's hydrologic and hydraulic modules has been completed. The converted code has been tested against HSPF's suite of "test" runs and shown good agreement and similar execution times while using the Numba compiler. Continued verification of the accuracy of the converted code against more complex legacy applications and improvement upon execution times by incorporating an intelligent network change detection tool is currently underway, and preliminary results will be presented.

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

PubMed Central

Dinov, Ivo; Lozev, Kamen; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Pierce, Jonathan; Zamanyan, Alen; Chakrapani, Shruthi; Van Horn, John; Parker, D. Stott; Magsipoc, Rico; Leung, Kelvin; Gutman, Boris; Woods, Roger; Toga, Arthur

2010-01-01

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges—management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu. PMID:20927408

Egas Moniz: 90 Years (1927–2017) from Cerebral Angiography

PubMed Central

Artico, Marco; Spoletini, Marialuisa; Fumagalli, Lorenzo; Biagioni, Francesca; Ryskalin, Larisa; Fornai, Francesco; Salvati, Maurizio; Frati, Alessandro; Pastore, Francesco Saverio; Taurone, Samanta

2017-01-01

In June 2017 we celebrate the 90th anniversary of the pioneer discovery of cerebral angiography, the seminal imaging technique used for visualizing cerebral blood vessels and vascular alterations as well as other intracranial disorders. Egas Moniz (1874–1955) was the first to describe the use of this revolutionary technique which, until 1975 (when computed tomography, CT, scan was introduced in the clinical practice), was the sole diagnostic tool to provide an imaging of cerebral vessels and therefore alterations due to intracranial pathology. Moniz introduced in the clinical practice this fundamental and important diagnostic tool. The present contribution wishes to pay a tribute to the Portuguese neurosurgeon, who was also a distinguished neurologist and statesman. Despite his tremendous contribution in modern brain imaging, Egas Moniz was awarded the Nobel Prize in Physiology or Medicine in 1949 for prefrontal leucotomy, the neurosurgical intervention nowadays unacceptable, but should rather be remembered for his key contribution to modern brain imaging. PMID:28974927

A New Network Modeling Tool for the Ground-based Nuclear Explosion Monitoring Community

NASA Astrophysics Data System (ADS)

Merchant, B. J.; Chael, E. P.; Young, C. J.

2013-12-01

Network simulations have long been used to assess the performance of monitoring networks to detect events for such purposes as planning station deployments and network resilience to outages. The standard tool has been the SAIC-developed NetSim package. With correct parameters, NetSim can produce useful simulations; however, the package has several shortcomings: an older language (FORTRAN), an emphasis on seismic monitoring with limited support for other technologies, limited documentation, and a limited parameter set. Thus, we are developing NetMOD (Network Monitoring for Optimal Detection), a Java-based tool designed to assess the performance of ground-based networks. NetMOD's advantages include: coded in a modern language that is multi-platform, utilizes modern computing performance (e.g. multi-core processors), incorporates monitoring technologies other than seismic, and includes a well-validated default parameter set for the IMS stations. NetMOD is designed to be extendable through a plugin infrastructure, so new phenomenological models can be added. Development of the Seismic Detection Plugin is being pursued first. Seismic location and infrasound and hydroacoustic detection plugins will follow. By making NetMOD an open-release package, it can hopefully provide a common tool that the monitoring community can use to produce assessments of monitoring networks and to verify assessments made by others.

The need for integration of drought monitoring tools for proactive food security management in sub-Saharan Africa

USGS Publications Warehouse

Tadesse, T.; Haile, M.; Senay, G.; Wardlow, B.D.; Knutson, C.L.

2008-01-01

Reducing the impact of drought and famine remains a challenge in sub-Saharan Africa despite ongoing drought relief assistance in recent decades. This is because drought and famine are primarily addressed through a crisis management approach when a disaster occurs, rather than stressing preparedness and risk management. Moreover, drought planning and food security efforts have been hampered by a lack of integrated drought monitoring tools, inadequate early warning systems (EWS), and insufficient information flow within and between levels of government in many sub-Saharan countries. The integration of existing drought monitoring tools for sub-Saharan Africa is essential for improving food security systems to reduce the impacts of drought and famine on society in this region. A proactive approach emphasizing integration requires the collective use of multiple tools, which can be used to detect trends in food availability and provide early indicators at local, national, and regional scales on the likely occurrence of food crises. In addition, improving the ability to monitor and disseminate critical drought-related information using available modern technologies (e.g., satellites, computers, and modern communication techniques) may help trigger timely and appropriate preventive responses and, ultimately, contribute to food security and sustainable development in sub-Saharan Africa. ?? 2008 United Nations.

75 FR 11914 - Chrysler, LLC, Mount Elliott Tool and Die, Including On-Site Leased Workers From Modern...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... Elliott Tool and Die, Including On-Site Leased Workers From Modern Professional Services, TAC Automotive... on-site leased workers from Modern Professional Services, TAC Automotive, Syncreon, CSC, and Resource... subject firm. The workers are engaged in the production of automotive dies and tooling. New information...

Scientific Computing Strategic Plan for the Idaho National Laboratory

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

Whiting, Eric Todd

Scientific computing is a critical foundation of modern science. Without innovations in the field of computational science, the essential missions of the Department of Energy (DOE) would go unrealized. Taking a leadership role in such innovations is Idaho National Laboratory’s (INL’s) challenge and charge, and is central to INL’s ongoing success. Computing is an essential part of INL’s future. DOE science and technology missions rely firmly on computing capabilities in various forms. Modeling and simulation, fueled by innovations in computational science and validated through experiment, are a critical foundation of science and engineering. Big data analytics from an increasing numbermore » of widely varied sources is opening new windows of insight and discovery. Computing is a critical tool in education, science, engineering, and experiments. Advanced computing capabilities in the form of people, tools, computers, and facilities, will position INL competitively to deliver results and solutions on important national science and engineering challenges. A computing strategy must include much more than simply computers. The foundational enabling component of computing at many DOE national laboratories is the combination of a showcase like data center facility coupled with a very capable supercomputer. In addition, network connectivity, disk storage systems, and visualization hardware are critical and generally tightly coupled to the computer system and co located in the same facility. The existence of these resources in a single data center facility opens the doors to many opportunities that would not otherwise be possible.« less

JINR cloud infrastructure evolution

NASA Astrophysics Data System (ADS)

Baranov, A. V.; Balashov, N. A.; Kutovskiy, N. A.; Semenov, R. N.

2016-09-01

To fulfil JINR commitments in different national and international projects related to the use of modern information technologies such as cloud and grid computing as well as to provide a modern tool for JINR users for their scientific research a cloud infrastructure was deployed at Laboratory of Information Technologies of Joint Institute for Nuclear Research. OpenNebula software was chosen as a cloud platform. Initially it was set up in simple configuration with single front-end host and a few cloud nodes. Some custom development was done to tune JINR cloud installation to fit local needs: web form in the cloud web-interface for resources request, a menu item with cloud utilization statistics, user authentication via Kerberos, custom driver for OpenVZ containers. Because of high demand in that cloud service and its resources over-utilization it was re-designed to cover increasing users' needs in capacity, availability and reliability. Recently a new cloud instance has been deployed in high-availability configuration with distributed network file system and additional computing power.

Contemporary imaging of mild TBI: the journey toward diffusion tensor imaging to assess neuronal damage.

PubMed

Fox, W Christopher; Park, Min S; Belverud, Shawn; Klugh, Arnett; Rivet, Dennis; Tomlin, Jeffrey M

2013-04-01

To follow the progression of neuroimaging as a means of non-invasive evaluation of mild traumatic brain injury (mTBI) in order to provide recommendations based on reproducible, defined imaging findings. A comprehensive literature review and analysis of contemporary published articles was performed to study the progression of neuroimaging findings as a non-invasive 'biomarker' for mTBI. Multiple imaging modalities exist to support the evaluation of patients with mTBI, including ultrasound (US), computed tomography (CT), single photon emission computed tomography (SPECT), positron emission tomography (PET), and magnetic resonance imaging (MRI). These techniques continue to evolve with the development of fractional anisotropy (FA), fiber tractography (FT), and diffusion tensor imaging (DTI). Modern imaging techniques, when applied in the appropriate clinical setting, may serve as a valuable tool for diagnosis and management of patients with mTBI. An understanding of modern neuroanatomical imaging will enhance our ability to analyse injury and recognize the manifestations of mTBI.

Design and Implementation of a Modern Automatic Deformation Monitoring System

NASA Astrophysics Data System (ADS)

Engel, Philipp; Schweimler, Björn

2016-03-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the University of Applied Sciences in Neubrandenburg (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

Accelerator Based Tools of Stockpile Stewardship

NASA Astrophysics Data System (ADS)

Seestrom, Susan

2017-01-01

The Manhattan Project had to solve difficult challenges in physics and materials science. During the cold war a large nuclear stockpile was developed. In both cases, the approach was largely empirical. Today that stockpile must be certified without nuclear testing, a task that becomes more difficult as the stockpile ages. I will discuss the role of modern accelerator based experiments, such as x-ray radiography, proton radiography, neutron and nuclear physics experiments, in stockpile stewardship. These new tools provide data of exceptional sensitivity and are answering questions about the stockpile, improving our scientific understanding, and providing validation for the computer simulations that are relied upon to certify todays' stockpile.

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2015-01-01

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

Method and computer program product for maintenance and modernization backlogging

DOEpatents

Mattimore, Bernard G; Reynolds, Paul E; Farrell, Jill M

2013-02-19

According to one embodiment, a computer program product for determining future facility conditions includes a computer readable medium having computer readable program code stored therein. The computer readable program code includes computer readable program code for calculating a time period specific maintenance cost, for calculating a time period specific modernization factor, and for calculating a time period specific backlog factor. Future facility conditions equal the time period specific maintenance cost plus the time period specific modernization factor plus the time period specific backlog factor. In another embodiment, a computer-implemented method for calculating future facility conditions includes calculating a time period specific maintenance cost, calculating a time period specific modernization factor, and calculating a time period specific backlog factor. Future facility conditions equal the time period specific maintenance cost plus the time period specific modernization factor plus the time period specific backlog factor. Other embodiments are also presented.

Network neuroscience

PubMed Central

Bassett, Danielle S; Sporns, Olaf

2017-01-01

Despite substantial recent progress, our understanding of the principles and mechanisms underlying complex brain function and cognition remains incomplete. Network neuroscience proposes to tackle these enduring challenges. Approaching brain structure and function from an explicitly integrative perspective, network neuroscience pursues new ways to map, record, analyze and model the elements and interactions of neurobiological systems. Two parallel trends drive the approach: the availability of new empirical tools to create comprehensive maps and record dynamic patterns among molecules, neurons, brain areas and social systems; and the theoretical framework and computational tools of modern network science. The convergence of empirical and computational advances opens new frontiers of scientific inquiry, including network dynamics, manipulation and control of brain networks, and integration of network processes across spatiotemporal domains. We review emerging trends in network neuroscience and attempt to chart a path toward a better understanding of the brain as a multiscale networked system. PMID:28230844

The future of medical diagnostics: large digitized databases.

PubMed

Kerr, Wesley T; Lau, Edward P; Owens, Gwen E; Trefler, Aaron

2012-09-01

The electronic health record mandate within the American Recovery and Reinvestment Act of 2009 will have a far-reaching affect on medicine. In this article, we provide an in-depth analysis of how this mandate is expected to stimulate the production of large-scale, digitized databases of patient information. There is evidence to suggest that millions of patients and the National Institutes of Health will fully support the mining of such databases to better understand the process of diagnosing patients. This data mining likely will reaffirm and quantify known risk factors for many diagnoses. This quantification may be leveraged to further develop computer-aided diagnostic tools that weigh risk factors and provide decision support for health care providers. We expect that creation of these databases will stimulate the development of computer-aided diagnostic support tools that will become an integral part of modern medicine.

Experimental validation of docking and capture using space robotics testbeds

NASA Technical Reports Server (NTRS)

Spofford, John; Schmitz, Eric; Hoff, William

1991-01-01

This presentation describes the application of robotic and computer vision systems to validate docking and capture operations for space cargo transfer vehicles. Three applications are discussed: (1) air bearing systems in two dimensions that yield high quality free-flying, flexible, and contact dynamics; (2) validation of docking mechanisms with misalignment and target dynamics; and (3) computer vision technology for target location and real-time tracking. All the testbeds are supported by a network of engineering workstations for dynamic and controls analyses. Dynamic simulation of multibody rigid and elastic systems are performed with the TREETOPS code. MATRIXx/System-Build and PRO-MATLAB/Simulab are the tools for control design and analysis using classical and modern techniques such as H-infinity and LQG/LTR. SANDY is a general design tool to optimize numerically a multivariable robust compensator with a user-defined structure. Mathematica and Macsyma are used to derive symbolically dynamic and kinematic equations.

Nonlinear Aerodynamics and the Design of Wing Tips

NASA Technical Reports Server (NTRS)

Kroo, Ilan

1991-01-01

The analysis and design of wing tips for fixed wing and rotary wing aircraft still remains part art, part science. Although the design of airfoil sections and basic planform geometry is well developed, the tip regions require more detailed consideration. This is important because of the strong impact of wing tip flow on wing drag; although the tip region constitutes a small portion of the wing, its effect on the drag can be significant. The induced drag of a wing is, for a given lift and speed, inversely proportional to the square of the wing span. Concepts are proposed as a means of reducing drag. Modern computational methods provide a tool for studying these issues in greater detail. The purpose of the current research program is to improve the understanding of the fundamental issues involved in the design of wing tips and to develop the range of computational and experimental tools needed for further study of these ideas.

Wood densitometry in 17th and 18th century Dutch, German, Austrian and French violins, compared to classical Cremonese and modern violins.

PubMed

Stoel, Berend C; Borman, Terry M; de Jongh, Ronald

2012-01-01

Classical violins produced by makers such as Antonio Stradivari and Guarneri del Gesu have long been considered the epitome of the luthier's art and the expressive tool of choice for the most celebrated violinists. It has been speculated these makers had access to wood that was unique in some way and that this was responsible for their acclaimed tonal characteristics. In an attempt to discern whether the above conjecture is true, we analyzed 17 modern and classical Dutch, German, Austrian and French violins by wood densitometry using computed tomography and correlated these results with our previous study of modern and Cremonese violins; in all studying 30 instruments of the violin family. In order to make this comparison possible we developed methods to cross calibrate results from different CT manufacturers using calibration wood pieces. We found no significant differences in median densities between modern and classical violins, or between classical violins from different origins. These results suggest that it is unlikely classical Cremonese makers had access to wood with significantly different wood density characteristics than that available to contemporaneous or modern makers.

Some recent applications of Navier-Stokes codes to rotorcraft

NASA Technical Reports Server (NTRS)

Mccroskey, W. J.

1992-01-01

Many operational limitations of helicopters and other rotary-wing aircraft are due to nonlinear aerodynamic phenomena incuding unsteady, three-dimensional transonic and separated flow near the surfaces and highly vortical flow in the wakes of rotating blades. Modern computational fluid dynamics (CFD) technology offers new tools to study and simulate these complex flows. However, existing Euler and Navier-Stokes codes have to be modified significantly for rotorcraft applications, and the enormous computational requirements presently limit their use in routine design applications. Nevertheless, the Euler/Navier-Stokes technology is progressing in anticipation of future supercomputers that will enable meaningful calculations to be made for complete rotorcraft configurations.

Trends in Programming Languages for Neuroscience Simulations

PubMed Central

Davison, Andrew P.; Hines, Michael L.; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing. PMID:20198154

Recent advances in fluidized bed drying

NASA Astrophysics Data System (ADS)

Haron, N. S.; Zakaria, J. H.; Mohideen Batcha, M. F.

2017-09-01

Fluidized bed drying are very well known to yield high heat and mass transfer and hence adopted to many industrial drying processes particularly agricultural products. In this paper, recent advances in fluidized bed drying were reviewed and focus is given to the drying related to the usage of Computational Fluid Dynamics (CFD). It can be seen that usage of modern computational tools such as CFD helps to optimize the fluidized bed dryer design and operation for lower energy consumption and thus better thermal efficiency. Among agricultural products that were reviewed in this paper were oil palm frond, wheat grains, olive pomace, coconut, pepper corn and millet.

Trends in programming languages for neuroscience simulations.

PubMed

Davison, Andrew P; Hines, Michael L; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing.

Space station data management system - A common GSE test interface for systems testing and verification

NASA Technical Reports Server (NTRS)

Martinez, Pedro A.; Dunn, Kevin W.

1987-01-01

This paper examines the fundamental problems and goals associated with test, verification, and flight-certification of man-rated distributed data systems. First, a summary of the characteristics of modern computer systems that affect the testing process is provided. Then, verification requirements are expressed in terms of an overall test philosophy for distributed computer systems. This test philosophy stems from previous experience that was gained with centralized systems (Apollo and the Space Shuttle), and deals directly with the new problems that verification of distributed systems may present. Finally, a description of potential hardware and software tools to help solve these problems is provided.

Evaluation of Proteus as a Tool for the Rapid Development of Models of Hydrologic Systems

NASA Astrophysics Data System (ADS)

Weigand, T. M.; Farthing, M. W.; Kees, C. E.; Miller, C. T.

2013-12-01

Models of modern hydrologic systems can be complex and involve a variety of operators with varying character. The goal is to implement approximations of such models that are both efficient for the developer and computationally efficient, which is a set of naturally competing objectives. Proteus is a Python-based toolbox that supports prototyping of model formulations as well as a wide variety of modern numerical methods and parallel computing. We used Proteus to develop numerical approximations for three models: Richards' equation, a brine flow model derived using the Thermodynamically Constrained Averaging Theory (TCAT), and a multiphase TCAT-based tumor growth model. For Richards' equation, we investigated discontinuous Galerkin solutions with higher order time integration based on the backward difference formulas. The TCAT brine flow model was implemented using Proteus and a variety of numerical methods were compared to hand coded solutions. Finally, an existing tumor growth model was implemented in Proteus to introduce more advanced numerics and allow the code to be run in parallel. From these three example models, Proteus was found to be an attractive open-source option for rapidly developing high quality code for solving existing and evolving computational science models.

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

PubMed

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

2006-01-01

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

The application of computer image analysis in life sciences and environmental engineering

NASA Astrophysics Data System (ADS)

Mazur, R.; Lewicki, A.; Przybył, K.; Zaborowicz, M.; Koszela, K.; Boniecki, P.; Mueller, W.; Raba, B.

2014-04-01

The main aim of the article was to present research on the application of computer image analysis in Life Science and Environmental Engineering. The authors used different methods of computer image analysis in developing of an innovative biotest in modern biomonitoring of water quality. Created tools were based on live organisms such as bioindicators Lemna minor L. and Hydra vulgaris Pallas as well as computer image analysis method in the assessment of negatives reactions during the exposition of the organisms to selected water toxicants. All of these methods belong to acute toxicity tests and are particularly essential in ecotoxicological assessment of water pollutants. Developed bioassays can be used not only in scientific research but are also applicable in environmental engineering and agriculture in the study of adverse effects on water quality of various compounds used in agriculture and industry.

DIC-CAM recipe for reverse engineering

NASA Astrophysics Data System (ADS)

Romero-Carrillo, P.; Lopez-Alba, E.; Dorado, R.; Diaz-Garrido, F. A.

2012-04-01

Reverse engineering (RE) tries to model and manufacture an object from measurements one of a reference object. Modern optical measurement systems and computer aided engineering software have improved reverse engineering procedures. We detail the main RE steps from 3D digitalization by Digital Image Correlation to manufacturing. The previous description is complemented with an application example, which portrays the performance of RE. The differences between original and manufactured objects are less than 2 mm (close to the tool radius).

KAGLVis - On-line 3D Visualisation of Earth-observing-satellite Data

NASA Astrophysics Data System (ADS)

Szuba, Marek; Ameri, Parinaz; Grabowski, Udo; Maatouki, Ahmad; Meyer, Jörg

2015-04-01

One of the goals of the Large-Scale Data Management and Analysis project is to provide a high-performance framework facilitating management of data acquired by Earth-observing satellites such as Envisat. On the client-facing facet of this framework, we strive to provide visualisation and basic analysis tool which could be used by scientists with minimal to no knowledge of the underlying infrastructure. Our tool, KAGLVis, is a JavaScript client-server Web application which leverages modern Web technologies to provide three-dimensional visualisation of satellite observables on a wide range of client systems. It takes advantage of the WebGL API to employ locally available GPU power for 3D rendering; this approach has been demonstrated to perform well even on relatively weak hardware such as integrated graphics chipsets found in modern laptop computers and with some user-interface tuning could even be usable on embedded devices such as smartphones or tablets. Data is fetched from the database back-end using a ReST API and cached locally, both in memory and using HTML5 Web Storage, to minimise network use. Computations, calculation of cloud altitude from cloud-index measurements for instance, can depending on configuration be performed on either the client or the server side. Keywords: satellite data, Envisat, visualisation, 3D graphics, Web application, WebGL, MEAN stack.

Legacy Code Modernization

NASA Technical Reports Server (NTRS)

Hribar, Michelle R.; Frumkin, Michael; Jin, Haoqiang; Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

Over the past decade, high performance computing has evolved rapidly; systems based on commodity microprocessors have been introduced in quick succession from at least seven vendors/families. Porting codes to every new architecture is a difficult problem; in particular, here at NASA, there are many large CFD applications that are very costly to port to new machines by hand. The LCM ("Legacy Code Modernization") Project is the development of an integrated parallelization environment (IPE) which performs the automated mapping of legacy CFD (Fortran) applications to state-of-the-art high performance computers. While most projects to port codes focus on the parallelization of the code, we consider porting to be an iterative process consisting of several steps: 1) code cleanup, 2) serial optimization,3) parallelization, 4) performance monitoring and visualization, 5) intelligent tools for automated tuning using performance prediction and 6) machine specific optimization. The approach for building this parallelization environment is to build the components for each of the steps simultaneously and then integrate them together. The demonstration will exhibit our latest research in building this environment: 1. Parallelizing tools and compiler evaluation. 2. Code cleanup and serial optimization using automated scripts 3. Development of a code generator for performance prediction 4. Automated partitioning 5. Automated insertion of directives. These demonstrations will exhibit the effectiveness of an automated approach for all the steps involved with porting and tuning a legacy code application for a new architecture.

On the computational modeling of the viscosity of colloidal dispersions and its relation with basic molecular interactions

NASA Astrophysics Data System (ADS)

Gama Goicochea, A.; Balderas Altamirano, M. A.; Lopez-Esparza, R.; Waldo-Mendoza, Miguel A.; Perez, E.

2015-09-01

The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and Brownian forces play in colloidal dispersions is also discussed. It is argued that many-body systems in which all these interactions take place can be accurately solved using computational simulation tools. One of those modern tools is the technique known as dissipative particle dynamics, which incorporates Brownian and hydrodynamic forces, as well as basic conservative interactions. A case study is reported, as an example of the applications of this technique, which consists of the prediction of the viscosity and friction between two opposing parallel surfaces covered with polymer chains, under the influence of a steady flow. This work is intended to serve as an introduction to the subject of colloidal dispersions and computer simulations, for final-year undergraduate students and beginning graduate students who are interested in beginning research in soft matter systems. To that end, a computational code is included that students can use right away to study complex fluids in equilibrium.

Atropos: specific, sensitive, and speedy trimming of sequencing reads.

PubMed

Didion, John P; Martin, Marcel; Collins, Francis S

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.

PubMed

Kawano, Shin; Ono, Hiromasa; Takagi, Toshihisa; Bono, Hidemasa

2012-03-01

In recent years, biological web resources such as databases and tools have become more complex because of the enormous amounts of data generated in the field of life sciences. Traditional methods of distributing tutorials include publishing textbooks and posting web documents, but these static contents cannot adequately describe recent dynamic web services. Due to improvements in computer technology, it is now possible to create dynamic content such as video with minimal effort and low cost on most modern computers. The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability.

Atropos: specific, sensitive, and speedy trimming of sequencing reads

PubMed Central

Collins, Francis S.

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos. PMID:28875074

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV

PubMed Central

Kawano, Shin; Ono, Hiromasa; Takagi, Toshihisa

2012-01-01

In recent years, biological web resources such as databases and tools have become more complex because of the enormous amounts of data generated in the field of life sciences. Traditional methods of distributing tutorials include publishing textbooks and posting web documents, but these static contents cannot adequately describe recent dynamic web services. Due to improvements in computer technology, it is now possible to create dynamic content such as video with minimal effort and low cost on most modern computers. The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability. PMID:21803786

Modeling NIF experimental designs with adaptive mesh refinement and Lagrangian hydrodynamics

NASA Astrophysics Data System (ADS)

Koniges, A. E.; Anderson, R. W.; Wang, P.; Gunney, B. T. N.; Becker, R.; Eder, D. C.; MacGowan, B. J.; Schneider, M. B.

2006-06-01

Incorporation of adaptive mesh refinement (AMR) into Lagrangian hydrodynamics algorithms allows for the creation of a highly powerful simulation tool effective for complex target designs with three-dimensional structure. We are developing an advanced modeling tool that includes AMR and traditional arbitrary Lagrangian-Eulerian (ALE) techniques. Our goal is the accurate prediction of vaporization, disintegration and fragmentation in National Ignition Facility (NIF) experimental target elements. Although our focus is on minimizing the generation of shrapnel in target designs and protecting the optics, the general techniques are applicable to modern advanced targets that include three-dimensional effects such as those associated with capsule fill tubes. Several essential computations in ordinary radiation hydrodynamics need to be redesigned in order to allow for AMR to work well with ALE, including algorithms associated with radiation transport. Additionally, for our goal of predicting fragmentation, we include elastic/plastic flow into our computations. We discuss the integration of these effects into a new ALE-AMR simulation code. Applications of this newly developed modeling tool as well as traditional ALE simulations in two and three dimensions are applied to NIF early-light target designs.

Development of Modern Performance Assessment Tools and Capabilities for Underground Disposal of Transuranic Waste at WIPP

NASA Astrophysics Data System (ADS)

Zeitler, T.; Kirchner, T. B.; Hammond, G. E.; Park, H.

2014-12-01

The Waste Isolation Pilot Plant (WIPP) has been developed by the U.S. Department of Energy (DOE) for the geologic (deep underground) disposal of transuranic (TRU) waste. Containment of TRU waste at the WIPP is regulated by the U.S. Environmental Protection Agency (EPA). The DOE demonstrates compliance with the containment requirements by means of performance assessment (PA) calculations. WIPP PA calculations estimate the probability and consequence of potential radionuclide releases from the repository to the accessible environment for a regulatory period of 10,000 years after facility closure. The long-term performance of the repository is assessed using a suite of sophisticated computational codes. In a broad modernization effort, the DOE has overseen the transfer of these codes to modern hardware and software platforms. Additionally, there is a current effort to establish new performance assessment capabilities through the further development of the PFLOTRAN software, a state-of-the-art massively parallel subsurface flow and reactive transport code. Improvements to the current computational environment will result in greater detail in the final models due to the parallelization afforded by the modern code. Parallelization will allow for relatively faster calculations, as well as a move from a two-dimensional calculation grid to a three-dimensional grid. The result of the modernization effort will be a state-of-the-art subsurface flow and transport capability that will serve WIPP PA into the future. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This research is funded by WIPP programs administered by the Office of Environmental Management (EM) of the U.S Department of Energy.

Seeing is believing: on the use of image databases for visually exploring plant organelle dynamics.

PubMed

Mano, Shoji; Miwa, Tomoki; Nishikawa, Shuh-ichi; Mimura, Tetsuro; Nishimura, Mikio

2009-12-01

Organelle dynamics vary dramatically depending on cell type, developmental stage and environmental stimuli, so that various parameters, such as size, number and behavior, are required for the description of the dynamics of each organelle. Imaging techniques are superior to other techniques for describing organelle dynamics because these parameters are visually exhibited. Therefore, as the results can be seen immediately, investigators can more easily grasp organelle dynamics. At present, imaging techniques are emerging as fundamental tools in plant organelle research, and the development of new methodologies to visualize organelles and the improvement of analytical tools and equipment have allowed the large-scale generation of image and movie data. Accordingly, image databases that accumulate information on organelle dynamics are an increasingly indispensable part of modern plant organelle research. In addition, image databases are potentially rich data sources for computational analyses, as image and movie data reposited in the databases contain valuable and significant information, such as size, number, length and velocity. Computational analytical tools support image-based data mining, such as segmentation, quantification and statistical analyses, to extract biologically meaningful information from each database and combine them to construct models. In this review, we outline the image databases that are dedicated to plant organelle research and present their potential as resources for image-based computational analyses.

Pedagogical Utilization and Assessment of the Statistic Online Computational Resource in Introductory Probability and Statistics Courses.

PubMed

Dinov, Ivo D; Sanchez, Juana; Christou, Nicolas

2008-01-01

Technology-based instruction represents a new recent pedagogical paradigm that is rooted in the realization that new generations are much more comfortable with, and excited about, new technologies. The rapid technological advancement over the past decade has fueled an enormous demand for the integration of modern networking, informational and computational tools with classical pedagogical instruments. Consequently, teaching with technology typically involves utilizing a variety of IT and multimedia resources for online learning, course management, electronic course materials, and novel tools of communication, engagement, experimental, critical thinking and assessment.The NSF-funded Statistics Online Computational Resource (SOCR) provides a number of interactive tools for enhancing instruction in various undergraduate and graduate courses in probability and statistics. These resources include online instructional materials, statistical calculators, interactive graphical user interfaces, computational and simulation applets, tools for data analysis and visualization. The tools provided as part of SOCR include conceptual simulations and statistical computing interfaces, which are designed to bridge between the introductory and the more advanced computational and applied probability and statistics courses. In this manuscript, we describe our designs for utilizing SOCR technology in instruction in a recent study. In addition, present the results of the effectiveness of using SOCR tools at two different course intensity levels on three outcome measures: exam scores, student satisfaction and choice of technology to complete assignments. Learning styles assessment was completed at baseline. We have used three very different designs for three different undergraduate classes. Each course included a treatment group, using the SOCR resources, and a control group, using classical instruction techniques. Our findings include marginal effects of the SOCR treatment per individual classes; however, pooling the results across all courses and sections, SOCR effects on the treatment groups were exceptionally robust and significant. Coupling these findings with a clear decrease in the variance of the quantitative examination measures in the treatment groups indicates that employing technology, like SOCR, in a sound pedagogical and scientific manner enhances overall the students' understanding and suggests better long-term knowledge retention.

Pedagogical Utilization and Assessment of the Statistic Online Computational Resource in Introductory Probability and Statistics Courses

PubMed Central

Dinov, Ivo D.; Sanchez, Juana; Christou, Nicolas

2009-01-01

Technology-based instruction represents a new recent pedagogical paradigm that is rooted in the realization that new generations are much more comfortable with, and excited about, new technologies. The rapid technological advancement over the past decade has fueled an enormous demand for the integration of modern networking, informational and computational tools with classical pedagogical instruments. Consequently, teaching with technology typically involves utilizing a variety of IT and multimedia resources for online learning, course management, electronic course materials, and novel tools of communication, engagement, experimental, critical thinking and assessment. The NSF-funded Statistics Online Computational Resource (SOCR) provides a number of interactive tools for enhancing instruction in various undergraduate and graduate courses in probability and statistics. These resources include online instructional materials, statistical calculators, interactive graphical user interfaces, computational and simulation applets, tools for data analysis and visualization. The tools provided as part of SOCR include conceptual simulations and statistical computing interfaces, which are designed to bridge between the introductory and the more advanced computational and applied probability and statistics courses. In this manuscript, we describe our designs for utilizing SOCR technology in instruction in a recent study. In addition, present the results of the effectiveness of using SOCR tools at two different course intensity levels on three outcome measures: exam scores, student satisfaction and choice of technology to complete assignments. Learning styles assessment was completed at baseline. We have used three very different designs for three different undergraduate classes. Each course included a treatment group, using the SOCR resources, and a control group, using classical instruction techniques. Our findings include marginal effects of the SOCR treatment per individual classes; however, pooling the results across all courses and sections, SOCR effects on the treatment groups were exceptionally robust and significant. Coupling these findings with a clear decrease in the variance of the quantitative examination measures in the treatment groups indicates that employing technology, like SOCR, in a sound pedagogical and scientific manner enhances overall the students’ understanding and suggests better long-term knowledge retention. PMID:19750185

Astro-tainment: Using modern and indigenous games to communicate astronomy

NASA Astrophysics Data System (ADS)

Manxoyi, S.

2008-06-01

Games are by their nature interactive, informative and developmental and in many cases full of fun and entertainment. SAAO has used modern and indigenous games to communicate astronomy to learners, educators and members of the public. These games include board, card, stone, pen and paper, domino, singalongs, ball and computer games. The use of games serves to simplify, demystify and communicate hard concepts in a fun way. They extend beyond the confines of institutions as games can be played at home and school. There is also no need for supervision when rules are mastered. This presentation also examines the principles (racing, collection, simulation and placing) which underpin our games as well seeking to demonstrate how simple materials can be transformed into communication and educational tools by infusing relevant astronomical knowledge.

Overview of computational structural methods for modern military aircraft

NASA Technical Reports Server (NTRS)

Kudva, J. N.

1992-01-01

Computational structural methods are essential for designing modern military aircraft. This briefing deals with computational structural methods (CSM) currently used. First a brief summary of modern day aircraft structural design procedures is presented. Following this, several ongoing CSM related projects at Northrop are discussed. Finally, shortcomings in this area, future requirements, and summary remarks are given.

Bioinformatics.

PubMed

Moore, Jason H

2007-11-01

Bioinformatics is an interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences such as biochemistry, cell biology, developmental biology, genetics, genomics, and physiology. An important goal of bioinformatics is to facilitate the management, analysis, and interpretation of data from biological experiments and observational studies. The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study. We review database resources as well as data mining software tools.

Full employment maintenance in the private sector

NASA Technical Reports Server (NTRS)

Young, G. A.

1976-01-01

Operationally, full employment can be accomplished by applying modern computer capabilities, game and decision concepts, and communication feedback possibilities, rather than accepted economic tools, to the problem of assuring invariant full employment. The government must provide positive direction to individual firms concerning the net number of employees that each firm must hire or refrain from hiring to assure national full employment. To preserve free enterprise and the decision making power of the individual manager, this direction must be based on each private firm's own numerical employment projections.

Assessing system reliability and allocating resources: a bayesian approach that integrates multi-level data

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

Graves, Todd L; Hamada, Michael S

2008-01-01

Good estimates of the reliability of a system make use of test data and expert knowledge at all available levels. Furthermore, by integrating all these information sources, one can determine how best to allocate scarce testing resources to reduce uncertainty. Both of these goals are facilitated by modern Bayesian computational methods. We apply these tools to examples that were previously solvable only through the use of ingenious approximations, and use genetic algorithms to guide resource allocation.

Computer simulation: A modern day crystal ball?

NASA Technical Reports Server (NTRS)

Sham, Michael; Siprelle, Andrew

1994-01-01

It has long been the desire of managers to be able to look into the future and predict the outcome of decisions. With the advent of computer simulation and the tremendous capability provided by personal computers, that desire can now be realized. This paper presents an overview of computer simulation and modeling, and discusses the capabilities of Extend. Extend is an iconic-driven Macintosh-based software tool that brings the power of simulation to the average computer user. An example of an Extend based model is presented in the form of the Space Transportation System (STS) Processing Model. The STS Processing Model produces eight shuttle launches per year, yet it takes only about ten minutes to run. In addition, statistical data such as facility utilization, wait times, and processing bottlenecks are produced. The addition or deletion of resources, such as orbiters or facilities, can be easily modeled and their impact analyzed. Through the use of computer simulation, it is possible to look into the future to see the impact of today's decisions.

Final Project Report: Data Locality Enhancement of Dynamic Simulations for Exascale Computing

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

Shen, Xipeng

The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future manycore systems, alleviating the memory performance issues for exascale computing. In the first three years, the PI and his group have achieves some significant progress towards the goal, producing a set of novel techniques for improving the memory performance and data locality in manycore systems, yielding 18 conference and workshop papers and 4 journal papers and graduating 6 Ph.Ds. This report summarizes the research results of thismore » project through that period.« less

Information Presentation and Control in a Modern Air Traffic Control Tower Simulator

NASA Technical Reports Server (NTRS)

Haines, Richard F.; Doubek, Sharon; Rabin, Boris; Harke, Stanton

1996-01-01

The proper presentation and management of information in America's largest and busiest (Level V) air traffic control towers calls for an in-depth understanding of many different human-computer considerations: user interface design for graphical, radar, and text; manual and automated data input hardware; information/display output technology; reconfigurable workstations; workload assessment; and many other related subjects. This paper discusses these subjects in the context of the Surface Development and Test Facility (SDTF) currently under construction at NASA's Ames Research Center, a full scale, multi-manned, air traffic control simulator which will provide the "look and feel" of an actual airport tower cab. Special emphasis will be given to the human-computer interfaces required for the different kinds of information displayed at the various controller and supervisory positions and to the computer-aided design (CAD) and other analytic, computer-based tools used to develop the facility.

LiPD and CSciBox: A Case Study in Why Data Standards are Important for Paleoscience

NASA Astrophysics Data System (ADS)

Weiss, I.; Bradley, E.; McKay, N.; Emile-Geay, J.; de Vesine, L. R.; Anderson, K. A.; White, J. W. C.; Marchitto, T. M., Jr.

2016-12-01

CSciBox [1] is an integrated software system that helps geoscientists build and evaluate age models. Its user chooses from a number of built-in analysis tools, composing them into an analysis workflow and applying it to paleoclimate proxy datasets. CSciBox employs modern database technology to store both the data and the analysis results in an easily accessible and searchable form, and offers the user access to the computational toolbox, the data, and the results via a graphical user interface and a sophisticated plotter. Standards are a staple of modern life, and underlie any form of automation. Without data standards, it is difficult, if not impossible, to construct effective computer tools for paleoscience analysis. The LiPD (Linked Paleo Data) framework [2] enables the storage of both data and metadata in systematic, meaningful, machine-readable ways. LiPD has been a primary enabler of CSciBox's goals of usability, interoperability, and reproducibility. Building LiPD capabilities into CSciBox's importer, for instance, eliminated the need to ask the user about file formats, variable names, relationships between columns in the input file, etc. Building LiPD capabilities into the exporter facilitated the storage of complete details about the input data-provenance, preprocessing steps, etc.-as well as full descriptions of any analyses that were performed using the CSciBox tool, along with citations to appropriate references. This comprehensive collection of data and metadata, which is all linked together in a semantically meaningful, machine-readable way, not only completely documents the analyses and makes them reproducible. It also enables interoperability with any other software system that employs the LiPD standard. [1] www.cs.colorado.edu/ lizb/cscience.html[2] McKay & Emile-Geay, Climate of the Past 12:1093 (2016)

A Parallel Numerical Micromagnetic Code Using FEniCS

NASA Astrophysics Data System (ADS)

Nagy, L.; Williams, W.; Mitchell, L.

2013-12-01

Many problems in the geosciences depend on understanding the ability of magnetic minerals to provide stable paleomagnetic recordings. Numerical micromagnetic modelling allows us to calculate the domain structures found in naturally occurring magnetic materials. However the computational cost rises exceedingly quickly with respect to the size and complexity of the geometries that we wish to model. This problem is compounded by the fact that the modern processor design no longer focuses on the speed at which calculations are performed, but rather on the number of computational units amongst which we may distribute our calculations. Consequently to better exploit modern computational resources our micromagnetic simulations must "go parallel". We present a parallel and scalable micromagnetics code written using FEniCS. FEniCS is a multinational collaboration involving several institutions (University of Cambridge, University of Chicago, The Simula Research Laboratory, etc.) that aims to provide a set of tools for writing scientific software; in particular software that employs the finite element method. The advantages of this approach are the leveraging of pre-existing projects from the world of scientific computing (PETSc, Trilinos, Metis/Parmetis, etc.) and exposing these so that researchers may pose problems in a manner closer to the mathematical language of their domain. Our code provides a scriptable interface (in Python) that allows users to not only run micromagnetic models in parallel, but also to perform pre/post processing of data.

NextGen Operational Improvements: Will they Improve Human Performance

NASA Technical Reports Server (NTRS)

Beard, Bettina L.; Johnston, James C.; Holbrook, Jon

2013-01-01

Modernization of the National Airspace System depends critically on the development of advanced technology, including cutting-edge automation, controller decision-support tools and integrated on-demand information. The Next Generation Air Transportation System national plan envisions air traffic control tower automation that proposes solutions for seven problems: 1) departure metering, 2) taxi routing, 3) taxi and runway scheduling, 4) departure runway assignments, 5) departure flow management, 6) integrated arrival and departure scheduling and 7) runway configuration management. Government, academia and industry are simultaneously pursuing the development of these tools. For each tool, the development process typically begins by assessing its potential benefits, and then progresses to designing preliminary versions of the tool, followed by testing the tool's strengths and weaknesses using computational modeling, human-in-the-loop simulation and/or field tests. We compiled the literature, evaluated the methodological rigor of the studies and served as referee for partisan conclusions that were sometimes overly optimistic. Here we provide the results of this review.

Space Shuttle Debris Impact Tool Assessment Using the Modern Design of Experiments

NASA Technical Reports Server (NTRS)

DeLoach, Richard; Rayos, Elonsio M.; Campbell, Charles H.; Rickman, Steven L.; Larsen, Curtis E.

2007-01-01

Complex computer codes are used to estimate thermal and structural reentry loads on the Shuttle Orbiter induced by ice and foam debris impact during ascent. Such debris can create cavities in the Shuttle Thermal Protection System. The sizes and shapes of these cavities are approximated to accommodate a code limitation that requires simple "shoebox" geometries to describe the cavities -- rectangular areas and planar walls that are at constant angles with respect to vertical. These approximations induce uncertainty in the code results. The Modern Design of Experiments (MDOE) has recently been applied to develop a series of resource-minimal computational experiments designed to generate low-order polynomial graduating functions to approximate the more complex underlying codes. These polynomial functions were then used to propagate cavity geometry errors to estimate the uncertainty they induce in the reentry load calculations performed by the underlying code. This paper describes a methodological study focused on evaluating the application of MDOE to future operational codes in a rapid and low-cost way to assess the effects of cavity geometry uncertainty.

Computational Studies of Snake Venom Toxins

PubMed Central

Ojeda, Paola G.; Caballero, Julio; Kaas, Quentin; González, Wendy

2017-01-01

Most snake venom toxins are proteins, and participate to envenomation through a diverse array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or neurotoxic effects. The venom of a single snake species contains hundreds of toxins, and the venoms of the 725 species of venomous snakes represent a large pool of potentially bioactive proteins. Despite considerable discovery efforts, most of the snake venom toxins are still uncharacterized. Modern bioinformatics tools have been recently developed to mine snake venoms, helping focus experimental research on the most potentially interesting toxins. Some computational techniques predict toxin molecular targets, and the binding mode to these targets. This review gives an overview of current knowledge on the ~2200 sequences, and more than 400 three-dimensional structures of snake toxins deposited in public repositories, as well as of molecular modeling studies of the interaction between these toxins and their molecular targets. We also describe how modern bioinformatics have been used to study the snake venom protein phospholipase A2, the small basic myotoxin Crotamine, and the three-finger peptide Mambalgin. PMID:29271884

CSciBox: An Intelligent Assistant for Dating Ice and Sediment Cores

NASA Astrophysics Data System (ADS)

Finlinson, K.; Bradley, E.; White, J. W. C.; Anderson, K. A.; Marchitto, T. M., Jr.; de Vesine, L. R.; Jones, T. R.; Lindsay, C. M.; Israelsen, B.

2015-12-01

CSciBox is an integrated software system for the construction and evaluation of age models of paleo-environmental archives. It incorporates a number of data-processing and visualization facilities, ranging from simple interpolation to reservoir-age correction and 14C calibration via the Calib algorithm, as well as a number of firn and ice-flow models. It employs modern database technology to store paleoclimate proxy data and analysis results in an easily accessible and searchable form, and offers the user access to those data and computational elements via a modern graphical user interface (GUI). In the case of truly large data or computations, CSciBox is parallelizable across modern multi-core processors, or clusters, or even the cloud. The code is open source and freely available on github, as are one-click installers for various versions of Windows and Mac OSX. The system's architecture allows users to incorporate their own software in the form of computational components that can be built smoothly into CSciBox workflows, taking advantage of CSciBox's GUI, data importing facilities, and plotting capabilities. To date, BACON and StratiCounter have been integrated into CSciBox as embedded components. The user can manipulate and compose all of these tools and facilities as she sees fit. Alternatively, she can employ CSciBox's automated reasoning engine, which uses artificial intelligence techniques to explore the gamut of age models and cross-dating scenarios automatically. The automated reasoning engine captures the knowledge of expert geoscientists, and can output a description of its reasoning.

Computer based guidance in the modern operating room: a historical perspective.

PubMed

Bova, Frank

2010-01-01

The past few decades have seen the introduction of many different and innovative approaches aimed at enhancing surgical technique. As microprocessors have decreased in size and increased in processing power, more sophisticated systems have been developed. Some systems have attempted to provide enhanced instrument control while others have attempted to provide tools for surgical guidance. These systems include robotics, image enhancements, and frame-based and frameless guidance procedures. In almost every case the system's design goals were achieved and surgical outcomes were enhanced, yet a vast majority of today's surgical procedures are conducted without the aid of these advances. As new tools are developed and existing tools refined, special attention to the systems interface and integration into the operating room environment will be required before increased utilization of these technologies can be realized.

Retraining the Modern Civil Engineer.

ERIC Educational Resources Information Center

Priscoli, Jerome Delli

1983-01-01

Discusses why modern engineering requires social science and the nature of planning. After these conceptional discussions, 12 practical tools which social science brings to engineering are reviewed. A tested approach to training engineers in these tools is then described. Tools include institutional analysis, policy profiling, and other impact…

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

The virtual digital nuclear power plant: A modern tool for supporting the lifecycle of VVER-based nuclear power units

NASA Astrophysics Data System (ADS)

Arkadov, G. V.; Zhukavin, A. P.; Kroshilin, A. E.; Parshikov, I. A.; Solov'ev, S. L.; Shishov, A. V.

2014-10-01

The article describes the "Virtual Digital VVER-Based Nuclear Power Plant" computerized system comprising a totality of verified initial data (sets of input data for a model intended for describing the behavior of nuclear power plant (NPP) systems in design and emergency modes of their operation) and a unified system of new-generation computation codes intended for carrying out coordinated computation of the variety of physical processes in the reactor core and NPP equipment. Experiments with the demonstration version of the "Virtual Digital VVER-Based NPP" computerized system has shown that it is in principle possible to set up a unified system of computation codes in a common software environment for carrying out interconnected calculations of various physical phenomena at NPPs constructed according to the standard AES-2006 project. With the full-scale version of the "Virtual Digital VVER-Based NPP" computerized system put in operation, the concerned engineering, design, construction, and operating organizations will have access to all necessary information relating to the NPP power unit project throughout its entire lifecycle. The domestically developed commercial-grade software product set to operate as an independently operating application to the project will bring about additional competitive advantages in the modern market of nuclear power technologies.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

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

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Superior model for fault tolerance computation in designing nano-sized circuit systems

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

Singh, N. S. S., E-mail: narinderjit@petronas.com.my; Muthuvalu, M. S., E-mail: msmuthuvalu@gmail.com; Asirvadam, V. S., E-mail: vijanth-sagayan@petronas.com.my

2014-10-24

As CMOS technology scales nano-metrically, reliability turns out to be a decisive subject in the design methodology of nano-sized circuit systems. As a result, several computational approaches have been developed to compute and evaluate reliability of desired nano-electronic circuits. The process of computing reliability becomes very troublesome and time consuming as the computational complexity build ups with the desired circuit size. Therefore, being able to measure reliability instantly and superiorly is fast becoming necessary in designing modern logic integrated circuits. For this purpose, the paper firstly looks into the development of an automated reliability evaluation tool based on the generalizationmore » of Probabilistic Gate Model (PGM) and Boolean Difference-based Error Calculator (BDEC) models. The Matlab-based tool allows users to significantly speed-up the task of reliability analysis for very large number of nano-electronic circuits. Secondly, by using the developed automated tool, the paper explores into a comparative study involving reliability computation and evaluation by PGM and, BDEC models for different implementations of same functionality circuits. Based on the reliability analysis, BDEC gives exact and transparent reliability measures, but as the complexity of the same functionality circuits with respect to gate error increases, reliability measure by BDEC tends to be lower than the reliability measure by PGM. The lesser reliability measure by BDEC is well explained in this paper using distribution of different signal input patterns overtime for same functionality circuits. Simulation results conclude that the reliability measure by BDEC depends not only on faulty gates but it also depends on circuit topology, probability of input signals being one or zero and also probability of error on signal lines.« less

An anatomy of industrial robots and their controls

NASA Astrophysics Data System (ADS)

Luh, J. Y. S.

1983-02-01

The modernization of manufacturing facilities by means of automation represents an approach for increasing productivity in industry. The three existing types of automation are related to continuous process controls, the use of transfer conveyor methods, and the employment of programmable automation for the low-volume batch production of discrete parts. The industrial robots, which are defined as computer controlled mechanics manipulators, belong to the area of programmable automation. Typically, the robots perform tasks of arc welding, paint spraying, or foundary operation. One may assign a robot to perform a variety of job assignments simply by changing the appropriate computer program. The present investigation is concerned with an evaluation of the potential of the robot on the basis of its basic structure and controls. It is found that robots function well in limited areas of industry. If the range of tasks which robots can perform is to be expanded, it is necessary to provide multiple-task sensors, or special tooling, or even automatic tooling.

Advanced 3D Characterization and Reconstruction of Reactor Materials FY16 Final Report

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

Fromm, Bradley; Hauch, Benjamin; Sridharan, Kumar

2016-12-01

A coordinated effort to link advanced materials characterization methods and computational modeling approaches is critical to future success for understanding and predicting the behavior of reactor materials that operate at extreme conditions. The difficulty and expense of working with nuclear materials have inhibited the use of modern characterization techniques on this class of materials. Likewise, mesoscale simulation efforts have been impeded due to insufficient experimental data necessary for initialization and validation of the computer models. The objective of this research is to develop methods to integrate advanced materials characterization techniques developed for reactor materials with state-of-the-art mesoscale modeling and simulationmore » tools. Research to develop broad-ion beam sample preparation, high-resolution electron backscatter diffraction, and digital microstructure reconstruction techniques; and methods for integration of these techniques into mesoscale modeling tools are detailed. Results for both irradiated and un-irradiated reactor materials are presented for FY14 - FY16 and final remarks are provided.« less

Integrating Xgrid into the HENP distributed computing model

NASA Astrophysics Data System (ADS)

Hajdu, L.; Kocoloski, A.; Lauret, J.; Miller, M.

2008-07-01

Modern Macintosh computers feature Xgrid, a distributed computing architecture built directly into Apple's OS X operating system. While the approach is radically different from those generally expected by the Unix based Grid infrastructures (Open Science Grid, TeraGrid, EGEE), opportunistic computing on Xgrid is nonetheless a tempting and novel way to assemble a computing cluster with a minimum of additional configuration. In fact, it requires only the default operating system and authentication to a central controller from each node. OS X also implements arbitrarily extensible metadata, allowing an instantly updated file catalog to be stored as part of the filesystem itself. The low barrier to entry allows an Xgrid cluster to grow quickly and organically. This paper and presentation will detail the steps that can be taken to make such a cluster a viable resource for HENP research computing. We will further show how to provide to users a unified job submission framework by integrating Xgrid through the STAR Unified Meta-Scheduler (SUMS), making tasks and jobs submission effortlessly at reach for those users already using the tool for traditional Grid or local cluster job submission. We will discuss additional steps that can be taken to make an Xgrid cluster a full partner in grid computing initiatives, focusing on Open Science Grid integration. MIT's Xgrid system currently supports the work of multiple research groups in the Laboratory for Nuclear Science, and has become an important tool for generating simulations and conducting data analyses at the Massachusetts Institute of Technology.

TRIM—3D: a three-dimensional model for accurate simulation of shallow water flow

USGS Publications Warehouse

Casulli, Vincenzo; Bertolazzi, Enrico; Cheng, Ralph T.

1993-01-01

A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is discussed. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that the resulting algorithm permits the use of large time steps at a minimal computational cost. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers. The high computational efficiency of this method has made it possible to provide the fine details of circulation structure in complex regions that previous studies were unable to obtain. For proper interpretation of the model results suitable interactive graphics is also an essential tool.

Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools.

PubMed

Profico, Antonio; Schlager, Stefan; Valoriani, Veronica; Buzi, Costantino; Melchionna, Marina; Veneziano, Alessio; Raia, Pasquale; Moggi-Cecchi, Jacopo; Manzi, Giorgio

2018-04-21

We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities. We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available. The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus. Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists. © 2018 Wiley Periodicals, Inc.

Advanced Test Reactor Core Modeling Update Project Annual Report for Fiscal Year 2012

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

David W. Nigg, Principal Investigator; Kevin A. Steuhm, Project Manager

Legacy computational reactor physics software tools and protocols currently used for support of Advanced Test Reactor (ATR) core fuel management and safety assurance, and to some extent, experiment management, are inconsistent with the state of modern nuclear engineering practice, and are difficult, if not impossible, to properly verify and validate (V&V) according to modern standards. Furthermore, the legacy staff knowledge required for application of these tools and protocols from the 1960s and 1970s is rapidly being lost due to staff turnover and retirements. In late 2009, the Idaho National Laboratory (INL) initiated a focused effort, the ATR Core Modeling Updatemore » Project, to address this situation through the introduction of modern high-fidelity computational software and protocols. This aggressive computational and experimental campaign will have a broad strategic impact on the operation of the ATR, both in terms of improved computational efficiency and accuracy for support of ongoing DOE programs as well as in terms of national and international recognition of the ATR National Scientific User Facility (NSUF). The ATR Core Modeling Update Project, targeted for full implementation in phase with the next anticipated ATR Core Internals Changeout (CIC) in the 2014-2015 time frame, began during the last quarter of Fiscal Year 2009, and has just completed its third full year. Key accomplishments so far have encompassed both computational as well as experimental work. A new suite of stochastic and deterministic transport theory based reactor physics codes and their supporting nuclear data libraries (HELIOS, KENO6/SCALE, NEWT/SCALE, ATTILA, and an extended implementation of MCNP5) has been installed at the INL under various licensing arrangements. Corresponding models of the ATR and ATRC are now operational with all five codes, demonstrating the basic feasibility of the new code packages for their intended purpose. Of particular importance, a set of as-run core depletion HELIOS calculations for all ATR cycles since August 2009, Cycle 145A through Cycle 151B, was successfully completed during 2012. This major effort supported a decision late in the year to proceed with the phased incorporation of the HELIOS methodology into the ATR Core Safety Analysis Package (CSAP) preparation process, in parallel with the established PDQ-based methodology, beginning late in Fiscal Year 2012. Acquisition of the advanced SERPENT (VTT-Finland) and MC21 (DOE-NR) Monte Carlo stochastic neutronics simulation codes was also initiated during the year and some initial applications of SERPENT to ATRC experiment analysis were demonstrated. These two new codes will offer significant additional capability, including the possibility of full-3D Monte Carlo fuel management support capabilities for the ATR at some point in the future. Finally, a capability for rigorous sensitivity analysis and uncertainty quantification based on the TSUNAMI system has been implemented and initial computational results have been obtained. This capability will have many applications as a tool for understanding the margins of uncertainty in the new models as well as for validation experiment design and interpretation.« less

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

PubMed

Borowiec, Marek L

2016-01-01

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

Working with the superabrasives industry to optimize tooling for grinding brittle materials

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

Taylor, J.S.; Piscotty, M.A.; Blaedel, K.L.

1996-05-01

The optics manufacturing industry is undertaking a significant modernization, as computer-numeric-controlled (CNC) equipment is joining or replacing open-loop equipment and hand lapping/polishing on the shop floor. Several prototype CNC lens grinding platforms employing ring tools are undergoing development and demonstration at the Center for Optics Manufacturing in Rochester, NY, and several machine tool companies have CNC product lines aimed at the optics industry. Benefits to using CNC ring tool grinding equipment include: essentially unlimited flexibility in selecting radii of curvature without special radiused tooling, the potential for CIM linkages to CAD workstations, and the cultural shift from craftsmen with undocumentedmore » procedures to CNC machine operators employing computerized routines for process control. In recent years, these developments, have inspired a number of US optics companies to invest in CNC equipment and participate in process development activities involving bound diamond tooling. This modernization process,extends beyond large optics companies that have historically embraced advanced equipment, to also include smaller optical shops where a shift to CNC equipment requires a significant company commitment. This paper addresses our efforts to optimize fine grinding wheels to support the new generation of CNC equipment. We begin with a discussion of how fine grinding fits into the optical production process, and then describe an initiative for improving the linkage between optics industry and the grinding wheel industry. For the purposes of this paper, we define fine wheels to have diamond sizes below 20 micrometers, which includes wheels used for what is sometimes called medium grinding (e.g. 10-20 micrometers diamond) and for fine grinding (e.g. 2-4 micrometers diamond).« less

The Development of Sociocultural Competence with the Help of Computer Technology

ERIC Educational Resources Information Center

Rakhimova, Alina E.; Yashina, Marianna E.; Mukhamadiarova, Albina F.; Sharipova, Astrid V.

2017-01-01

The article deals with the description of the process of development sociocultural knowledge and competences using computer technologies. On the whole the development of modern computer technologies allows teachers to broaden trainees' sociocultural outlook and trace their progress online. Observation of modern computer technologies and estimation…

Ganalyzer: A Tool for Automatic Galaxy Image Analysis

NASA Astrophysics Data System (ADS)

Shamir, Lior

2011-08-01

We describe Ganalyzer, a model-based tool that can automatically analyze and classify galaxy images. Ganalyzer works by separating the galaxy pixels from the background pixels, finding the center and radius of the galaxy, generating the radial intensity plot, and then computing the slopes of the peaks detected in the radial intensity plot to measure the spirality of the galaxy and determine its morphological class. Unlike algorithms that are based on machine learning, Ganalyzer is based on measuring the spirality of the galaxy, a task that is difficult to perform manually, and in many cases can provide a more accurate analysis compared to manual observation. Ganalyzer is simple to use, and can be easily embedded into other image analysis applications. Another advantage is its speed, which allows it to analyze ~10,000,000 galaxy images in five days using a standard modern desktop computer. These capabilities can make Ganalyzer a useful tool in analyzing large data sets of galaxy images collected by autonomous sky surveys such as SDSS, LSST, or DES. The software is available for free download at http://vfacstaff.ltu.edu/lshamir/downloads/ganalyzer, and the data used in the experiment are available at http://vfacstaff.ltu.edu/lshamir/downloads/ganalyzer/GalaxyImages.zip.

Modern data-driven decision support systems: the role of computing with words and computational linguistics

NASA Astrophysics Data System (ADS)

Kacprzyk, Janusz; Zadrożny, Sławomir

2010-05-01

We present how the conceptually and numerically simple concept of a fuzzy linguistic database summary can be a very powerful tool for gaining much insight into the very essence of data. The use of linguistic summaries provides tools for the verbalisation of data analysis (mining) results which, in addition to the more commonly used visualisation, e.g. via a graphical user interface, can contribute to an increased human consistency and ease of use, notably for supporting decision makers via the data-driven decision support system paradigm. Two new relevant aspects of the analysis are also outlined which were first initiated by the authors. First, following Kacprzyk and Zadrożny, it is further considered how linguistic data summarisation is closely related to some types of solutions used in natural language generation (NLG). This can make it possible to use more and more effective and efficient tools and techniques developed in NLG. Second, similar remarks are given on relations to systemic functional linguistics. Moreover, following Kacprzyk and Zadrożny, comments are given on an extremely relevant aspect of scalability of linguistic summarisation of data, using a new concept of a conceptual scalability.

Modern morphometry: new perspectives in physical anthropology.

PubMed

Mantini, Simone; Ripani, Maurizio

2009-06-01

In the past one hundred years physical anthropology has recourse to more and more efficient methods, which provide several new information regarding, human evolution and biology. Apart from the molecular approach, the introduction of new computed assisted techniques gave rise to a new concept of morphometry. Computed tomography and 3D-imaging, allowed providing anatomical description of the external and inner structures exceeding the problems encountered with the traditional morphometric methods. Furthermore, the support of geometric morphometrics, allowed creating geometric models to investigate morphological variation in terms of evolution, ontogeny and variability. The integration of these new tools gave rise to the virtual anthropology and to a new image of the anthropologist in which anatomical, biological, mathematical statistical and data processing information are fused in a multidisciplinary approach.

Parallel-hierarchical processing and classification of laser beam profile images based on the GPU-oriented architecture

NASA Astrophysics Data System (ADS)

Yarovyi, Andrii A.; Timchenko, Leonid I.; Kozhemiako, Volodymyr P.; Kokriatskaia, Nataliya I.; Hamdi, Rami R.; Savchuk, Tamara O.; Kulyk, Oleksandr O.; Surtel, Wojciech; Amirgaliyev, Yedilkhan; Kashaganova, Gulzhan

2017-08-01

The paper deals with a problem of insufficient productivity of existing computer means for large image processing, which do not meet modern requirements posed by resource-intensive computing tasks of laser beam profiling. The research concentrated on one of the profiling problems, namely, real-time processing of spot images of the laser beam profile. Development of a theory of parallel-hierarchic transformation allowed to produce models for high-performance parallel-hierarchical processes, as well as algorithms and software for their implementation based on the GPU-oriented architecture using GPGPU technologies. The analyzed performance of suggested computerized tools for processing and classification of laser beam profile images allows to perform real-time processing of dynamic images of various sizes.

Diagnosis of the Computer-Controlled Milling Machine, Definition of the Working Errors and Input Corrections on the Basis of Mathematical Model

NASA Astrophysics Data System (ADS)

Starikov, A. I.; Nekrasov, R. Yu; Teploukhov, O. J.; Soloviev, I. V.; Narikov, K. A.

2016-10-01

Manufactures, machinery and equipment improve of constructively as science advances and technology, and requirements are improving of quality and longevity. That is, the requirements for surface quality and precision manufacturing, oil and gas equipment parts are constantly increasing. Production of oil and gas engineering products on modern machine tools with computer numerical control - is a complex synthesis of technical and electrical equipment parts, as well as the processing procedure. Technical machine part wears during operation and in the electrical part are accumulated mathematical errors. Thus, the above-mentioned disadvantages of any of the following parts of metalworking equipment affect the manufacturing process of products in general, and as a result lead to the flaw.

Designers workbench: toward real-time immersive modeling

NASA Astrophysics Data System (ADS)

Kuester, Falko; Duchaineau, Mark A.; Hamann, Bernd; Joy, Kenneth I.; Ma, Kwan-Liu

2000-05-01

This paper introduces the Designers Workbench, a semi- immersive virtual environment for two-handed modeling, sculpting and analysis tasks. The paper outlines the fundamental tools, design metaphors and hardware components required for an intuitive real-time modeling system. As companies focus on streamlining productivity to cope with global competition, the migration to computer-aided design (CAD), computer-aided manufacturing, and computer-aided engineering systems has established a new backbone of modern industrial product development. However, traditionally a product design frequently originates form a clay model that, after digitization, forms the basis for the numerical description of CAD primitives. The Designers Workbench aims at closing this technology or 'digital gap' experienced by design and CAD engineers by transforming the classical design paradigm into its fully integrate digital and virtual analog allowing collaborative development in a semi- immersive virtual environment. This project emphasizes two key components form the classical product design cycle: freeform modeling and analysis. In the freedom modeling stage, content creation in the form of two-handed sculpting of arbitrary objects using polygonal, volumetric or mathematically defined primitives is emphasized, whereas the analysis component provides the tools required for pre- and post-processing steps for finite element analysis tasks applied to the created models.

OLTARIS: On-Line Tool for the Assessment of Radiation in Space

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Blattnig, Steve R.; Clowdsley, Martha S.; Qualls, Garry D.; Sandridge, Christopher A.; Simonsen, Lisa C.; Norbury, John W.; Slaba, Tony C.; Walker, Steven A.; Badavi, Francis F.;

Google Tools in the Classroom

NASA Astrophysics Data System (ADS)

Albee, E. M.; Koons, P. O.; Schauffler, M.; Zhu, Y.; Segee, B. E.

2009-12-01

The Maine Learning Technology Initiative provides every seventh and eighth grade student in the state with MacBook laptop computers. Limitless education possibilities exist with the inclusion of Google Tools and laptops as learning tools in our modern classrooms. Google Applications allow students to create documents, spreadsheets, charts, graphs, forms, and presentations and easily allows the sharing of information with their fellow classmates and teachers. These applications invite the use of inquiry and critical thinking skills, collaboration among peers, and subject integration to teach students crucial concepts. The benefits for teachers extend into the realm of using Google sites to easily create a teacher website and blog to upload classroom information and create a communication connection for parents and students as well as collaborations between the teachers and University researchers and educators. Google Applications further enhances the possibilities for learning, sharing a wealth of information, and enhancing communication inside and outside of the classroom.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

PubMed

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

Using the CAE technologies of engineering analysis for designing steam turbines at ZAO Ural Turbine Works

NASA Astrophysics Data System (ADS)

Goloshumova, V. N.; Kortenko, V. V.; Pokhoriler, V. L.; Kultyshev, A. Yu.; Ivanovskii, A. A.

2008-08-01

We describe the experience ZAO Ural Turbine Works specialists gained from mastering the series of CAD/CAE/CAM/PDM technologies, which are modern software tools of computer-aided engineering. We also present the results obtained from mathematical simulation of the process through which high-and intermediate-pressure rotors are heated for revealing the most thermally stressed zones, as well as the results from mathematical simulation of a new design of turbine cylinder shells for improving the maneuverability of these turbines.

Articles on Practical Cybernetics. Computer-Developed Computers; Heuristics and Modern Sciences; Linguistics and Practice; Cybernetics and Moral-Ethical Considerations; and Men and Machines at the Chessboard.

ERIC Educational Resources Information Center

Berg, A. I.; And Others

Five articles which were selected from a Russian language book on cybernetics and then translated are presented here. They deal with the topics of: computer-developed computers, heuristics and modern sciences, linguistics and practice, cybernetics and moral-ethical considerations, and computer chess programs. (Author/JY)

Smartphones and the plastic surgeon.

PubMed

Al-Hadithy, Nada; Ghosh, Sudip

2013-06-01

Surgical trainees are facing limited training opportunities since the introduction of the European Working Time Directive. Smartphone sales are increasing and have usurped computer sales for the first time. In this context, smartphones are an important portable reference and educational tool, already in the possession of the majority of surgeons in training. Technology in the palm of our hands has led to a revolution of accessible information for the plastic surgery trainee and surgeon. This article reviews the uses of smartphones and applications for plastic surgeons in education, telemedicine and global health. A comprehensive guide to existing and upcoming learning materials and clinical tools for the plastic surgeon is included. E-books, podcasts, educational videos, guidelines, work-based assessment tools and online logbooks are presented. In the limited resource setting of modern clinical practice, savvy plastic surgeons can select technological tools to democratise access to education and best clinical care. Copyright © 2013 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Can Wireless Technology Enable New Diabetes Management Tools?

PubMed Central

Hedtke, Paul A.

2008-01-01

Mobile computing and communications technology embodied in the modern cell phone device can be employed to improve the lives of diabetes patients by giving them better tools for self-management. Several companies are working on the development of diabetes management tools that leverage the ubiquitous cell phone to bring self-management tools to the hand of the diabetes patient. Integration of blood glucose monitoring (BGM) technology with the cell phone platform adds a level of convenience for the person with diabetes, but, more importantly, allows BGM data to be automatically captured, logged, and processed in near real time in order to provide the diabetes patient with assistance in managing their blood glucose levels. Other automatic measurements can estimate physical activity, and information regarding medication events and food intake can be captured and analyzed in order to provide the diabetes patient with continual assistance in managing their therapy and behaviors in order to improve glycemic control. The path to realization of such solutions is not, however, without obstacles. PMID:19885187

Can wireless technology enable new diabetes management tools?

PubMed

Hedtke, Paul A

2008-01-01

Mobile computing and communications technology embodied in the modern cell phone device can be employed to improve the lives of diabetes patients by giving them better tools for self-management. Several companies are working on the development of diabetes management tools that leverage the ubiquitous cell phone to bring self-management tools to the hand of the diabetes patient. Integration of blood glucose monitoring (BGM) technology with the cell phone platform adds a level of convenience for the person with diabetes, but, more importantly, allows BGM data to be automatically captured, logged, and processed in near real time in order to provide the diabetes patient with assistance in managing their blood glucose levels. Other automatic measurements can estimate physical activity, and information regarding medication events and food intake can be captured and analyzed in order to provide the diabetes patient with continual assistance in managing their therapy and behaviors in order to improve glycemic control. The path to realization of such solutions is not, however, without obstacles.

Using m-learning on nursing courses to improve learning.

PubMed

de Marcos Ortega, Luis; Barchino Plata, Roberto; Jiménez Rodríguez, María Lourdes; Hilera González, José Ramón; Martínez Herráiz, José Javier; Gutiérrez de Mesa, José Antonio; Gutiérrez Martínez, José María; Otón Tortosa, Salvador

2011-05-01

Modern handheld devices and wireless communications foster new kinds of communication and interaction that can define new approaches to teaching and learning. Mobile learning (m-learning) seeks to use them extensively, exactly in the same way in which e-learning uses personal computers and wired communication technologies. In this new mobile environment, new applications and educational models need to be created and tested to confirm (or reject) their validity and usefulness. In this article, we present a mobile tool aimed at self-assessment, which allows students to test their knowledge at any place and at any time. The degree to which the students' achievement improved is also evaluated, and a survey on the students' opinion of the new tool was also conducted. An experimental group of 20- to 21-year-old nursing students was chosen to test the tool. Results show that this kind of tool improves students' achievement and does not make necessary to introduce substantial changes in current teaching activities and methodology.

Integrating reliability and maintainability into a concurrent engineering environment

NASA Astrophysics Data System (ADS)

Phillips, Clifton B.; Peterson, Robert R.

1993-02-01

This paper describes the results of a reliability and maintainability study conducted at the University of California, San Diego and supported by private industry. Private industry thought the study was important and provided the university access to innovative tools under cooperative agreement. The current capability of reliability and maintainability tools and how they fit into the design process is investigated. The evolution of design methodologies leading up to today's capability is reviewed for ways to enhance the design process while keeping cost under control. A method for measuring the consequences of reliability and maintainability policy for design configurations in an electronic environment is provided. The interaction of selected modern computer tool sets is described for reliability, maintainability, operations, and other elements of the engineering design process. These tools provide a robust system evaluation capability that brings life cycle performance improvement information to engineers and their managers before systems are deployed, and allow them to monitor and track performance while it is in operation.

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

A survey study on student preferences regarding pathology teaching in Germany: a call for curricular modernization.

PubMed

Herrmann, Florian E M; Lenski, Markus; Steffen, Julius; Kailuweit, Magdalena; Nikolaus, Marc; Koteeswaran, Rajasekaran; Sailer, Andreas; Hanszke, Anna; Wintergerst, Maximilian; Dittmer, Sissi; Mayr, Doris; Genzel-Boroviczény, Orsolya; Eley, Diann S; Fischer, Martin R

2015-06-02

Pathology is a discipline that provides the basis of the understanding of disease in medicine. The past decades have seen a decline in the emphasis laid on pathology teaching in medical schools and outdated pathology curricula have worsened the situation. Student opinions and thoughts are central to the questions of whether and how such curricula should be modernized. A survey was conducted among 1018 German medical students regarding their preferences in pathology teaching modalities and their satisfaction with lecture-based courses. A qualitative analysis was performed comparing a recently modernized pathology curriculum with a traditional lecture-based curriculum. The differences in modalities of teaching used were investigated. Student satisfaction with the lecture-based curriculum positively correlated with student grades (spearman's correlation coefficient 0.24). Additionally, students with lower grades supported changing the curriculum (spearman's correlation coefficient 0.47). The majority supported virtual microscopy, autopsies, seminars and podcasts as preferred didactic methods. The data supports the implementation of a pathology curriculum where tutorials, autopsies and supplementary computer-based learning tools play important roles.

Twenty-Five Year Site Plan FY2013 - FY2037

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

Jones, William H.

2012-07-12

Los Alamos National Laboratory (the Laboratory) is the nation's premier national security science laboratory. Its mission is to develop and apply science and technology to ensure the safety, security, and reliability of the United States (U.S.) nuclear stockpile; reduce the threat of weapons of mass destruction, proliferation, and terrorism; and solve national problems in defense, energy, and the environment. The fiscal year (FY) 2013-2037 Twenty-Five Year Site Plan (TYSP) is a vital component for planning to meet the National Nuclear Security Administration (NNSA) commitment to ensure the U.S. has a safe, secure, and reliable nuclear deterrent. The Laboratory also usesmore » the TYSP as an integrated planning tool to guide development of an efficient and responsive infrastructure that effectively supports the Laboratory's missions and workforce. Emphasizing the Laboratory's core capabilities, this TYSP reflects the Laboratory's role as a prominent contributor to NNSA missions through its programs and campaigns. The Laboratory is aligned with Nuclear Security Enterprise (NSE) modernization activities outlined in the NNSA Strategic Plan (May 2011) which include: (1) ensuring laboratory plutonium space effectively supports pit manufacturing and enterprise-wide special nuclear materials consolidation; (2) constructing the Chemistry and Metallurgy Research Replacement Nuclear Facility (CMRR-NF); (3) establishing shared user facilities to more cost effectively manage high-value, experimental, computational and production capabilities; and (4) modernizing enduring facilities while reducing the excess facility footprint. Th is TYSP is viewed by the Laboratory as a vital planning tool to develop an effi cient and responsive infrastructure. Long range facility and infrastructure development planning are critical to assure sustainment and modernization. Out-year re-investment is essential for sustaining existing facilities, and will be re-evaluated on an annual basis. At the same time, major modernization projects will require new line-item funding. This document is, in essence, a roadmap that defines a path forward for the Laboratory to modernize, streamline, consolidate, and sustain its infrastructure to meet its national security mission.« 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.

FluxSuite: a New Scientific Tool for Advanced Network Management and Cross-Sharing of Next-Generation Flux Stations

NASA Astrophysics Data System (ADS)

Burba, G. G.; Johnson, D.; Velgersdyk, M.; Beaty, K.; Forgione, A.; Begashaw, I.; Allyn, D.

2015-12-01

Significant increases in data generation and computing power in recent years have greatly improved spatial and temporal flux data coverage on multiple scales, from a single station to continental flux networks. At the same time, operating budgets for flux teams and stations infrastructure are getting ever more difficult to acquire and sustain. With more stations and networks, larger data flows from each station, and smaller operating budgets, modern tools are needed to effectively and efficiently handle the entire process. This would help maximize time dedicated to answering research questions, and minimize time and expenses spent on data processing, quality control and station management. Cross-sharing the stations with external institutions may also help leverage available funding, increase scientific collaboration, and promote data analyses and publications. FluxSuite, a new advanced tool combining hardware, software and web-service, was developed to address these specific demands. It automates key stages of flux workflow, minimizes day-to-day site management, and modernizes the handling of data flows: Each next-generation station measures all parameters needed for flux computations Field microcomputer calculates final fully-corrected flux rates in real time, including computation-intensive Fourier transforms, spectra, co-spectra, multiple rotations, stationarity, footprint, etc. Final fluxes, radiation, weather and soil data are merged into a single quality-controlled file Multiple flux stations are linked into an automated time-synchronized network Flux network manager, or PI, can see all stations in real time, including fluxes, supporting data, automated reports, and email alerts PI can assign rights, allow or restrict access to stations and data: selected stations can be shared via rights-managed access internally or with external institutions Researchers without stations could form "virtual networks" for specific projects by collaborating with PIs from different actual networks This presentation provides detailed examples of FluxSuite currently utilized by two large flux networks in China (National Academy of Sciences & Agricultural Academy of Sciences), and smaller networks with stations in the USA, Germany, Ireland, Malaysia and other locations around the globe.

Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

NASA Astrophysics Data System (ADS)

Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha; Kalinkin, Alexander A.

2017-02-01

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, which is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,'bottom-up' and 'top-down', are illustrated. Preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.

Application of Reduced Order Transonic Aerodynamic Influence Coefficient Matrix for Design Optimization

NASA Technical Reports Server (NTRS)

Pak, Chan-gi; Li, Wesley W.

2009-01-01

Supporting the Aeronautics Research Mission Directorate guidelines, the National Aeronautics and Space Administration [NASA] Dryden Flight Research Center is developing a multidisciplinary design, analysis, and optimization [MDAO] tool. This tool will leverage existing tools and practices, and allow the easy integration and adoption of new state-of-the-art software. Today s modern aircraft designs in transonic speed are a challenging task due to the computation time required for the unsteady aeroelastic analysis using a Computational Fluid Dynamics [CFD] code. Design approaches in this speed regime are mainly based on the manual trial and error. Because of the time required for unsteady CFD computations in time-domain, this will considerably slow down the whole design process. These analyses are usually performed repeatedly to optimize the final design. As a result, there is considerable motivation to be able to perform aeroelastic calculations more quickly and inexpensively. This paper will describe the development of unsteady transonic aeroelastic design methodology for design optimization using reduced modeling method and unsteady aerodynamic approximation. The method requires the unsteady transonic aerodynamics be represented in the frequency or Laplace domain. Dynamically linear assumption is used for creating Aerodynamic Influence Coefficient [AIC] matrices in transonic speed regime. Unsteady CFD computations are needed for the important columns of an AIC matrix which corresponded to the primary modes for the flutter. Order reduction techniques, such as Guyan reduction and improved reduction system, are used to reduce the size of problem transonic flutter can be found by the classic methods, such as Rational function approximation, p-k, p, root-locus etc. Such a methodology could be incorporated into MDAO tool for design optimization at a reasonable computational cost. The proposed technique is verified using the Aerostructures Test Wing 2 actually designed, built, and tested at NASA Dryden Flight Research Center. The results from the full order model and the approximate reduced order model are analyzed and compared.

Mechanistic Insights and Computational Design of Transition-Metal Catalysts for Hydrogenation and Dehydrogenation Reactions.

PubMed

Chen, Xiangyang; Yang, Xinzheng

2016-10-01

Catalytic hydrogenation and dehydrogenation reactions are fundamentally important in chemical synthesis and industrial processes, as well as potential applications in the storage and conversion of renewable energy. Modern computational quantum chemistry has already become a powerful tool in understanding the structures and properties of compounds and elucidating mechanistic insights of chemical reactions, and therefore, holds great promise in the design of new catalysts. Herein, we review our computational studies on the catalytic hydrogenation of carbon dioxide and small organic carbonyl compounds, and on the dehydrogenation of amine-borane and alcohols with an emphasis on elucidating reaction mechanisms and predicting new catalytic reactions, and in return provide some general ideas for the design of high-efficiency, low-cost transition-metal complexes for hydrogenation and dehydrogenation reactions. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Current Lewis Turbomachinery Research: Building on our Legacy of Excellence

NASA Technical Reports Server (NTRS)

Povinelli, Louis A.

1997-01-01

This Wu Chang-Hua lecture is concerned with the development of analysis and computational capability for turbomachinery flows which is based on detailed flow field physics. A brief review of the work of Professor Wu is presented as well as a summary of the current NASA aeropropulsion programs. Two major areas of research are described in order to determine our predictive capabilities using modern day computational tools evolved from the work of Professor Wu. In one of these areas, namely transonic rotor flow, it is demonstrated that a high level of accuracy is obtainable provided sufficient geometric detail is simulated. In the second case, namely turbine heat transfer, our capability is lacking for rotating blade rows and experimental correlations will provide needed information in the near term. It is believed that continuing progress will allow us to realize the full computational potential and its impact on design time and cost.

GPU accelerated implementation of NCI calculations using promolecular density.

PubMed

Rubez, Gaëtan; Etancelin, Jean-Matthieu; Vigouroux, Xavier; Krajecki, Michael; Boisson, Jean-Charles; Hénon, Eric

2017-05-30

The NCI approach is a modern tool to reveal chemical noncovalent interactions. It is particularly attractive to describe ligand-protein binding. A custom implementation for NCI using promolecular density is presented. It is designed to leverage the computational power of NVIDIA graphics processing unit (GPU) accelerators through the CUDA programming model. The code performances of three versions are examined on a test set of 144 systems. NCI calculations are particularly well suited to the GPU architecture, which reduces drastically the computational time. On a single compute node, the dual-GPU version leads to a 39-fold improvement for the biggest instance compared to the optimal OpenMP parallel run (C code, icc compiler) with 16 CPU cores. Energy consumption measurements carried out on both CPU and GPU NCI tests show that the GPU approach provides substantial energy savings. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Computational Chemistry Using Modern Electronic Structure Methods

ERIC Educational Resources Information Center

Bell, Stephen; Dines, Trevor J.; Chowdhry, Babur Z.; Withnall, Robert

2007-01-01

Various modern electronic structure methods are now days used to teach computational chemistry to undergraduate students. Such quantum calculations can now be easily used even for large size molecules.

The role of load-carrying in the evolution of modern body proportions.

PubMed

Wang, W-J; Crompton, R H

2004-05-01

The first unquestionably bipedal early human ancestors, the species Australopithecus afarensis, were markedly different to ourselves in body proportions, having a long trunk and short legs. Some have argued that 'chimpanzee-like' features such as these suggest a 'bent-hip, bent-knee' (BHBK) posture would have been adopted during gait. Computer modelling studies, however, indicate that this early human ancestor could have walked in a reasonably efficient upright posture, whereas BHBK posture would have nearly doubled the mechanical energy cost of locomotion, as it does the physiological cost of locomotion in ourselves. More modern body proportions first appear at around 1.8-1.5 Ma, with Homo ergaster (early African Homo erectus), represented by the Nariokotome skeleton KNM-WT 15000, in which the legs were considerably longer in relation to the trunk than they are in human adults, although this skeleton represents an adolescent. Several authors have suggested that this morphology would have allowed faster, more endurant walking. But during the same period, the archaeological record indicates a sharp rise in distances over which stone tools or raw materials are transported. Is this coincidental, or can load-carrying also be implicated in selection for a more modern morphology? Computer simulations of loaded walking, verified against kinetic data for humans, show that BHBK gait is even more ineffective while load-carrying. However, walking erect, the Nariokotome individual could have carried loads of 10-15% body mass for less cost, relative to body size, than AL 288-1 walking erect but unloaded. In fact, to the extent that our sample of humans is typical, KNM-WT 15000 would have had better mechanical effectiveness in bearing light loads on the back than modern human adults. Thus, selection for effectiveness in load-carrying, as well as in endurant walking, is indeed likely to have been implicated in the evolution of modern body proportions.

The role of load-carrying in the evolution of modern body proportions

PubMed Central

Wang, W -J; Crompton, R H

2004-01-01

The first unquestionably bipedal early human ancestors, the species Australopithecus afarensis, were markedly different to ourselves in body proportions, having a long trunk and short legs. Some have argued that ′chimpanzee-like′ features such as these suggest a ‘bent-hip, bent-knee’ (BHBK) posture would have been adopted during gait. Computer modelling studies, however, indicate that this early human ancestor could have walked in a reasonably efficient upright posture, whereas BHBK posture would have nearly doubled the mechanical energy cost of locomotion, as it does the physiological cost of locomotion in ourselves. More modern body proportions first appear at around 1.8–1.5 Ma, with Homo ergaster (early African Homo erectus), represented by the Nariokotome skeleton KNM-WT 15000, in which the legs were considerably longer in relation to the trunk than they are in human adults, although this skeleton represents an adolescent. Several authors have suggested that this morphology would have allowed faster, more endurant walking. But during the same period, the archaeological record indicates a sharp rise in distances over which stone tools or raw materials are transported. Is this coincidental, or can load-carrying also be implicated in selection for a more modern morphology? Computer simulations of loaded walking, verified against kinetic data for humans, show that BHBK gait is even more ineffective while load-carrying. However, walking erect, the Nariokotome individual could have carried loads of 10–15% body mass for less cost, relative to body size, than AL 288-1 walking erect but unloaded. In fact, to the extent that our sample of humans is typical, KNM-WT 15000 would have had better mechanical effectiveness in bearing light loads on the back than modern human adults. Thus, selection for effectiveness in load-carrying, as well as in endurant walking, is indeed likely to have been implicated in the evolution of modern body proportions. PMID:15198704

GPURFSCREEN: a GPU based virtual screening tool using random forest classifier.

PubMed

Jayaraj, P B; Ajay, Mathias K; Nufail, M; Gopakumar, G; Jaleel, U C A

2016-01-01

In-silico methods are an integral part of modern drug discovery paradigm. Virtual screening, an in-silico method, is used to refine data models and reduce the chemical space on which wet lab experiments need to be performed. Virtual screening of a ligand data model requires large scale computations, making it a highly time consuming task. This process can be speeded up by implementing parallelized algorithms on a Graphical Processing Unit (GPU). Random Forest is a robust classification algorithm that can be employed in the virtual screening. A ligand based virtual screening tool (GPURFSCREEN) that uses random forests on GPU systems has been proposed and evaluated in this paper. This tool produces optimized results at a lower execution time for large bioassay data sets. The quality of results produced by our tool on GPU is same as that on a regular serial environment. Considering the magnitude of data to be screened, the parallelized virtual screening has a significantly lower running time at high throughput. The proposed parallel tool outperforms its serial counterpart by successfully screening billions of molecules in training and prediction phases.

Role of computational fluid dynamics in unsteady aerodynamics for aeroelasticity

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.; Goorjian, Peter M.

1989-01-01

In the last two decades there have been extensive developments in computational unsteady transonic aerodynamics. Such developments are essential since the transonic regime plays an important role in the design of modern aircraft. Therefore, there has been a large effort to develop computational tools with which to accurately perform flutter analysis at transonic speeds. In the area of Computational Fluid Dynamics (CFD), unsteady transonic aerodynamics are characterized by the feature of modeling the motion of shock waves over aerodynamic bodies, such as wings. This modeling requires the solution of nonlinear partial differential equations. Most advanced codes such as XTRAN3S use the transonic small perturbation equation. Currently, XTRAN3S is being used for generic research in unsteady aerodynamics and aeroelasticity of almost full aircraft configurations. Use of Euler/Navier Stokes equations for simple typical sections has just begun. A brief history of the development of CFD for aeroelastic applications is summarized. The development of unsteady transonic aerodynamics and aeroelasticity are also summarized.

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.

Human-machine interface for a VR-based medical imaging environment

NASA Astrophysics Data System (ADS)

Krapichler, Christian; Haubner, Michael; Loesch, Andreas; Lang, Manfred K.; Englmeier, Karl-Hans

1997-05-01

Modern 3D scanning techniques like magnetic resonance imaging (MRI) or computed tomography (CT) produce high- quality images of the human anatomy. Virtual environments open new ways to display and to analyze those tomograms. Compared with today's inspection of 2D image sequences, physicians are empowered to recognize spatial coherencies and examine pathological regions more facile, diagnosis and therapy planning can be accelerated. For that purpose a powerful human-machine interface is required, which offers a variety of tools and features to enable both exploration and manipulation of the 3D data. Man-machine communication has to be intuitive and efficacious to avoid long accustoming times and to enhance familiarity with and acceptance of the interface. Hence, interaction capabilities in virtual worlds should be comparable to those in the real work to allow utilization of our natural experiences. In this paper the integration of hand gestures and visual focus, two important aspects in modern human-computer interaction, into a medical imaging environment is shown. With the presented human- machine interface, including virtual reality displaying and interaction techniques, radiologists can be supported in their work. Further, virtual environments can even alleviate communication between specialists from different fields or in educational and training applications.

Heliophysics Legacy Data Restoration

NASA Astrophysics Data System (ADS)

Candey, R. M.; Bell, E. V., II; Bilitza, D.; Chimiak, R.; Cooper, J. F.; Garcia, L. N.; Grayzeck, E. J.; Harris, B. T.; Hills, H. K.; Johnson, R. C.; Kovalick, T. J.; Lal, N.; Leckner, H. A.; Liu, M. H.; McCaslin, P. W.; McGuire, R. E.; Papitashvili, N. E.; Rhodes, S. A.; Roberts, D. A.; Yurow, R. E.

2016-12-01

The Space Physics Data Facility (SPDF) , in collaboration with the National Space Science Data Coordinated Archive (NSSDCA), is converting datasets from older NASA missions to online storage. Valuable science is still buried within these datasets, particularly by applying modern algorithms on computers with vastly more storage and processing power than available when originally measured, and when analyzed in conjunction with other data and models. The data were also not readily accessible as archived on 7- and 9-track tapes, microfilm and microfiche and other media. Although many datasets have now been moved online in formats that are readily analyzed, others will still require some deciphering to puzzle out the data values and scientific meaning. There is an ongoing effort to convert the datasets to a modern Common Data Format (CDF) and add metadata for use in browse and analysis tools such as CDAWeb .

A brief historical introduction to Euler's formula for polyhedra, topology, graph theory and networks

NASA Astrophysics Data System (ADS)

Debnath, Lokenath

2010-09-01

This article is essentially devoted to a brief historical introduction to Euler's formula for polyhedra, topology, theory of graphs and networks with many examples from the real-world. Celebrated Königsberg seven-bridge problem and some of the basic properties of graphs and networks for some understanding of the macroscopic behaviour of real physical systems are included. We also mention some important and modern applications of graph theory or network problems from transportation to telecommunications. Graphs or networks are effectively used as powerful tools in industrial, electrical and civil engineering, communication networks in the planning of business and industry. Graph theory and combinatorics can be used to understand the changes that occur in many large and complex scientific, technical and medical systems. With the advent of fast large computers and the ubiquitous Internet consisting of a very large network of computers, large-scale complex optimization problems can be modelled in terms of graphs or networks and then solved by algorithms available in graph theory. Many large and more complex combinatorial problems dealing with the possible arrangements of situations of various kinds, and computing the number and properties of such arrangements can be formulated in terms of networks. The Knight's tour problem, Hamilton's tour problem, problem of magic squares, the Euler Graeco-Latin squares problem and their modern developments in the twentieth century are also included.

Design of Launch Vehicle Flight Control Systems Using Ascent Vehicle Stability Analysis Tool

NASA Technical Reports Server (NTRS)

Jang, Jiann-Woei; Alaniz, Abran; Hall, Robert; Bedossian, Nazareth; Hall, Charles; Jackson, Mark

2011-01-01

A launch vehicle represents a complicated flex-body structural environment for flight control system design. The Ascent-vehicle Stability Analysis Tool (ASAT) is developed to address the complicity in design and analysis of a launch vehicle. The design objective for the flight control system of a launch vehicle is to best follow guidance commands while robustly maintaining system stability. A constrained optimization approach takes the advantage of modern computational control techniques to simultaneously design multiple control systems in compliance with required design specs. "Tower Clearance" and "Load Relief" designs have been achieved for liftoff and max dynamic pressure flight regions, respectively, in the presence of large wind disturbances. The robustness of the flight control system designs has been verified in the frequency domain Monte Carlo analysis using ASAT.

Applied mediation analyses: a review and tutorial.

PubMed

Lange, Theis; Hansen, Kim Wadt; Sørensen, Rikke; Galatius, Søren

2017-01-01

In recent years, mediation analysis has emerged as a powerful tool to disentangle causal pathways from an exposure/treatment to clinically relevant outcomes. Mediation analysis has been applied in scientific fields as diverse as labour market relations and randomized clinical trials of heart disease treatments. In parallel to these applications, the underlying mathematical theory and computer tools have been refined. This combined review and tutorial will introduce the reader to modern mediation analysis including: the mathematical framework; required assumptions; and software implementation in the R package medflex. All results are illustrated using a recent study on the causal pathways stemming from the early invasive treatment of acute coronary syndrome, for which the rich Danish population registers allow us to follow patients' medication use and more after being discharged from hospital.

FESetup: Automating Setup for Alchemical Free Energy Simulations.

PubMed

Loeffler, Hannes H; Michel, Julien; Woods, Christopher

2015-12-28

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Möckel, M.; Wiedemann, C.; Flegel, S.; Gelhaus, J.; Vörsmann, P.; Klinkrad, H.; Krag, H.

2011-07-01

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction to OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Moeckel, Marek; Wiedemann, Carsten; Flegel, Sven Kevin; Gelhaus, Johannes; Klinkrad, Heiner; Krag, Holger; Voersmann, Peter

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction of OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Advanced Test Reactor Core Modeling Update Project Annual Report for Fiscal Year 2011

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

David W. Nigg; Devin A. Steuhm

2011-09-01

Legacy computational reactor physics software tools and protocols currently used for support of Advanced Test Reactor (ATR) core fuel management and safety assurance and, to some extent, experiment management are obsolete, inconsistent with the state of modern nuclear engineering practice, and are becoming increasingly difficult to properly verify and validate (V&V). Furthermore, the legacy staff knowledge required for application of these tools and protocols from the 1960s and 1970s is rapidly being lost due to staff turnover and retirements. In 2009 the Idaho National Laboratory (INL) initiated a focused effort to address this situation through the introduction of modern high-fidelitymore » computational software and protocols, with appropriate V&V, within the next 3-4 years via the ATR Core Modeling and Simulation and V&V Update (or 'Core Modeling Update') Project. This aggressive computational and experimental campaign will have a broad strategic impact on the operation of the ATR, both in terms of improved computational efficiency and accuracy for support of ongoing DOE programs as well as in terms of national and international recognition of the ATR National Scientific User Facility (NSUF). The ATR Core Modeling Update Project, targeted for full implementation in phase with the anticipated ATR Core Internals Changeout (CIC) in the 2014 time frame, began during the last quarter of Fiscal Year 2009, and has just completed its first full year. Key accomplishments so far have encompassed both computational as well as experimental work. A new suite of stochastic and deterministic transport theory based reactor physics codes and their supporting nuclear data libraries (SCALE, KENO-6, HELIOS, NEWT, and ATTILA) have been installed at the INL under various permanent sitewide license agreements and corresponding baseline models of the ATR and ATRC are now operational, demonstrating the basic feasibility of these code packages for their intended purpose. Furthermore, a capability for rigorous sensitivity analysis and uncertainty quantification based on the TSUNAMI system is being implemented and initial computational results have been obtained. This capability will have many applications in 2011 and beyond as a tool for understanding the margins of uncertainty in the new models as well as for validation experiment design and interpretation. Finally we note that although full implementation of the new computational models and protocols will extend over a period 3-4 years as noted above, interim applications in the much nearer term have already been demonstrated. In particular, these demonstrations included an analysis that was useful for understanding the cause of some issues in December 2009 that were triggered by a larger than acceptable discrepancy between the measured excess core reactivity and a calculated value that was based on the legacy computational methods. As the Modeling Update project proceeds we anticipate further such interim, informal, applications in parallel with formal qualification of the system under the applicable INL Quality Assurance procedures and standards.« less

Xarray: multi-dimensional data analysis in Python

NASA Astrophysics Data System (ADS)

Hoyer, Stephan; Hamman, Joe; Maussion, Fabien

2017-04-01

xarray (http://xarray.pydata.org) is an open source project and Python package that provides a toolkit and data structures for N-dimensional labeled arrays, which are the bread and butter of modern geoscientific data analysis. Key features of the package include label-based indexing and arithmetic, interoperability with the core scientific Python packages (e.g., pandas, NumPy, Matplotlib, Cartopy), out-of-core computation on datasets that don't fit into memory, a wide range of input/output options, and advanced multi-dimensional data manipulation tools such as group-by and resampling. In this contribution we will present the key features of the library and demonstrate its great potential for a wide range of applications, from (big-)data processing on super computers to data exploration in front of a classroom.

Epilepsy analytic system with cloud computing.

PubMed

Shen, Chia-Ping; Zhou, Weizhi; Lin, Feng-Seng; Sung, Hsiao-Ya; Lam, Yan-Yu; Chen, Wei; Lin, Jeng-Wei; Pan, Ming-Kai; Chiu, Ming-Jang; Lai, Feipei

2013-01-01

Biomedical data analytic system has played an important role in doing the clinical diagnosis for several decades. Today, it is an emerging research area of analyzing these big data to make decision support for physicians. This paper presents a parallelized web-based tool with cloud computing service architecture to analyze the epilepsy. There are many modern analytic functions which are wavelet transform, genetic algorithm (GA), and support vector machine (SVM) cascaded in the system. To demonstrate the effectiveness of the system, it has been verified by two kinds of electroencephalography (EEG) data, which are short term EEG and long term EEG. The results reveal that our approach achieves the total classification accuracy higher than 90%. In addition, the entire training time accelerate about 4.66 times and prediction time is also meet requirements in real time.

Recent advances in imaging technologies in dentistry.

PubMed

Shah, Naseem; Bansal, Nikhil; Logani, Ajay

2014-10-28

Dentistry has witnessed tremendous advances in all its branches over the past three decades. With these advances, the need for more precise diagnostic tools, specially imaging methods, have become mandatory. From the simple intra-oral periapical X-rays, advanced imaging techniques like computed tomography, cone beam computed tomography, magnetic resonance imaging and ultrasound have also found place in modern dentistry. Changing from analogue to digital radiography has not only made the process simpler and faster but also made image storage, manipulation (brightness/contrast, image cropping, etc.) and retrieval easier. The three-dimensional imaging has made the complex cranio-facial structures more accessible for examination and early and accurate diagnosis of deep seated lesions. This paper is to review current advances in imaging technology and their uses in different disciplines of dentistry.

Recent advances in imaging technologies in dentistry

PubMed Central

Shah, Naseem; Bansal, Nikhil; Logani, Ajay

2014-01-01

Dentistry has witnessed tremendous advances in all its branches over the past three decades. With these advances, the need for more precise diagnostic tools, specially imaging methods, have become mandatory. From the simple intra-oral periapical X-rays, advanced imaging techniques like computed tomography, cone beam computed tomography, magnetic resonance imaging and ultrasound have also found place in modern dentistry. Changing from analogue to digital radiography has not only made the process simpler and faster but also made image storage, manipulation (brightness/contrast, image cropping, etc.) and retrieval easier. The three-dimensional imaging has made the complex cranio-facial structures more accessible for examination and early and accurate diagnosis of deep seated lesions. This paper is to review current advances in imaging technology and their uses in different disciplines of dentistry. PMID:25349663

Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

DOE PAGES

Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha; ...

2017-03-20

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, whichmore » is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,‘bottom-up’ and ‘top-down’, are illustrated. Here, preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.« less

Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

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

Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, whichmore » is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,‘bottom-up’ and ‘top-down’, are illustrated. Here, preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.« less

Simulation training tools for nonlethal weapons using gaming environments

NASA Astrophysics Data System (ADS)

Donne, Alexsana; Eagan, Justin; Tse, Gabriel; Vanderslice, Tom; Woods, Jerry

2006-05-01

Modern simulation techniques have a growing role for evaluating new technologies and for developing cost-effective training programs. A mission simulator facilitates the productive exchange of ideas by demonstration of concepts through compellingly realistic computer simulation. Revolutionary advances in 3D simulation technology have made it possible for desktop computers to process strikingly realistic and complex interactions with results depicted in real-time. Computer games now allow for multiple real human players and "artificially intelligent" (AI) simulated robots to play together. Advances in computer processing power have compensated for the inherent intensive calculations required for complex simulation scenarios. The main components of the leading game-engines have been released for user modifications, enabling game enthusiasts and amateur programmers to advance the state-of-the-art in AI and computer simulation technologies. It is now possible to simulate sophisticated and realistic conflict situations in order to evaluate the impact of non-lethal devices as well as conflict resolution procedures using such devices. Simulations can reduce training costs as end users: learn what a device does and doesn't do prior to use, understand responses to the device prior to deployment, determine if the device is appropriate for their situational responses, and train with new devices and techniques before purchasing hardware. This paper will present the status of SARA's mission simulation development activities, based on the Half-Life gameengine, for the purpose of evaluating the latest non-lethal weapon devices, and for developing training tools for such devices.

New Frontiers for Applications of Thermal Infrared Imaging Devices: Computational Psychopshysiology in the Neurosciences

PubMed Central

Cardone, Daniela; Merla, Arcangelo

2017-01-01

Thermal infrared imaging has been proposed, and is now used, as a tool for the non-contact and non-invasive computational assessment of human autonomic nervous activity and psychophysiological states. Thanks to a new generation of high sensitivity infrared thermal detectors and the development of computational models of the autonomic control of the facial cutaneous temperature, several autonomic variables can be computed through thermal infrared imaging, including localized blood perfusion rate, cardiac pulse rate, breath rate, sudomotor and stress responses. In fact, all of these parameters impact on the control of the cutaneous temperature. The physiological information obtained through this approach, could then be used to infer about a variety of psychophysiological or emotional states, as proved by the increasing number of psychophysiology or neurosciences studies that use thermal infrared imaging. This paper presents a review of the principal achievements of thermal infrared imaging in computational psychophysiology, focusing on the capability of the technique for providing ubiquitous and unwired monitoring of psychophysiological activity and affective states. It also presents a summary on the modern, up-to-date infrared sensors technology. PMID:28475155

New Frontiers for Applications of Thermal Infrared Imaging Devices: Computational Psychopshysiology in the Neurosciences.

PubMed

Cardone, Daniela; Merla, Arcangelo

2017-05-05

Thermal infrared imaging has been proposed, and is now used, as a tool for the non-contact and non-invasive computational assessment of human autonomic nervous activity and psychophysiological states. Thanks to a new generation of high sensitivity infrared thermal detectors and the development of computational models of the autonomic control of the facial cutaneous temperature, several autonomic variables can be computed through thermal infrared imaging, including localized blood perfusion rate, cardiac pulse rate, breath rate, sudomotor and stress responses. In fact, all of these parameters impact on the control of the cutaneous temperature. The physiological information obtained through this approach, could then be used to infer about a variety of psychophysiological or emotional states, as proved by the increasing number of psychophysiology or neurosciences studies that use thermal infrared imaging. This paper presents a review of the principal achievements of thermal infrared imaging in computational psychophysiology, focusing on the capability of the technique for providing ubiquitous and unwired monitoring of psychophysiological activity and affective states. It also presents a summary on the modern, up-to-date infrared sensors technology.

Computational chemistry

NASA Technical Reports Server (NTRS)

Arnold, J. O.

1987-01-01

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

A Microarray Tool Provides Pathway and GO Term Analysis.

PubMed

Koch, Martin; Royer, Hans-Dieter; Wiese, Michael

2011-12-01

Analysis of gene expression profiles is no longer exclusively a task for bioinformatic experts. However, gaining statistically significant results is challenging and requires both biological knowledge and computational know-how. Here we present a novel, user-friendly microarray reporting tool called maRt. The software provides access to bioinformatic resources, like gene ontology terms and biological pathways by use of the DAVID and the BioMart web-service. Results are summarized in structured HTML reports, each presenting a different layer of information. In these report, contents of diverse sources are integrated and interlinked. To speed up processing, maRt takes advantage of the multi-core technology of modern desktop computers by using parallel processing. Since the software is built upon a RCP infrastructure it might be an outset for developers aiming to integrate novel R based applications. Installer, documentation and various kinds of tutorials are available under LGPL license at the website of our institute http://www.pharma.uni-bonn.de/www/mart. This software is free for academic use. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The classification of lung cancers and their degree of malignancy by FTIR, PCA-LDA analysis, and a physics-based computational model.

PubMed

Kaznowska, E; Depciuch, J; Łach, K; Kołodziej, M; Koziorowska, A; Vongsvivut, J; Zawlik, I; Cholewa, M; Cebulski, J

2018-08-15

Lung cancer has the highest mortality rate of all malignant tumours. The current effects of cancer treatment, as well as its diagnostics, are unsatisfactory. Therefore it is very important to introduce modern diagnostic tools, which will allow for rapid classification of lung cancers and their degree of malignancy. For this purpose, the authors propose the use of Fourier Transform InfraRed (FTIR) spectroscopy combined with Principal Component Analysis-Linear Discriminant Analysis (PCA-LDA) and a physics-based computational model. The results obtained for lung cancer tissues, adenocarcinoma and squamous cell carcinoma FTIR spectra, show a shift in wavenumbers compared to control tissue FTIR spectra. Furthermore, in the FTIR spectra of adenocarcinoma there are no peaks corresponding to glutamate or phospholipid functional groups. Moreover, in the case of G2 and G3 malignancy of adenocarcinoma lung cancer, the absence of an OH groups peak was noticed. Thus, it seems that FTIR spectroscopy is a valuable tool to classify lung cancer and to determine the degree of its malignancy. Copyright © 2018 Elsevier B.V. All rights reserved.

Science in the cloud (SIC): A use case in MRI connectomics

PubMed Central

Gorgolewski, Krzysztof J.; Kleissas, Dean; Roncal, William Gray; Litt, Brian; Wandell, Brian; Poldrack, Russel A.; Wiener, Martin; Vogelstein, R. Jacob; Burns, Randal

2017-01-01

Abstract Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools that drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries. Our proposed solution leverages these existing technologies and standards, and provides an accessible and extensible model for reproducible research, called ‘science in the cloud’ (SIC). Exploiting scientific containers, cloud computing, and cloud data services, we show the capability to compute in the cloud and run a web service that enables intimate interaction with the tools and data presented. We hope this model will inspire the community to produce reproducible and, importantly, extensible results that will enable us to collectively accelerate the rate at which scientific breakthroughs are discovered, replicated, and extended. PMID:28327935

The benefits of virtual reality simulator training for laparoscopic surgery.

PubMed

Hart, Roger; Karthigasu, Krishnan

2007-08-01

Virtual reality is a computer-generated system that provides a representation of an environment. This review will analyse the literature with regard to any benefit to be derived from training with virtual reality equipment and to describe the current equipment available. Virtual reality systems are not currently realistic of the live operating environment because they lack tactile sensation, and do not represent a complete operation. The literature suggests that virtual reality training is a valuable learning tool for gynaecologists in training, particularly those in the early stages of their careers. Furthermore, it may be of benefit for the ongoing audit of surgical skills and for the early identification of a surgeon's deficiencies before operative incidents occur. It is only a matter of time before realistic virtual reality models of most complete gynaecological operations are available, with improved haptics as a result of improved computer technology. It is inevitable that in the modern climate of litigation virtual reality training will become an essential part of clinical training, as evidence for its effectiveness as a training tool exists, and in many countries training by operating on live animals is not possible.

Science in the cloud (SIC): A use case in MRI connectomics.

PubMed

Kiar, Gregory; Gorgolewski, Krzysztof J; Kleissas, Dean; Roncal, William Gray; Litt, Brian; Wandell, Brian; Poldrack, Russel A; Wiener, Martin; Vogelstein, R Jacob; Burns, Randal; Vogelstein, Joshua T

2017-05-01

Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools that drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries. Our proposed solution leverages these existing technologies and standards, and provides an accessible and extensible model for reproducible research, called 'science in the cloud' (SIC). Exploiting scientific containers, cloud computing, and cloud data services, we show the capability to compute in the cloud and run a web service that enables intimate interaction with the tools and data presented. We hope this model will inspire the community to produce reproducible and, importantly, extensible results that will enable us to collectively accelerate the rate at which scientific breakthroughs are discovered, replicated, and extended. © The Author 2017. Published by Oxford University Press.

The Generic Mapping Tools 6: Classic versus Modern Mode

NASA Astrophysics Data System (ADS)

Wessel, P.; Uieda, L.; Luis, J. M. F.; Scharroo, R.; Smith, W. H. F.; Wobbe, F.

2017-12-01

The Generic Mapping Tools (GMT; gmt.soest.hawaii.edu) is a 25-year old, mature open-source software package for the analysis and display of geoscience data (e.g., interpolate, filter, manipulate, project and plot temporal and spatial data). The GMT "toolbox" includes about 80 core and 40 supplemental modules sharing a common set of command options, file structures, and documentation. GMT5, when released in 2013, introduced an application programming interface (API) to allow programmatic access to GMT from other computing environments. Since then, we have released a GMT/MATLAB toolbox, an experimental GMT/Julia package, and will soon introduce a GMT/Python module. In developing these extensions, we wanted to simplify the GMT learning curve but quickly realized the main stumbling blocks to GMT command-line mastery would be ported to the external environments unless we introduced major changes. With thousands of GMT scripts already in use by scientists around the world, we were acutely aware of the need for backwards compatibility. Our solution, to be released as GMT 6, was to add a modern run mode that complements the classic mode offered so far. Modern mode completely eliminates the top three obstacles for new (and not so new) GMT users: (1) The responsibility to properly stack PostScript layers manually (i.e., the -O -K dance), (2) the responsibility of handling output redirection of PostScript (create versus append), and (3) the need to provide commands with repeated information about regions (-R) and projections (-J). Thus, modern mode results in shorter, simpler scripts with fewer pitfalls, without interfering with classic scripts. Our implementation adds five new commands that begin and end a modern session, simplify figure management, automate the conversion of PostScript to more suitable formats, automate region detection, and offer a new automated subplot environment for multi-panel illustrations. Here, we highlight the GMT modern mode and the simplifications it offers, both for command-line use and in external environments. GMT 6 is in beta mode but accessible from our repository. Numerous improvements have been added in addition to modern mode; we expect a formal release in early 2018. Publication partially supported by FCT project UID/GEO/50019/2013 - Instituto D. Luiz.

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

PubMed Central

Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano

2014-01-01

Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads. PMID:24842718

Mid-frequency Band Dynamics of Large Space Structures

NASA Technical Reports Server (NTRS)

Coppolino, Robert N.; Adams, Douglas S.

2004-01-01

High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

Computational models of epilepsy.

PubMed

Stefanescu, Roxana A; Shivakeshavan, R G; Talathi, Sachin S

2012-12-01

Approximately 30% of epilepsy patients suffer from medically refractory epilepsy, in which seizures can not controlled by the use of anti-epileptic drugs (AEDs). Understanding the mechanisms underlying these forms of drug-resistant epileptic seizures and the development of alternative effective treatment strategies are fundamental challenges for modern epilepsy research. In this context, computational modeling has gained prominence as an important tool for tackling the complexity of the epileptic phenomenon. In this review article, we present a survey of computational models of epilepsy from the point of view that epilepsy is a dynamical brain disease that is primarily characterized by unprovoked spontaneous epileptic seizures. We introduce key concepts from the mathematical theory of dynamical systems, such as multi-stability and bifurcations, and explain how these concepts aid in our understanding of the brain mechanisms involved in the emergence of epileptic seizures. We present a literature survey of the different computational modeling approaches that are used in the study of epilepsy. Special emphasis is placed on highlighting the fine balance between the degree of model simplification and the extent of biological realism that modelers seek in order to address relevant questions. In this context, we discuss three specific examples from published literature, which exemplify different approaches used for developing computational models of epilepsy. We further explore the potential of recently developed optogenetics tools to provide novel avenue for seizure control. We conclude with a discussion on the utility of computational models for the development of new epilepsy treatment protocols. Copyright © 2012 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Shuttle Debris Impact Tool Assessment Using the Modern Design of Experiments

NASA Technical Reports Server (NTRS)

DeLoach, R.; Rayos, E. M.; Campbell, C. H.; Rickman, S. L.

2006-01-01

Computational tools have been developed to estimate thermal and mechanical reentry loads experienced by the Space Shuttle Orbiter as the result of cavities in the Thermal Protection System (TPS). Such cavities can be caused by impact from ice or insulating foam debris shed from the External Tank (ET) on liftoff. The reentry loads depend on cavity geometry and certain Shuttle state variables, among other factors. Certain simplifying assumptions have been made in the tool development about the cavity geometry variables. For example, the cavities are all modeled as shoeboxes , with rectangular cross-sections and planar walls. So an actual cavity is typically approximated with an idealized cavity described in terms of its length, width, and depth, as well as its entry angle, exit angle, and side angles (assumed to be the same for both sides). As part of a comprehensive assessment of the uncertainty in reentry loads estimated by the debris impact assessment tools, an effort has been initiated to quantify the component of the uncertainty that is due to imperfect geometry specifications for the debris impact cavities. The approach is to compute predicted loads for a set of geometry factor combinations sufficient to develop polynomial approximations to the complex, nonparametric underlying computational models. Such polynomial models are continuous and feature estimable, continuous derivatives, conditions that facilitate the propagation of independent variable errors. As an additional benefit, once the polynomial models have been developed, they require fewer computational resources to execute than the underlying finite element and computational fluid dynamics codes, and can generate reentry loads estimates in significantly less time. This provides a practical screening capability, in which a large number of debris impact cavities can be quickly classified either as harmless, or subject to additional analysis with the more comprehensive underlying computational tools. The polynomial models also provide useful insights into the sensitivity of reentry loads to various cavity geometry variables, and reveal complex interactions among those variables that indicate how the sensitivity of one variable depends on the level of one or more other variables. For example, the effect of cavity length on certain reentry loads depends on the depth of the cavity. Such interactions are clearly displayed in the polynomial response models.

Towards a Unified Architecture for Data-Intensive Seismology in VERCE

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Automation based on knowledge modeling theory and its applications in engine diagnostic systems using Space Shuttle Main Engine vibrational data. M.S. Thesis

NASA Technical Reports Server (NTRS)

Kim, Jonnathan H.

1995-01-01

Humans can perform many complicated tasks without explicit rules. This inherent and advantageous capability becomes a hurdle when a task is to be automated. Modern computers and numerical calculations require explicit rules and discrete numerical values. In order to bridge the gap between human knowledge and automating tools, a knowledge model is proposed. Knowledge modeling techniques are discussed and utilized to automate a labor and time intensive task of detecting anomalous bearing wear patterns in the Space Shuttle Main Engine (SSME) High Pressure Oxygen Turbopump (HPOTP).

Satellite -Based Networks for U-Health & U-Learning

NASA Astrophysics Data System (ADS)

Graschew, G.; Roelofs, T. A.; Rakowsky, S.; Schlag, P. M.

2008-08-01

The use of modern Information and Communication Technologies (ICT) as enabling tools for healthcare services (eHealth) introduces new ways of creating ubiquitous access to high-level medical care for all, anytime and anywhere (uHealth). Satellite communication constitutes one of the most flexible methods of broadband communication offering high reliability and cost-effectiveness of connections meeting telemedicine communication requirements. Global networks and the use of computers for educational purposes stimulate and support the development of virtual universities for e-learning. Especially real-time interactive applications can play an important role in tailored and personalised services.

[The development of hospital medical supplies information management system].

PubMed

Cao, Shaoping; Gu, Hongqing; Zhang, Peng; Wang, Qiang

2010-05-01

The information management of medical materials by using high-tech computer, in order to improve the efficiency of the consumption of medical supplies, hospital supplies and develop a new technology way to manage the hospital and material support. Using C # NET, JAVA techniques to develop procedures for the establishment of hospital material management information system, set the various management modules, production of various statistical reports, standard operating procedures. The system is convenient, functional and strong, fluent statistical functions. It can always fully grasp and understand the whole hospital supplies run dynamic information, as a modern and effective tool for hospital materials management.

[Data collection in anesthesia. Experiences with the inauguration of a new information system].

PubMed

Zbinden, A M; Rothenbühler, H; Häberli, B

1997-06-01

In many institutions information systems are used to process off-line anaesthesia data for invoices, statistical purposes, and quality assurance. Information systems are also increasingly being used to improve process control in order to reduce costs. Most of today's systems were created when information technology and working processes in anaesthesia were very different from those in use today. Thus, many institutions must now replace their computer systems but are probably not aware of how complex this change will be. Modern information systems mostly use client-server architecture and relational data bases. Substituting an old system with a new one is frequently a greater task than designing a system from scratch. This article gives the conclusions drawn from the experience obtained when a large departmental computer system is redesigned in an university hospital. The new system was based on a client-server architecture and was developed by an external company without preceding conceptual analysis. Modules for patient, anaesthesia, surgical, and pain-service data were included. Data were analysed using a separate statistical package (RS/1 from Bolt Beranek), taking advantage of its powerful precompiled procedures. Development and introduction of the new system took much more time and effort than expected despite the use of modern software tools. Introduction of the new program required intensive user training despite the choice of modem graphic screen layouts. Automatic data-reading systems could not be used, as too many faults occurred and the effort for the user was too high. However, after the initial problems were solved the system turned out to be a powerful tool for quality control (both process and outcome quality), billing, and scheduling. The statistical analysis of the data resulted in meaningful and relevant conclusions. Before creating a new information system, the working processes have to be analysed and, if possible, made more efficient; a detailed programme specification must then be made. A servicing and maintenance contract should be drawn up before the order is given to a company. Time periods of equal duration have to be scheduled for defining, writing, testing and introducing the program. Modern client-server systems with relational data bases are by no means simpler to establish and maintain than previous mainframe systems with hierarchical data bases, and thus, experienced computer specialists need to be close at hand. We recommend collecting data only once for both statistics and quality control. To verify data quality, a system of random spot-sampling has to be established. Despite the large investments needed to build up such a system, we consider it a powerful tool for helping to solve the difficult daily problems of managing a surgical and anaesthesia unit.

A synthetic design environment for ship design

NASA Technical Reports Server (NTRS)

Chipman, Richard R.

1995-01-01

Rapid advances in computer science and information system technology have made possible the creation of synthetic design environments (SDE) which use virtual prototypes to increase the efficiency and agility of the design process. This next generation of computer-based design tools will rely heavily on simulation and advanced visualization techniques to enable integrated product and process teams to concurrently conceptualize, design, and test a product and its fabrication processes. This paper summarizes a successful demonstration of the feasibility of using a simulation based design environment in the shipbuilding industry. As computer science and information science technologies have evolved, there have been many attempts to apply and integrate the new capabilities into systems for the improvement of the process of design. We see the benefits of those efforts in the abundance of highly reliable, technologically complex products and services in the modern marketplace. Furthermore, the computer-based technologies have been so cost effective that the improvements embodied in modern products have been accompanied by lowered costs. Today the state-of-the-art in computerized design has advanced so dramatically that the focus is no longer on merely improving design methodology; rather the goal is to revolutionize the entire process by which complex products are conceived, designed, fabricated, tested, deployed, operated, maintained, refurbished and eventually decommissioned. By concurrently addressing all life-cycle issues, the basic decision making process within an enterprise will be improved dramatically, leading to new levels of quality, innovation, efficiency, and customer responsiveness. By integrating functions and people with an enterprise, such systems will change the fundamental way American industries are organized, creating companies that are more competitive, creative, and productive.

[Computing in medical practice].

PubMed

Wechsler, Rudolf; Anção, Meide S; de Campos, Carlos José Reis; Sigulem, Daniel

2003-05-01

Currently, information technology is part of several aspects of our daily life. The objective of this paper is to analyze and discuss the use of information technology in both medical education and/or medical practice. Information was gathered through non-systematic bibliographic review, including articles, official regulations, book chapters and annals. Direct search and search of electronic databanks in Medline and Lilacs databases were also performed. This paper was structured in topics. First, there is a discussion on the electronic medical record. The following aspects are presented: history, functions, costs, benefits, ethical and legal issues, and positive and negative characteristics. Medical decision-support systems are also evaluated in view of the huge amount of information produced every year regarding healthcare. The impact of the Internet on the production and diffusion of knowledge is also analyzed. Telemedicine is assessed, since it presents new challenges to medical practice, and raises important ethical issues such as "virtual medical consultation." Finally, a practical experience of modernization of a pediatric outpatient center by the introduction of computers and telecommunication tools is described. Medical computing offers tools and instruments that support the administrative organization of medical visits, gather, store and process patient's data, generate diagnoses, provide therapeutical advice and access to information in order to improve medical knowledge and to make it available whenever and wherever adequate decision-making is required.

Designers Workbench: Towards Real-Time Immersive Modeling

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

Kuester, F; Duchaineau, M A; Hamann, B

2001-10-03

This paper introduces the DesignersWorkbench, a semi-immersive virtual environment for two-handed modeling, sculpting and analysis tasks. The paper outlines the fundamental tools, design metaphors and hardware components required for an intuitive real-time modeling system. As companies focus on streamlining productivity to cope with global competition, the migration to computer-aided design (CAD), computer-aided manufacturing (CAM), and computer-aided engineering (CAE) systems has established a new backbone of modern industrial product development. However, traditionally a product design frequently originates from a clay model that, after digitization, forms the basis for the numerical description of CAD primitives. The DesignersWorkbench aims at closing this technologymore » or ''digital gap'' experienced by design and CAD engineers by transforming the classical design paradigm into its filly integrated digital and virtual analog allowing collaborative development in a semi-immersive virtual environment. This project emphasizes two key components from the classical product design cycle: freeform modeling and analysis. In the freeform modeling stage, content creation in the form of two-handed sculpting of arbitrary objects using polygonal, volumetric or mathematically defined primitives is emphasized, whereas the analysis component provides the tools required for pre- and post-processing steps for finite element analysis tasks applied to the created models.« less

Bildung as a Powerful Tool in Modern University Teaching

ERIC Educational Resources Information Center

Olesen, Mogens Noergaard

2009-01-01

In this paper we will demonstrate how powerful "Bildung" is as a tool in modern university teaching. The concept of "Bildung" was originally introduced by the German philosopher Immanuel Kant (Kant 1787, 1798, 1804) and the Prussian lawyer and politician Wilhelm von Humboldt (Humboldt 1792, Bohlin 2008). From 1810…

Fast computation of derivative based sensitivities of PSHA models via algorithmic differentiation

NASA Astrophysics Data System (ADS)

Leövey, Hernan; Molkenthin, Christian; Scherbaum, Frank; Griewank, Andreas; Kuehn, Nicolas; Stafford, Peter

2015-04-01

Probabilistic seismic hazard analysis (PSHA) is the preferred tool for estimation of potential ground-shaking hazard due to future earthquakes at a site of interest. A modern PSHA represents a complex framework which combines different models with possible many inputs. Sensitivity analysis is a valuable tool for quantifying changes of a model output as inputs are perturbed, identifying critical input parameters and obtaining insight in the model behavior. Differential sensitivity analysis relies on calculating first-order partial derivatives of the model output with respect to its inputs. Moreover, derivative based global sensitivity measures (Sobol' & Kucherenko '09) can be practically used to detect non-essential inputs of the models, thus restricting the focus of attention to a possible much smaller set of inputs. Nevertheless, obtaining first-order partial derivatives of complex models with traditional approaches can be very challenging, and usually increases the computation complexity linearly with the number of inputs appearing in the models. In this study we show how Algorithmic Differentiation (AD) tools can be used in a complex framework such as PSHA to successfully estimate derivative based sensitivities, as is the case in various other domains such as meteorology or aerodynamics, without no significant increase in the computation complexity required for the original computations. First we demonstrate the feasibility of the AD methodology by comparing AD derived sensitivities to analytically derived sensitivities for a basic case of PSHA using a simple ground-motion prediction equation. In a second step, we derive sensitivities via AD for a more complex PSHA study using a ground motion attenuation relation based on a stochastic method to simulate strong motion. The presented approach is general enough to accommodate more advanced PSHA studies of higher complexity.

New media applications and their potential for the advancement of public perceptions of archaeoastronomy and for the testing of archaeoastronomical hypotheses.

NASA Astrophysics Data System (ADS)

MacDonald, J.

This paper looks at the use of astronomical programmes and the development of new media modeling techniques as a means to better understand archaeoastronomy. The paper also suggests that these new methods and technologies are a means of furthering the public perceptions of archaeoastronomy and the important role that 'astronomy' played in the history and development of human culture. This discussion is rooted in a computer simulation of Stonehenge and its land and skyscape. The integration of the astronomy software allows viewing horizon astronomical lignments in relation to digitally recreated Neolithic/Early Bronze Age (EBA) monumental architecture. This work shows how modern virtual modelling techniques can be a tool for testing archaeoastronomical hypotheses, as well as a demonstrative tool for teaching and promoting archaeoastronomy in mainstream media.

Field Science Ethnography: Methods For Systematic Observation on an Expedition

NASA Technical Reports Server (NTRS)

Clancey, William J.; Clancy, Daniel (Technical Monitor)

2001-01-01

The Haughton-Mars expedition is a multidisciplinary project, exploring an impact crater in an extreme environment to determine how people might live and work on Mars. The expedition seeks to understand and field test Mars facilities, crew roles, operations, and computer tools. I combine an ethnographic approach to establish a baseline understanding of how scientists prefer to live and work when relatively unemcumbered, with a participatory design approach of experimenting with procedures and tools in the context of use. This paper focuses on field methods for systematically recording and analyzing the expedition's activities. Systematic photography and time-lapse video are combined with concept mapping to organize and present information. This hybrid approach is generally applicable to the study of modern field expeditions having a dozen or more multidisciplinary participants, spread over a large terrain during multiple field seasons.

The Genome Portal of the Department of Energy Joint Genome Institute

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

Nordberg, Henrik; Cantor, Michael; Dushekyo, Serge

2014-03-14

The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Genome Portal in the past 2 years was significantly updated, with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. A critical aspect of handling big data in genomics is the development of visualization and analysis tools that allow scientists to derive meaning from what are otherwise terrabases ofmore » inert sequence. An interactive visualization tool developed in the group allows us to explore contigs resulting from a single metagenome assembly. Implemented with modern web technologies that take advantage of the power of the computer's graphical processing unit (gpu), the tool allows the user to easily navigate over a 100,000 data points in multiple dimensions, among many biologically meaningful parameters of a dataset such as relative abundance, contig length, and G+C content.« less

Applying "Climate" system to teaching basic climatology and raising public awareness of climate change issues

NASA Astrophysics Data System (ADS)

Gordova, Yulia; Okladnikov, Igor; Titov, Alexander; Gordov, Evgeny

2016-04-01

While there is a strong demand for innovation in digital learning, available training programs in the environmental sciences have no time to adapt to rapid changes in the domain content. A joint group of scientists and university teachers develops and implements an educational environment for new learning experiences in basics of climatic science and its applications. This so-called virtual learning laboratory "Climate" contains educational materials and interactive training courses developed to provide undergraduate and graduate students with profound understanding of changes in regional climate and environment. The main feature of this Laboratory is that students perform their computational tasks on climate modeling and evaluation and assessment of climate change using the typical tools of the "Climate" information-computational system, which are usually used by real-life practitioners performing such kind of research. Students have an opportunity to perform computational laboratory works using information-computational tools of the system and improve skills of their usage simultaneously with mastering the subject. We did not create an artificial learning environment to pass the trainings. On the contrary, the main purpose of association of the educational block and computational information system was to familiarize students with the real existing technologies for monitoring and analysis of data on the state of the climate. Trainings are based on technologies and procedures which are typical for Earth system sciences. Educational courses are designed to permit students to conduct their own investigations of ongoing and future climate changes in a manner that is essentially identical to the techniques used by national and international climate research organizations. All trainings are supported by lectures, devoted to the basic aspects of modern climatology, including analysis of current climate change and its possible impacts ensuring effective links between theory and practice. Along with its usage in graduate and postgraduate education, "Climate" is used as a framework for a developed basic information course on climate change for common public. In this course basic concepts and problems of modern climate change and its possible consequences are described for non-specialists. The course will also include links to relevant information resources on topical issues of Earth Sciences and a number of case studies, which are carried out for a selected region to consolidate the received knowledge.

Feasibility study of basic characterization of MAGAT polymer gel using CBCT attached in linear accelerator: Preliminary study

NASA Astrophysics Data System (ADS)

Sathiyaraj, P.; Samuel, E. James jebaseelan

2018-01-01

The aim of this study is to evaluate the methacrylic acid, gelatin and tetrakis (hydroxymethyl) phosphonium chloride gel (MAGAT) by cone beam computed tomography (CBCT) attached with modern linear accelerator. To compare the results of standard diagnostic computed tomography (CT) with CBCT, different parameters such as linearity, sensitivity and temporal stability were checked. MAGAT gel showed good linearity for both diagnostic CT and CBCT measurements. Sensitivity and temporal stability were also comparable with diagnostic CT measurements. In both the modalities, the sensitivity of the MAGAT increased to 4 days and decreased till the 10th day of post irradiation. Since all measurements (linearity, sensitivity and temporal stability) from diagnostic CT and CBCT were comparable, CBCT could be a potential tool for dose analysis study for polymer gel dosimeter.

WASP (Write a Scientific Paper) using Excel - 1: Data entry and validation.

PubMed

Grech, Victor

2018-02-01

Data collection for the purposes of analysis, after the planning and execution of a research study, commences with data input and validation. The process of data entry and analysis may appear daunting to the uninitiated, but as pointed out in the 1970s in a series of papers by British Medical Journal Deputy Editor TDV Swinscow, modern hardware and software (he was then referring to the availability of hand calculators) permits the performance of statistical testing outside a computer laboratory. In this day and age, modern software, such as the ubiquitous and almost universally familiar Microsoft Excel™ greatly facilitates this process. This first paper comprises the first of a collection of papers which will emulate Swinscow's series, in his own words, "addressed to readers who want to start at the beginning, not to those who are already skilled statisticians." These papers will have less focus on the actual arithmetic, and more emphasis on how to actually implement simple statistics, step by step, using Excel, thereby constituting the equivalent of Swinscow's papers in the personal computer age. Data entry can be facilitated by several underutilised features in Excel. This paper will explain Excel's little-known form function, data validation implementation at input stage, simple coding tips and data cleaning tools. Copyright © 2018 Elsevier B.V. All rights reserved.

Intra-individual metameric variation expressed at the enamel-dentine junction of lower post-canine dentition of South African fossil hominins and modern humans.

PubMed

Pan, Lei; Thackeray, John Francis; Dumoncel, Jean; Zanolli, Clément; Oettlé, Anna; de Beer, Frikkie; Hoffman, Jakobus; Duployer, Benjamin; Tenailleau, Christophe; Braga, José

2017-08-01

The aim of this study is to compare the degree and patterning of inter- and intra-individual metameric variation in South African australopiths, early Homo and modern humans. Metameric variation likely reflects developmental and taxonomical issues, and could also be used to infer ecological and functional adaptations. However, its patterning along the early hominin postcanine dentition, particularly among South African fossil hominins, remains unexplored. Using microfocus X-ray computed tomography (µXCT) and geometric morphometric tools, we studied the enamel-dentine junction (EDJ) morphology and we investigated the intra- and inter-individual EDJ metameric variation among eight australopiths and two early Homo specimens from South Africa, as well as 32 modern humans. Along post-canine dentition, shape changes between metameres represented by relative positions and height of dentine horns, outlines of the EDJ occlusal table are reported in modern and fossil taxa. Comparisons of EDJ mean shapes and multivariate analyses reveal substantial variation in the direction and magnitude of metameric shape changes among taxa, but some common trends can be found. In modern humans, both the direction and magnitude of metameric shape change show increased variability in M 2 -M 3 compared to M 1 -M 2 . Fossil specimens are clustered together showing similar magnitudes of shape change. Along M 2 -M 3 , the lengths of their metameric vectors are not as variable as those of modern humans, but they display considerable variability in the direction of shape change. The distalward increase of metameric variation along the modern human molar row is consistent with the odontogenetic models of molar row structure (inhibitory cascade model). Though much remains to be tested, the variable trends and magnitudes in metamerism in fossil hominins reported here, together with differences in the scale of shape change between modern humans and fossil hominins may provide valuable information regarding functional morphology and developmental processes in fossil species. © 2017 Wiley Periodicals, Inc.

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

PubMed

Dreuw, Andreas

2006-11-13

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

Estimating population diversity with CatchAll

PubMed Central

Bunge, John; Woodard, Linda; Böhning, Dankmar; Foster, James A.; Connolly, Sean; Allen, Heather K.

2012-01-01

Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments. Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample ‘frequency count’ data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program. Availability: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall. Contact: jab18@cornell.edu PMID:22333246

Exploiting current-generation graphics hardware for synthetic-scene generation

NASA Astrophysics Data System (ADS)

Tanner, Michael A.; Keen, Wayne A.

2010-04-01

Increasing seeker frame rate and pixel count, as well as the demand for higher levels of scene fidelity, have driven scene generation software for hardware-in-the-loop (HWIL) and software-in-the-loop (SWIL) testing to higher levels of parallelization. Because modern PC graphics cards provide multiple computational cores (240 shader cores for a current NVIDIA Corporation GeForce and Quadro cards), implementation of phenomenology codes on graphics processing units (GPUs) offers significant potential for simultaneous enhancement of simulation frame rate and fidelity. To take advantage of this potential requires algorithm implementation that is structured to minimize data transfers between the central processing unit (CPU) and the GPU. In this paper, preliminary methodologies developed at the Kinetic Hardware In-The-Loop Simulator (KHILS) will be presented. Included in this paper will be various language tradeoffs between conventional shader programming, Compute Unified Device Architecture (CUDA) and Open Computing Language (OpenCL), including performance trades and possible pathways for future tool development.

StarTrax --- The Next Generation User Interface

NASA Astrophysics Data System (ADS)

Richmond, Alan; White, Nick

StarTrax is a software package to be distributed to end users for installation on their local computing infrastructure. It will provide access to many services of the HEASARC, i.e. bulletins, catalogs, proposal and analysis tools, initially for the ROSAT MIPS (Mission Information and Planning System), later for the Next Generation Browse. A user activating the GUI will reach all HEASARC capabilities through a uniform view of the system, independent of the local computing environment and of the networking method of accessing StarTrax. Use it if you prefer the point-and-click metaphor of modern GUI technology, to the classical command-line interfaces (CLI). Notable strengths include: easy to use; excellent portability; very robust server support; feedback button on every dialog; painstakingly crafted User Guide. It is designed to support a large number of input devices including terminals, workstations and personal computers. XVT's Portability Toolkit is used to build the GUI in C/C++ to run on: OSF/Motif (UNIX or VMS), OPEN LOOK (UNIX), or Macintosh, or MS-Windows (DOS), or character systems.

The next generation of command post computing

NASA Astrophysics Data System (ADS)

Arnold, Ross D.; Lieb, Aaron J.; Samuel, Jason M.; Burger, Mitchell A.

2015-05-01

The future of command post computing demands an innovative new solution to address a variety of challenging operational needs. The Command Post of the Future is the Army's primary command and control decision support system, providing situational awareness and collaborative tools for tactical decision making, planning, and execution management from Corps to Company level. However, as the U.S. Army moves towards a lightweight, fully networked battalion, disconnected operations, thin client architecture and mobile computing become increasingly essential. The Command Post of the Future is not designed to support these challenges in the coming decade. Therefore, research into a hybrid blend of technologies is in progress to address these issues. This research focuses on a new command and control system utilizing the rich collaboration framework afforded by Command Post of the Future coupled with a new user interface consisting of a variety of innovative workspace designs. This new system is called Tactical Applications. This paper details a brief history of command post computing, presents the challenges facing the modern Army, and explores the concepts under consideration for Tactical Applications that meet these challenges in a variety of innovative ways.

LCFM - LIVING COLOR FRAME MAKER: PC GRAPHICS GENERATION AND MANAGEMENT TOOL FOR REAL-TIME APPLICATIONS

NASA Technical Reports Server (NTRS)

Truong, L. V.

1994-01-01

Computer graphics are often applied for better understanding and interpretation of data under observation. These graphics become more complicated when animation is required during "run-time", as found in many typical modern artificial intelligence and expert systems. Living Color Frame Maker is a solution to many of these real-time graphics problems. Living Color Frame Maker (LCFM) is a graphics generation and management tool for IBM or IBM compatible personal computers. To eliminate graphics programming, the graphic designer can use LCFM to generate computer graphics frames. The graphical frames are then saved as text files, in a readable and disclosed format, which can be easily accessed and manipulated by user programs for a wide range of "real-time" visual information applications. For example, LCFM can be implemented in a frame-based expert system for visual aids in management of systems. For monitoring, diagnosis, and/or controlling purposes, circuit or systems diagrams can be brought to "life" by using designated video colors and intensities to symbolize the status of hardware components (via real-time feedback from sensors). Thus status of the system itself can be displayed. The Living Color Frame Maker is user friendly with graphical interfaces, and provides on-line help instructions. All options are executed using mouse commands and are displayed on a single menu for fast and easy operation. LCFM is written in C++ using the Borland C++ 2.0 compiler for IBM PC series computers and compatible computers running MS-DOS. The program requires a mouse and an EGA/VGA display. A minimum of 77K of RAM is also required for execution. The documentation is provided in electronic form on the distribution medium in WordPerfect format. A sample MS-DOS executable is provided on the distribution medium. The standard distribution medium for this program is one 5.25 inch 360K MS-DOS format diskette. The contents of the diskette are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. The Living Color Frame Maker tool was developed in 1992.

Charting, navigating, and populating natural product chemical space for drug discovery.

PubMed

Lachance, Hugo; Wetzel, Stefan; Kumar, Kamal; Waldmann, Herbert

2012-07-12

Natural products are a heterogeneous group of compounds with diverse, yet particular molecular properties compared to synthetic compounds and drugs. All relevant analyses show that natural products indeed occupy parts of chemical space not explored by available screening collections while at the same time largely adhering to the rule-of-five. This renders them a valuable, unique, and necessary component of screening libraries used in drug discovery. With ChemGPS-NP on the Web and Scaffold Hunter two tools are available to the scientific community to guide exploration of biologically relevant NP chemical space in a focused and targeted fashion with a view to guide novel synthesis approaches. Several of the examples given illustrate the possibility of bridging the gap between computational methods and compound library synthesis and the possibility of integrating cheminformatics and chemical space analyses with synthetic chemistry and biochemistry to successfully explore chemical space for the identification of novel small molecule modulators of protein function.The examples also illustrate the synergistic potential of the chemical space concept and modern chemical synthesis for biomedical research and drug discovery. Chemical space analysis can map under explored biologically relevant parts of chemical space and identify the structure types occupying these parts. Modern synthetic methodology can then be applied to efficiently fill this “virtual space” with real compounds.From a cheminformatics perspective, there is a clear demand for open-source and easy to use tools that can be readily applied by educated nonspecialist chemists and biologists in their daily research. This will include further development of Scaffold Hunter, ChemGPS-NP, and related approaches on the Web. Such a “cheminformatics toolbox” would enable chemists and biologists to mine their own data in an intuitive and highly interactive process and without the need for specialized computer science and cheminformatics expertise. We anticipate that it may be a viable, if not necessary, step for research initiatives based on large high-throughput screening campaigns,in particular in the pharmaceutical industry, to make the most out of the recent advances in computational tools in order to leverage and take full advantage of the large data sets generated and available in house. There are “holes” in these data sets that can and should be identified and explored by chemistry and biology.

Making Research Fly in Schools: "Drosophila" as a Powerful Modern Tool for Teaching Biology

ERIC Educational Resources Information Center

Harbottle, Jennifer; Strangward, Patrick; Alnuamaani, Catherine; Lawes, Surita; Patel, Sanjai; Prokop, Andreas

2016-01-01

The "droso4schools" project aims to introduce the fruit fly "Drosophila" as a powerful modern teaching tool to convey curriculum-relevant specifications in biology lessons. Flies are easy and cheap to breed and have been at the forefront of biology research for a century, providing unique conceptual understanding of biology and…

Magnetic resonance imaging of granular materials

NASA Astrophysics Data System (ADS)

Stannarius, Ralf

2017-05-01

Magnetic Resonance Imaging (MRI) has become one of the most important tools to screen humans in medicine; virtually every modern hospital is equipped with a Nuclear Magnetic Resonance (NMR) tomograph. The potential of NMR in 3D imaging tasks is by far greater, but there is only "a handful" of MRI studies of particulate matter. The method is expensive, time-consuming, and requires a deep understanding of pulse sequences, signal acquisition, and processing. We give a short introduction into the physical principles of this imaging technique, describe its advantages and limitations for the screening of granular matter, and present a number of examples of different application purposes, from the exploration of granular packing, via the detection of flow and particle diffusion, to real dynamic measurements. Probably, X-ray computed tomography is preferable in most applications, but fast imaging of single slices with modern MRI techniques is unmatched, and the additional opportunity to retrieve spatially resolved flow and diffusion profiles without particle tracking is a unique feature.

Imaging with organic indicators and high-speed charge-coupled device cameras in neurons: some applications where these classic techniques have advantages.

PubMed

Ross, William N; Miyazaki, Kenichi; Popovic, Marko A; Zecevic, Dejan

2015-04-01

Dynamic calcium and voltage imaging is a major tool in modern cellular neuroscience. Since the beginning of their use over 40 years ago, there have been major improvements in indicators, microscopes, imaging systems, and computers. While cutting edge research has trended toward the use of genetically encoded calcium or voltage indicators, two-photon microscopes, and in vivo preparations, it is worth noting that some questions still may be best approached using more classical methodologies and preparations. In this review, we highlight a few examples in neurons where the combination of charge-coupled device (CCD) imaging and classical organic indicators has revealed information that has so far been more informative than results using the more modern systems. These experiments take advantage of the high frame rates, sensitivity, and spatial integration of the best CCD cameras. These cameras can respond to the faster kinetics of organic voltage and calcium indicators, which closely reflect the fast dynamics of the underlying cellular events.

Computer Synthesis Approaches of Hyperboloid Gear Drives with Linear Contact

NASA Astrophysics Data System (ADS)

Abadjiev, Valentin; Kawasaki, Haruhisa

2014-09-01

The computer design has improved forming different type software for scientific researches in the field of gearing theory as well as performing an adequate scientific support of the gear drives manufacture. Here are attached computer programs that are based on mathematical models as a result of scientific researches. The modern gear transmissions require the construction of new mathematical approaches to their geometric, technological and strength analysis. The process of optimization, synthesis and design is based on adequate iteration procedures to find out an optimal solution by varying definite parameters. The study is dedicated to accepted methodology in the creation of soft- ware for the synthesis of a class high reduction hyperboloid gears - Spiroid and Helicon ones (Spiroid and Helicon are trademarks registered by the Illinois Tool Works, Chicago, Ill). The developed basic computer products belong to software, based on original mathematical models. They are based on the two mathematical models for the synthesis: "upon a pitch contact point" and "upon a mesh region". Computer programs are worked out on the basis of the described mathematical models, and the relations between them are shown. The application of the shown approaches to the synthesis of commented gear drives is illustrated.

Peer-to-peer Monte Carlo simulation of photon migration in topical applications of biomedical optics

NASA Astrophysics Data System (ADS)

Doronin, Alexander; Meglinski, Igor

2012-09-01

In the framework of further development of the unified approach of photon migration in complex turbid media, such as biological tissues we present a peer-to-peer (P2P) Monte Carlo (MC) code. The object-oriented programming is used for generalization of MC model for multipurpose use in various applications of biomedical optics. The online user interface providing multiuser access is developed using modern web technologies, such as Microsoft Silverlight, ASP.NET. The emerging P2P network utilizing computers with different types of compute unified device architecture-capable graphics processing units (GPUs) is applied for acceleration and to overcome the limitations, imposed by multiuser access in the online MC computational tool. The developed P2P MC was validated by comparing the results of simulation of diffuse reflectance and fluence rate distribution for semi-infinite scattering medium with known analytical results, results of adding-doubling method, and with other GPU-based MC techniques developed in the past. The best speedup of processing multiuser requests in a range of 4 to 35 s was achieved using single-precision computing, and the double-precision computing for floating-point arithmetic operations provides higher accuracy.

Peer-to-peer Monte Carlo simulation of photon migration in topical applications of biomedical optics.

PubMed

Doronin, Alexander; Meglinski, Igor

2012-09-01

In the framework of further development of the unified approach of photon migration in complex turbid media, such as biological tissues we present a peer-to-peer (P2P) Monte Carlo (MC) code. The object-oriented programming is used for generalization of MC model for multipurpose use in various applications of biomedical optics. The online user interface providing multiuser access is developed using modern web technologies, such as Microsoft Silverlight, ASP.NET. The emerging P2P network utilizing computers with different types of compute unified device architecture-capable graphics processing units (GPUs) is applied for acceleration and to overcome the limitations, imposed by multiuser access in the online MC computational tool. The developed P2P MC was validated by comparing the results of simulation of diffuse reflectance and fluence rate distribution for semi-infinite scattering medium with known analytical results, results of adding-doubling method, and with other GPU-based MC techniques developed in the past. The best speedup of processing multiuser requests in a range of 4 to 35 s was achieved using single-precision computing, and the double-precision computing for floating-point arithmetic operations provides higher accuracy.

Modelling the influence of noise of the image sensor for blood cells recognition in computer microscopy

NASA Astrophysics Data System (ADS)

Nikitaev, V. G.; Nagornov, O. V.; Pronichev, A. N.; Polyakov, E. V.; Dmitrieva, V. V.

2017-12-01

The first stage of diagnostics of blood cancer is the analysis of blood smears. The application of decision-making support systems would reduce the subjectivity of the diagnostic process and avoid errors, resulting in often irreversible changes in the patient's condition. In this regard, the solution of this problem requires the use of modern technology. One of the tools of the program classification of blood cells are texture features, and the task of finding informative among them is promising. The paper investigates the effect of noise of the image sensor to informative texture features with application of methods of mathematical modelling.

A hybrid Gerchberg-Saxton-like algorithm for DOE and CGH calculation

NASA Astrophysics Data System (ADS)

Wang, Haichao; Yue, Weirui; Song, Qiang; Liu, Jingdan; Situ, Guohai

2017-02-01

The Gerchberg-Saxton (GS) algorithm is widely used in various disciplines of modern sciences and technologies where phase retrieval is required. However, this legendary algorithm most likely stagnates after a few iterations. Many efforts have been taken to improve this situation. Here we propose to introduce the strategy of gradient descent and weighting technique to the GS algorithm, and demonstrate it using two examples: design of a diffractive optical element (DOE) to achieve off-axis illumination in lithographic tools, and design of a computer generated hologram (CGH) for holographic display. Both numerical simulation and optical experiments are carried out for demonstration.

Coprocessors for quantum devices

NASA Astrophysics Data System (ADS)

Kay, Alastair

2018-03-01

Quantum devices, from simple fixed-function tools to the ultimate goal of a universal quantum computer, will require high-quality, frequent repetition of a small set of core operations, such as the preparation of entangled states. These tasks are perfectly suited to realization by a coprocessor or supplementary instruction set, as is common practice in modern CPUs. In this paper, we present two quintessentially quantum coprocessor functions: production of a Greenberger-Horne-Zeilinger state and implementation of optimal universal (asymmetric) quantum cloning. Both are based on the evolution of a fixed Hamiltonian. We introduce a technique for deriving the parameters of these Hamiltonians based on the numerical integration of Toda-like flows.

Community Near-Port Modeling System (C-PORT): Briefing for ...

EPA Pesticide Factsheets

What C-PORT is: Screening level tool for assessing port activities and exploring the range of potential impacts that changes to port operations might have on local air quality; Analysis of decision alternatives through mapping of the likely pattern of potential pollutant dispersion and an estimated change in pollutant concentrations for user-designated scenarios; Designed primarily to evaluate the local air quality impacts of proposed port expansion or modernization, as well as to identify options for mitigating any impacts; Currently includes data from 21 US seaports and features a map-based interface similar to the widely used Google Earth; Still under development, C-PORT is designed as an easy-to-use computer modeling tool for users, such as state air quality managers and planners. This is part of our product outreach prior to model public release and to solicit for additional beta testers.

Ontology-based tools to expedite predictive model construction.

PubMed

Haug, Peter; Holmen, John; Wu, Xinzi; Mynam, Kumar; Ebert, Matthew; Ferraro, Jeffrey

2014-01-01

Large amounts of medical data are collected electronically during the course of caring for patients using modern medical information systems. This data presents an opportunity to develop clinically useful tools through data mining and observational research studies. However, the work necessary to make sense of this data and to integrate it into a research initiative can require substantial effort from medical experts as well as from experts in medical terminology, data extraction, and data analysis. This slows the process of medical research. To reduce the effort required for the construction of computable, diagnostic predictive models, we have developed a system that hybridizes a medical ontology with a large clinical data warehouse. Here we describe components of this system designed to automate the development of preliminary diagnostic models and to provide visual clues that can assist the researcher in planning for further analysis of the data behind these models.

A revolution in diagnostic imaging.

PubMed

Mamula, Paul W

2003-03-01

In November 1966, Sandy Koufax, the star left-handed pitcher of the Los Angeles Dodgers, retired after spending his final season coping with traumatic arthritis in his elbow, the compounded effects of a sliding injury to his pitching arm the previous season and 12 years of hard throwing.1 Had his career begun a few years later, he might have been able to benefit from the advances in diagnostic imaging and treatment that were introduced at that time. Modern arthroscopy and computed tomography (CT) did not become available until the mid 1970s,2 and the first elbow reconstruction was done by Frank Jobe, MD, about 10 years after Koufax retired.1 Arthroscopy was first used as a diagnostic tool, but it later became a surgical tool, affecting treatment of knees, then, later, shoulders. Since 1973, when The Physician and Sportsmedicine was launched, we have witnessed a revolution in diagnostic imaging and are continuing to see an evolution of modalities.

Shared Memory Parallelism for 3D Cartesian Discrete Ordinates Solver

NASA Astrophysics Data System (ADS)

Moustafa, Salli; Dutka-Malen, Ivan; Plagne, Laurent; Ponçot, Angélique; Ramet, Pierre

2014-06-01

This paper describes the design and the performance of DOMINO, a 3D Cartesian SN solver that implements two nested levels of parallelism (multicore+SIMD) on shared memory computation nodes. DOMINO is written in C++, a multi-paradigm programming language that enables the use of powerful and generic parallel programming tools such as Intel TBB and Eigen. These two libraries allow us to combine multi-thread parallelism with vector operations in an efficient and yet portable way. As a result, DOMINO can exploit the full power of modern multi-core processors and is able to tackle very large simulations, that usually require large HPC clusters, using a single computing node. For example, DOMINO solves a 3D full core PWR eigenvalue problem involving 26 energy groups, 288 angular directions (S16), 46 × 106 spatial cells and 1 × 1012 DoFs within 11 hours on a single 32-core SMP node. This represents a sustained performance of 235 GFlops and 40:74% of the SMP node peak performance for the DOMINO sweep implementation. The very high Flops/Watt ratio of DOMINO makes it a very interesting building block for a future many-nodes nuclear simulation tool.

Urban Flow and Pollutant Dispersion Simulation with Multi-scale coupling of Meteorological Model with Computational Fluid Dynamic Analysis

NASA Astrophysics Data System (ADS)

Liu, Yushi; Poh, Hee Joo

2014-11-01

The Computational Fluid Dynamics analysis has become increasingly important in modern urban planning in order to create highly livable city. This paper presents a multi-scale modeling methodology which couples Weather Research and Forecasting (WRF) Model with open source CFD simulation tool, OpenFOAM. This coupling enables the simulation of the wind flow and pollutant dispersion in urban built-up area with high resolution mesh. In this methodology meso-scale model WRF provides the boundary condition for the micro-scale CFD model OpenFOAM. The advantage is that the realistic weather condition is taken into account in the CFD simulation and complexity of building layout can be handled with ease by meshing utility of OpenFOAM. The result is validated against the Joint Urban 2003 Tracer Field Tests in Oklahoma City and there is reasonably good agreement between the CFD simulation and field observation. The coupling of WRF- OpenFOAM provide urban planners with reliable environmental modeling tool in actual urban built-up area; and it can be further extended with consideration of future weather conditions for the scenario studies on climate change impact.

Computer-aided modelling and analysis of PV systems: a comparative study.

PubMed

Koukouvaos, Charalambos; Kandris, Dionisis; Samarakou, Maria

2014-01-01

Modern scientific advances have enabled remarkable efficacy for photovoltaic systems with regard to the exploitation of solar energy, boosting them into having a rapidly growing position among the systems developed for the production of renewable energy. However, in many cases the design, analysis, and control of photovoltaic systems are tasks which are quite complex and thus difficult to be carried out. In order to cope with this kind of problems, appropriate software tools have been developed either as standalone products or parts of general purpose software platforms used to model and simulate the generation, transmission, and distribution of solar energy. The utilization of this kind of software tools may be extremely helpful to the successful performance evaluation of energy systems with maximum accuracy and minimum cost in time and effort. The work presented in this paper aims on a first level at the performance analysis of various configurations of photovoltaic systems through computer-aided modelling. On a second level, it provides a comparative evaluation of the credibility of two of the most advanced graphical programming environments, namely, Simulink and LabVIEW, with regard to their application in photovoltaic systems.

Computer-Aided Modelling and Analysis of PV Systems: A Comparative Study

PubMed Central

Koukouvaos, Charalambos

2014-01-01

Modern scientific advances have enabled remarkable efficacy for photovoltaic systems with regard to the exploitation of solar energy, boosting them into having a rapidly growing position among the systems developed for the production of renewable energy. However, in many cases the design, analysis, and control of photovoltaic systems are tasks which are quite complex and thus difficult to be carried out. In order to cope with this kind of problems, appropriate software tools have been developed either as standalone products or parts of general purpose software platforms used to model and simulate the generation, transmission, and distribution of solar energy. The utilization of this kind of software tools may be extremely helpful to the successful performance evaluation of energy systems with maximum accuracy and minimum cost in time and effort. The work presented in this paper aims on a first level at the performance analysis of various configurations of photovoltaic systems through computer-aided modelling. On a second level, it provides a comparative evaluation of the credibility of two of the most advanced graphical programming environments, namely, Simulink and LabVIEW, with regard to their application in photovoltaic systems. PMID:24772007

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

Generative models for clinical applications in computational psychiatry.

PubMed

Frässle, Stefan; Yao, Yu; Schöbi, Dario; Aponte, Eduardo A; Heinzle, Jakob; Stephan, Klaas E

2018-05-01

Despite the success of modern neuroimaging techniques in furthering our understanding of cognitive and pathophysiological processes, translation of these advances into clinically relevant tools has been virtually absent until now. Neuromodeling represents a powerful framework for overcoming this translational deadlock, and the development of computational models to solve clinical problems has become a major scientific goal over the last decade, as reflected by the emergence of clinically oriented neuromodeling fields like Computational Psychiatry, Computational Neurology, and Computational Psychosomatics. Generative models of brain physiology and connectivity in the human brain play a key role in this endeavor, striving for computational assays that can be applied to neuroimaging data from individual patients for differential diagnosis and treatment prediction. In this review, we focus on dynamic causal modeling (DCM) and its use for Computational Psychiatry. DCM is a widely used generative modeling framework for functional magnetic resonance imaging (fMRI) and magneto-/electroencephalography (M/EEG) data. This article reviews the basic concepts of DCM, revisits examples where it has proven valuable for addressing clinically relevant questions, and critically discusses methodological challenges and recent methodological advances. We conclude this review with a more general discussion of the promises and pitfalls of generative models in Computational Psychiatry and highlight the path that lies ahead of us. This article is categorized under: Neuroscience > Computation Neuroscience > Clinical Neuroscience. © 2018 Wiley Periodicals, Inc.

Speaking Spontaneously in the Modern Foreign Languages Classroom: Tools for Supporting Successful Target Language Conversation

ERIC Educational Resources Information Center

Christie, Colin

2016-01-01

This article reports on the findings of a study into the conditions which promote spontaneous learner talk in the target language in the modern foreign languages (MFL) classroom. A qualitative case study approach was adopted. French lessons, with school students aged 11-16 years old, were observed and analysed with the aim of identifying tools and…

Modern Languages and Specific Learning Difficulties (SpLD): Implications of Teaching Adult Learners with Dyslexia in Distance Learning

ERIC Educational Resources Information Center

Gallardo, Matilde; Heiser, Sarah; Arias McLaughlin, Ximena

2015-01-01

In modern language (ML) distance learning programmes, teachers and students use online tools to facilitate, reinforce and support independent learning. This makes it essential for teachers to develop pedagogical expertise in using online communication tools to perform their role. Teachers frequently raise questions of how best to support the needs…

3D treatment planning systems.

PubMed

Saw, Cheng B; Li, Sicong

2018-01-01

Three-dimensional (3D) treatment planning systems have evolved and become crucial components of modern radiation therapy. The systems are computer-aided designing or planning softwares that speed up the treatment planning processes to arrive at the best dose plans for the patients undergoing radiation therapy. Furthermore, the systems provide new technology to solve problems that would not have been considered without the use of computers such as conformal radiation therapy (CRT), intensity-modulated radiation therapy (IMRT), and volumetric modulated arc therapy (VMAT). The 3D treatment planning systems vary amongst the vendors and also the dose delivery systems they are designed to support. As such these systems have different planning tools to generate the treatment plans and convert the treatment plans into executable instructions that can be implemented by the dose delivery systems. The rapid advancements in computer technology and accelerators have facilitated constant upgrades and the introduction of different and unique dose delivery systems than the traditional C-arm type medical linear accelerators. The focus of this special issue is to gather relevant 3D treatment planning systems for the radiation oncology community to keep abreast of technology advancement by assess the planning tools available as well as those unique "tricks or tips" used to support the different dose delivery systems. Copyright © 2018 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

Intelligent Manufacturing of Commercial Optics Final Report CRADA No. TC-0313-92

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

Taylor, J. S.; Pollicove, H.

The project combined the research and development efforts of LLNL and the University of Rochester Center for Manufacturing Optics (COM), to develop a new generation of flexible computer controlled optics· grinding machines. COM's principal near term development effort is to commercialize the OPTICAM-SM, a new prototype spherical grinding machine. A crucial requirement for commercializing the OPTICAM-SM is the development of a predictable and repeatable material removal process ( deterministic micro-grinding) that yields high quality surfaces that minimize non-deterministic polishing. OPTICAM machine tools and the fabrication process development studies are part of COM' s response to the DOD (ARPA) request tomore » implement a modernization strategy for revitalizing the U.S. optics manufacturing base. This project was entered into in order to develop a new generation of :flexible, computer-controlled optics grinding machines.« less

Solution x-ray scattering and structure formation in protein dynamics

NASA Astrophysics Data System (ADS)

Nasedkin, Alexandr; Davidsson, Jan; Niemi, Antti J.; Peng, Xubiao

2017-12-01

We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

Automatic detection and severity measurement of eczema using image processing.

PubMed

Alam, Md Nafiul; Munia, Tamanna Tabassum Khan; Tavakolian, Kouhyar; Vasefi, Fartash; MacKinnon, Nick; Fazel-Rezai, Reza

2016-08-01

Chronic skin diseases like eczema may lead to severe health and financial consequences for patients if not detected and controlled early. Early measurement of disease severity, combined with a recommendation for skin protection and use of appropriate medication can prevent the disease from worsening. Current diagnosis can be costly and time-consuming. In this paper, an automatic eczema detection and severity measurement model are presented using modern image processing and computer algorithm. The system can successfully detect regions of eczema and classify the identified region as mild or severe based on image color and texture feature. Then the model automatically measures skin parameters used in the most common assessment tool called "Eczema Area and Severity Index (EASI)," by computing eczema affected area score, eczema intensity score, and body region score of eczema allowing both patients and physicians to accurately assess the affected skin.

Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

PubMed

Yu, Jia; Blom, Jochen; Sczyrba, Alexander; Goesmann, Alexander

2017-09-10

The introduction of next generation sequencing has caused a steady increase in the amounts of data that have to be processed in modern life science. Sequence alignment plays a key role in the analysis of sequencing data e.g. within whole genome sequencing or metagenome projects. BLAST is a commonly used alignment tool that was the standard approach for more than two decades, but in the last years faster alternatives have been proposed including RapSearch, GHOSTX, and DIAMOND. Here we introduce HAMOND, an application that uses Apache Hadoop to parallelize DIAMOND computation in order to scale-out the calculation of alignments. HAMOND is fault tolerant and scalable by utilizing large cloud computing infrastructures like Amazon Web Services. HAMOND has been tested in comparative genomics analyses and showed promising results both in efficiency and accuracy. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Introduction to Cosmology, Proceedings of the Polish Astronomical Society volume 4

NASA Astrophysics Data System (ADS)

Biernacka, Monika; Bajan, Katarzyna; Stachowski, Grzegorz; Pollo, Agnieszka

2016-07-01

On 11-23 July 2016, Jan Kochanowski University in Kielce was the host of the Second Cosmological School "Introduction to Cosmology". The main purpose of the School was to provide an introduction to a selection of the most interesting topics in modern cosmology, both in theory and observations. The program included a series of mini-workshops on cosmological simulations, Virtual Observatory database and tools and Spectral Energy Distribution tting. The School was intended for undergraduate, MSc and PhD students, as well as young postdoctoral researchers. The School was co-organized by the Polish Astronomical Society, the Jan Kochanowski University in Kielce, the Jagiellonian University in Cracow, the Nuclear Centre for Nuclear Research and the N. Copernicus Astronomical Center in Warsaw. The Interdisciplinary Centre for Mathematical and Computational Modeling kindly provided us with the possibility to remotely use their computing facilities.

Introduction to Cosmology, Proceedings of the Polish Astronomical Society volume 4

NASA Astrophysics Data System (ADS)

Biernacka, Monika; Bajan, Katarzyna; Stachowski, Grzegorz; Pollo, Agnieszka

2017-08-01

On 11-23 July 2016, Jan Kochanowski University in Kielce was the host of the Second Cosmological School "Introduction to Cosmology". The main purpose of the School was to provide an introduction to a selection of the most interesting topics in modern cosmology, both in theory and observations. The program included a series of mini-workshops on cosmological simulations, Virtual Observatory database and tools and Spectral Energy Distribution tting. The School was intended for undergraduate, MSc and PhD students, as well as young postdoctoral researchers. The School was co-organized by the Polish Astronomical Society, the Jan Kochanowski University in Kielce, the Jagiellonian University in Cracow, the Nuclear Centre for Nuclear Research and the N. Copernicus Astronomical Center in Warsaw. The Interdisciplinary Centre for Mathematical and Computational Modeling kindly provided us with the possibility to remotely use their computing facilities.

Rapid Parallel Calculation of shell Element Based On GPU

NASA Astrophysics Data System (ADS)

Wanga, Jian Hua; Lia, Guang Yao; Lib, Sheng; Li, Guang Yao

2010-06-01

Long computing time bottlenecked the application of finite element. In this paper, an effective method to speed up the FEM calculation by using the existing modern graphic processing unit and programmable colored rendering tool was put forward, which devised the representation of unit information in accordance with the features of GPU, converted all the unit calculation into film rendering process, solved the simulation work of all the unit calculation of the internal force, and overcame the shortcomings of lowly parallel level appeared ever before when it run in a single computer. Studies shown that this method could improve efficiency and shorten calculating hours greatly. The results of emulation calculation about the elasticity problem of large number cells in the sheet metal proved that using the GPU parallel simulation calculation was faster than using the CPU's. It is useful and efficient to solve the project problems in this way.

Telescience workstation

NASA Technical Reports Server (NTRS)

Brown, Robert L.; Doyle, Dee; Haines, Richard F.; Slocum, Michael

1989-01-01

As part of the Telescience Testbed Pilot Program, the Universities Space Research Association/ Research Institute for Advanced Computer Science (USRA/RIACS) proposed to support remote communication by providing a network of human/machine interfaces, computer resources, and experimental equipment which allows: remote science, collaboration, technical exchange, and multimedia communication. The telescience workstation is intended to provide a local computing environment for telescience. The purpose of the program are as follows: (1) to provide a suitable environment to integrate existing and new software for a telescience workstation; (2) to provide a suitable environment to develop new software in support of telescience activities; (3) to provide an interoperable environment so that a wide variety of workstations may be used in the telescience program; (4) to provide a supportive infrastructure and a common software base; and (5) to advance, apply, and evaluate the telescience technolgy base. A prototype telescience computing environment designed to bring practicing scientists in domains other than their computer science into a modern style of doing their computing was created and deployed. This environment, the Telescience Windowing Environment, Phase 1 (TeleWEn-1), met some, but not all of the goals stated above. The TeleWEn-1 provided a window-based workstation environment and a set of tools for text editing, document preparation, electronic mail, multimedia mail, raster manipulation, and system management.

Automatic and accurate reconstruction of distal humerus contours through B-Spline fitting based on control polygon deformation.

PubMed

Mostafavi, Kamal; Tutunea-Fatan, O Remus; Bordatchev, Evgueni V; Johnson, James A

2014-12-01

The strong advent of computer-assisted technologies experienced by the modern orthopedic surgery prompts for the expansion of computationally efficient techniques to be built on the broad base of computer-aided engineering tools that are readily available. However, one of the common challenges faced during the current developmental phase continues to remain the lack of reliable frameworks to allow a fast and precise conversion of the anatomical information acquired through computer tomography to a format that is acceptable to computer-aided engineering software. To address this, this study proposes an integrated and automatic framework capable to extract and then postprocess the original imaging data to a common planar and closed B-Spline representation. The core of the developed platform relies on the approximation of the discrete computer tomography data by means of an original two-step B-Spline fitting technique based on successive deformations of the control polygon. In addition to its rapidity and robustness, the developed fitting technique was validated to produce accurate representations that do not deviate by more than 0.2 mm with respect to alternate representations of the bone geometry that were obtained through different-contact-based-data acquisition or data processing methods. © IMechE 2014.

Topology optimization aided structural design: Interpretation, computational aspects and 3D printing.

PubMed

Kazakis, Georgios; Kanellopoulos, Ioannis; Sotiropoulos, Stefanos; Lagaros, Nikos D

2017-10-01

Construction industry has a major impact on the environment that we spend most of our life. Therefore, it is important that the outcome of architectural intuition performs well and complies with the design requirements. Architects usually describe as "optimal design" their choice among a rather limited set of design alternatives, dictated by their experience and intuition. However, modern design of structures requires accounting for a great number of criteria derived from multiple disciplines, often of conflicting nature. Such criteria derived from structural engineering, eco-design, bioclimatic and acoustic performance. The resulting vast number of alternatives enhances the need for computer-aided architecture in order to increase the possibility of arriving at a more preferable solution. Therefore, the incorporation of smart, automatic tools in the design process, able to further guide designer's intuition becomes even more indispensable. The principal aim of this study is to present possibilities to integrate automatic computational techniques related to topology optimization in the phase of intuition of civil structures as part of computer aided architectural design. In this direction, different aspects of a new computer aided architectural era related to the interpretation of the optimized designs, difficulties resulted from the increased computational effort and 3D printing capabilities are covered here in.

Overcoming the fragility - X-ray computed micro-tomography elucidates brachiopod endoskeletons.

PubMed

Seidel, Ronald; Lüter, Carsten

2014-01-01

The calcareous shells of brachiopods offer a wealth of informative characters for taxonomic and phylogenetic investigations. In particular scanning electron microscopy (SEM) has been used for decades to visualise internal structures of the shell. However, to produce informative SEM data, brachiopod shells need to be opened after chemical removal of the soft tissue. This preparation occasionally damages the shell. Additionally, skeletal elements of taxonomic/systematic interest such as calcareous spicules which are loosely embedded in the lophophore and mantle connective tissue become disintegrated during the preparation process. Using a nondestructive micro-computed tomography (μCT) approach, the entire fragile endoskeleton of brachiopods is documented for the first time. New insights on the structure and position of tissue-bound skeletal elements (spicules) are given as add ons to existing descriptions of brachiopod shell anatomy, thereby enhancing the quality and quantity of informative characters needed for both taxonomic and phylogenetic studies. Here, we present five modern, articulated brachiopods (Rectocalathis schemmgregoryi n. gen., n. sp., Eucalathis sp., Gryphus vitreus, Liothyrella neozelanica and Terebratulina retusa) that were X-rayed using a Phoenix Nanotom XS 180 NF. We provide links to download 3D models of these species, and additional five species with spicules can be accessed in the Supplemental Material. In total, 17 brachiopod genera covering all modern articulated subgroups and 2 inarticulated genera were X-rayed for morphological analysis. Rectocalathis schemmgregoryi n. gen., n. sp. is fully described. Micro-CT is an excellent non-destructive tool for investigating calcified structures in the exo- and endoskeletons of brachiopods. With high quality images and interactive 3D models, this study provides a comprehensive description of the profound differences in shell anatomy, facilitates the detection of new delicate morphological characters of the endoskeleton and gives new insights into the body plan of modern brachiopods.

Modern Functions of a Textbook on Social Sciences and Humanities as an Informational Management Tool of University Education

ERIC Educational Resources Information Center

Nikonova, Elina I.; Sharonov, Ivan A.; Sorokoumova, Svetlana N.; Suvorova, Olga V.; Sorokoumova, Elena A.

2016-01-01

The relevance of the study is conditioned by the changes in the content of socio-humanitarian education, aimed at the acquisition of knowledge, the development of tolerance, civic and moral education. The purpose of the paper is to identify the modern functions of a textbook on social sciences and humanities as an informational management tool of…

Aeroelastic Ground Wind Loads Analysis Tool for Launch Vehicles

NASA Technical Reports Server (NTRS)

Ivanco, Thomas G.

2016-01-01

Launch vehicles are exposed to ground winds during rollout and on the launch pad that can induce static and dynamic loads. Of particular concern are the dynamic loads caused by vortex shedding from nearly-cylindrical structures. When the frequency of vortex shedding nears that of a lowly-damped structural mode, the dynamic loads can be more than an order of magnitude greater than mean drag loads. Accurately predicting vehicle response to vortex shedding during the design and analysis cycles is difficult and typically exceeds the practical capabilities of modern computational fluid dynamics codes. Therefore, mitigating the ground wind loads risk typically requires wind-tunnel tests of dynamically-scaled models that are time consuming and expensive to conduct. In recent years, NASA has developed a ground wind loads analysis tool for launch vehicles to fill this analytical capability gap in order to provide predictions for prelaunch static and dynamic loads. This paper includes a background of the ground wind loads problem and the current state-of-the-art. It then discusses the history and significance of the analysis tool and the methodology used to develop it. Finally, results of the analysis tool are compared to wind-tunnel and full-scale data of various geometries and Reynolds numbers.

Explorationists and dinosaurs

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

French, W.S.

1993-02-01

The exploration industry is changing, exploration technology is changing and the explorationist's job is changing. Resource companies are diversifying internationally and their central organizations are providing advisors rather than services. As a result, the relationship between the resource company and the contractor is changing. Resource companies are promoting standards so that all contract services in all parts of the world will look the same to their advisors. Contractors, for competitive reasons, want to look [open quotes]different[close quotes] from other contractors. The resource companies must encourage competition between contractors to insure the availability of new technology but must also resist themore » current trend of burdening the contractor with more and more of the risk involved in exploration. It is becoming more and more obvious that geophysical expenditures represent the best [open quotes]value added[close quotes] expenditures in exploration and development budgets. As a result, seismic-related contractors represent the growth component of our industry. The predominant growth is in 3-D seismic technology, and this growth is being further propelled by the computational power of the new generation of massively parallel computers and by recent advances in computer graphic techniques. Interpretation of seismic data involves the analysis of wavelet shapes and amplitudes prior to stacking the data. Thus, modern interpretation involves understanding compressional waves, shear waves, and propagating modes which create noise and interference. Modern interpretation and processing are carried out simultaneously, iteratively, and interactively and involve many physics-related concepts. These concepts are not merely tools for the interpretation, they are the interpretation. Explorationists who do not recognize this fact are going the way of the dinosaurs.« less

ASDF - A Modern Data Format for Seismology

NASA Astrophysics Data System (ADS)

Krischer, Lion; Smith, James; Lei, Wenjie; Lefebvre, Matthieu; Ruan, Youyi; Sales de Andrade, Elliot; Podhorszki, Norbert; Bozdag, Ebru; Tromp, Jeroen

2017-04-01

Seismology as a science is driven by observing and understanding data and it is thus vital to make this as easy and accessible as possible. The growing volume of freely available data coupled with ever expanding computational power enables scientists to take on new and bigger problems. This evolution is to some part hindered as existing data formats have not been designed with it in mind. We present ASDF (http://seismic-data.org), the Adaptable Seismic Data Format, a novel, modern, and especially practical data format for all branches of seismology with particular focus on how it is incorporated into seismic full waveform inversion workflows. The format aims to solve five key issues: Efficiency: Fast I/O operations especially in high performance computing environments, especially limiting the total number of files. Data organization: Different types of data are needed for a variety of tasks. This results in ad hoc data organization and formats that are hard to maintain, integrate, reproduce, and exchange. Data exchange: We want to exchange complex and complete data sets. Reproducibility: Oftentimes just not existing but crucial to advance our science. Mining, visualization, and understanding of data: As data volumes grow, more complex, new techniques to query and visualize large datasets are needed. ASDF tackles these by defining a structure on top of HDF5 reusing as many existing standards (QuakeML, StationXML, PROV) as possible. An essential trait of ASDF is that it empowers the construction of completely self-describing data sets including waveform, station, and event data together with non-waveform data and a provenance description of everything. This for example for the first time enables the proper archival and exchange of processed or synthetic waveforms. To aid community adoption we developed mature tools in Python as well as in C and Fortran. Additionally we provide a formal definition of the format, a validation tool, and integration into widely used tools like ObsPy (http://obspy.org), SPECFEM GLOBE (https://geodynamics.org/cig/software/specfem3d_globe/), and Salvus (http://salvus.io).

Solubility prediction, solvate and cocrystal screening as tools for rational crystal engineering.

PubMed

Loschen, Christoph; Klamt, Andreas

2015-06-01

The fact that novel drug candidates are becoming increasingly insoluble is a major problem of current drug development. Computational tools may address this issue by screening for suitable solvents or by identifying potential novel cocrystal formers that increase bioavailability. In contrast to other more specialized methods, the fluid phase thermodynamics approach COSMO-RS (conductor-like screening model for real solvents) allows for a comprehensive treatment of drug solubility, solvate and cocrystal formation and many other thermodynamics properties in liquids. This article gives an overview of recent COSMO-RS developments that are of interest for drug development and contains several new application examples for solubility prediction and solvate/cocrystal screening. For all property predictions COSMO-RS has been used. The basic concept of COSMO-RS consists of using the screening charge density as computed from first principles calculations in combination with fast statistical thermodynamics to compute the chemical potential of a compound in solution. The fast and accurate assessment of drug solubility and the identification of suitable solvents, solvate or cocrystal formers is nowadays possible and may be used to complement modern drug development. Efficiency is increased by avoiding costly quantum-chemical computations using a database of previously computed molecular fragments. COSMO-RS theory can be applied to a range of physico-chemical properties, which are of interest in rational crystal engineering. Most notably, in combination with experimental reference data, accurate quantitative solubility predictions in any solvent or solvent mixture are possible. Additionally, COSMO-RS can be extended to the prediction of cocrystal formation, which results in considerable predictive accuracy concerning coformer screening. In a recent variant costly quantum chemical calculations are avoided resulting in a significant speed-up and ease-of-use. © 2015 Royal Pharmaceutical Society.

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

OLTARIS: On-Line Tool for the Assessment of Radiation in Space

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Blattnig, Steve R.; Clowdsley, Martha S.; Qualls, Garry D.; Sandridge, Chris A.; Simonsen, Lisa C.; Norbury, John W.; Slaba, Tony C.; Walker, Steve A.; Badavi, Francis F.;

Surgical treatment of secondary peritonitis : A continuing problem.

PubMed

van Ruler, O; Boermeester, M A

2017-01-01

Secondary peritonitis remains associated with high mortality and morbidity rates. Treatment of secondary peritonitis is challenging even in modern medicine. Surgical intervention for source control remains the cornerstone of treatment, beside adequate antimicrobial therapy and resuscitation. A randomized clinical trial showed that relaparotomy on demand (ROD) after initial emergency surgery is the preferred treatment strategy, irrespective of the severity and extent of peritonitis. The effective and safe use of ROD requires intensive monitoring of the patient in a setting where diagnostic tests and decision making about relaparotomy are guaranteed round the clock. The lack of knowledge on timely and adequate patient selection, together with the lack of use of easy but reliable monitoring tools, seems to hamper full implementation of ROD. The accuracy of the relap decision tool is reasonable for prediction of ongoing peritonitis and selection for computer tomography (CT). The value of CT in an early postoperative phase is unclear. Future research and innovative technologies should focus on the additive value of CT in cases of operated secondary peritonitis and on the further optimization of bedside prediction tools to enhance adequate patient selection for intervention in a multidisciplinary setting.

A paperless course on structural engineering programming: investing in educational technology in the times of the Greek financial recession

NASA Astrophysics Data System (ADS)

Sextos, Anastasios G.

2014-01-01

This paper presents the structure of an undergraduate course entitled 'programming techniques and the use of specialised software in structural engineering' which is offered to the fifth (final) year students of the Civil Engineering Department of Aristotle University Thessaloniki in Greece. The aim of this course is to demonstrate the use of new information technologies in the field of structural engineering and to teach modern programming and finite element simulation techniques that the students can in turn apply in both research and everyday design of structures. The course also focuses on the physical interpretation of structural engineering problems, in a way that the students become familiar with the concept of computational tools without losing perspective from the engineering problem studied. For this purpose, a wide variety of structural engineering problems are studied in class, involving structural statics, dynamics, earthquake engineering, design of reinforced concrete and steel structures as well as data and information management. The main novelty of the course is that it is taught and examined solely in the computer laboratory ensuring that each student can accomplish the prescribed 'hands-on' training on a dedicated computer, strictly on a 1:1 student over hardware ratio. Significant effort has also been put so that modern educational techniques and tools are utilised to offer the course in an essentially paperless mode. This involves electronic educational material, video tutorials, student information in real time and exams given and assessed electronically through an ad hoc developed, personalised, electronic system. The positive feedback received from the students reveals that the concept of a paperless course is not only applicable in real academic conditions but is also a promising approach that significantly increases student productivity and engagement. The question, however, is whether such an investment in educational technology is indeed timely during economic recession, where the academic priorities are rapidly changing. In the light of this unfavourable and unstable financial environment, a critical overview of the strengths, the weaknesses, the opportunities and the threats of this effort is presented herein, hopefully contributing to the discussion on the future of higher education in the time of crisis.

Securing Secrets and Managing Trust in Modern Computing Applications

ERIC Educational Resources Information Center

Sayler, Andy

2016-01-01

The amount of digital data generated and stored by users increases every day. In order to protect this data, modern computing systems employ numerous cryptographic and access control solutions. Almost all of such solutions, however, require the keeping of certain secrets as the basis of their security models. How best to securely store and control…

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

NASA Astrophysics Data System (ADS)

Fisher, Ward

2014-05-01

Planning software compatibility across forthcoming generations of computing platforms is a problem commonly encountered in software engineering and development. While this problem can affect any class of software, data analysis and visualization programs are particularly vulnerable. This is due in part to their inherent dependency on specialized hardware and computing environments. A number of strategies and tools have been designed to aid software engineers with this task. While generally embraced by developers at 'traditional' software companies, these methodologies are often dismissed by the scientific software community as unwieldy, inefficient and unnecessary. As a result, many important and storied scientific software packages can struggle to adapt to a new computing environment; for example, one in which much work is carried out on sub-laptop devices (such as tablets and smartphones). Rewriting these packages for a new platform often requires significant investment in terms of development time and developer expertise. In many cases, porting older software to modern devices is neither practical nor possible. As a result, replacement software must be developed from scratch, wasting resources better spent on other projects. Enabled largely by the rapid rise and adoption of cloud computing platforms, 'Application Streaming' technologies allow legacy visualization and analysis software to be operated wholly from a client device (be it laptop, tablet or smartphone) while retaining full functionality and interactivity. It mitigates much of the developer effort required by other more traditional methods while simultaneously reducing the time it takes to bring the software to a new platform. This work will provide an overview of Application Streaming and how it compares against other technologies which allow scientific visualization software to be executed from a remote computer. We will discuss the functionality and limitations of existing application streaming frameworks and how a developer might prepare their software for application streaming. We will also examine the secondary benefits realized by moving legacy software to the cloud. Finally, we will examine the process by which a legacy Java application, the Integrated Data Viewer (IDV), is to be adapted for tablet computing via Application Streaming.

Computational ecology as an emerging science

PubMed Central

Petrovskii, Sergei; Petrovskaya, Natalia

2012-01-01

It has long been recognized that numerical modelling and computer simulations can be used as a powerful research tool to understand, and sometimes to predict, the tendencies and peculiarities in the dynamics of populations and ecosystems. It has been, however, much less appreciated that the context of modelling and simulations in ecology is essentially different from those that normally exist in other natural sciences. In our paper, we review the computational challenges arising in modern ecology in the spirit of computational mathematics, i.e. with our main focus on the choice and use of adequate numerical methods. Somewhat paradoxically, the complexity of ecological problems does not always require the use of complex computational methods. This paradox, however, can be easily resolved if we recall that application of sophisticated computational methods usually requires clear and unambiguous mathematical problem statement as well as clearly defined benchmark information for model validation. At the same time, many ecological problems still do not have mathematically accurate and unambiguous description, and available field data are often very noisy, and hence it can be hard to understand how the results of computations should be interpreted from the ecological viewpoint. In this scientific context, computational ecology has to deal with a new paradigm: conventional issues of numerical modelling such as convergence and stability become less important than the qualitative analysis that can be provided with the help of computational techniques. We discuss this paradigm by considering computational challenges arising in several specific ecological applications. PMID:23565336

Re-Computation of Numerical Results Contained in NACA Report No. 496

NASA Technical Reports Server (NTRS)

Perry, Boyd, III

2015-01-01

An extensive examination of NACA Report No. 496 (NACA 496), "General Theory of Aerodynamic Instability and the Mechanism of Flutter," by Theodore Theodorsen, is described. The examination included checking equations and solution methods and re-computing interim quantities and all numerical examples in NACA 496. The checks revealed that NACA 496 contains computational shortcuts (time- and effort-saving devices for engineers of the time) and clever artifices (employed in its solution methods), but, unfortunately, also contains numerous tripping points (aspects of NACA 496 that have the potential to cause confusion) and some errors. The re-computations were performed employing the methods and procedures described in NACA 496, but using modern computational tools. With some exceptions, the magnitudes and trends of the original results were in fair-to-very-good agreement with the re-computed results. The exceptions included what are speculated to be computational errors in the original in some instances and transcription errors in the original in others. Independent flutter calculations were performed and, in all cases, including those where the original and re-computed results differed significantly, were in excellent agreement with the re-computed results. Appendix A contains NACA 496; Appendix B contains a Matlab(Reistered) program that performs the re-computation of results; Appendix C presents three alternate solution methods, with examples, for the two-degree-of-freedom solution method of NACA 496; Appendix D contains the three-degree-of-freedom solution method (outlined in NACA 496 but never implemented), with examples.

Oscillatory threshold logic.

PubMed

Borresen, Jon; Lynch, Stephen

2012-01-01

In the 1940s, the first generation of modern computers used vacuum tube oscillators as their principle components, however, with the development of the transistor, such oscillator based computers quickly became obsolete. As the demand for faster and lower power computers continues, transistors are themselves approaching their theoretical limit and emerging technologies must eventually supersede them. With the development of optical oscillators and Josephson junction technology, we are again presented with the possibility of using oscillators as the basic components of computers, and it is possible that the next generation of computers will be composed almost entirely of oscillatory devices. Here, we demonstrate how coupled threshold oscillators may be used to perform binary logic in a manner entirely consistent with modern computer architectures. We describe a variety of computational circuitry and demonstrate working oscillator models of both computation and memory.

Enabling a new Paradigm to Address Big Data and Open Science Challenges

NASA Astrophysics Data System (ADS)

Ramamurthy, Mohan; Fisher, Ward

2017-04-01

Data are not only the lifeblood of the geosciences but they have become the currency of the modern world in science and society. Rapid advances in computing, communi¬cations, and observational technologies — along with concomitant advances in high-resolution modeling, ensemble and coupled-systems predictions of the Earth system — are revolutionizing nearly every aspect of our field. Modern data volumes from high-resolution ensemble prediction/projection/simulation systems and next-generation remote-sensing systems like hyper-spectral satellite sensors and phased-array radars are staggering. For example, CMIP efforts alone will generate many petabytes of climate projection data for use in assessments of climate change. And NOAA's National Climatic Data Center projects that it will archive over 350 petabytes by 2030. For researchers and educators, this deluge and the increasing complexity of data brings challenges along with the opportunities for discovery and scientific breakthroughs. The potential for big data to transform the geosciences is enormous, but realizing the next frontier depends on effectively managing, analyzing, and exploiting these heterogeneous data sources, extracting knowledge and useful information from heterogeneous data sources in ways that were previously impossible, to enable discoveries and gain new insights. At the same time, there is a growing focus on the area of "Reproducibility or Replicability in Science" that has implications for Open Science. The advent of cloud computing has opened new avenues for not only addressing both big data and Open Science challenges to accelerate scientific discoveries. However, to successfully leverage the enormous potential of cloud technologies, it will require the data providers and the scientific communities to develop new paradigms to enable next-generation workflows and transform the conduct of science. Making data readily available is a necessary but not a sufficient condition. Data providers also need to give scientists an ecosystem that includes data, tools, workflows and other services needed to perform analytics, integration, interpretation, and synthesis - all in the same environment or platform. Instead of moving data to processing systems near users, as is the tradition, the cloud permits one to bring processing, computing, analysis and visualization to data - so called data proximate workbench capabilities, also known as server-side processing. In this talk, I will present the ongoing work at Unidata to facilitate a new paradigm for doing science by offering a suite of tools, resources, and platforms to leverage cloud technologies for addressing both big data and Open Science/reproducibility challenges. That work includes the development and deployment of new protocols for data access and server-side operations and Docker container images of key applications, JupyterHub Python notebook tools, and cloud-based analysis and visualization capability via the CloudIDV tool to enable reproducible workflows and effectively use the accessed data.

Increasing the reliability of ecological models using modern software engineering techniques

Treesearch

Robert M. Scheller; Brian R. Sturtevant; Eric J. Gustafson; Brendan C. Ward; David J. Mladenoff

2009-01-01

Modern software development techniques are largely unknown to ecologists. Typically, ecological models and other software tools are developed for limited research purposes, and additional capabilities are added later, usually in an ad hoc manner. Modern software engineering techniques can substantially increase scientific rigor and confidence in ecological models and...

PyNEST: A Convenient Interface to the NEST Simulator.

PubMed

Eppler, Jochen Martin; Helias, Moritz; Muller, Eilif; Diesmann, Markus; Gewaltig, Marc-Oliver

2008-01-01

The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10(4) neurons and 10(7) to 10(9) synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST's efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST's native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used.

PyNEST: A Convenient Interface to the NEST Simulator

PubMed Central

Eppler, Jochen Martin; Helias, Moritz; Muller, Eilif; Diesmann, Markus; Gewaltig, Marc-Oliver

2008-01-01

The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 104 neurons and 107 to 109 synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST's efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST's native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used. PMID:19198667

Symmetric log-domain diffeomorphic Registration: a demons-based approach.

PubMed

Vercauteren, Tom; Pennec, Xavier; Perchant, Aymeric; Ayache, Nicholas

2008-01-01

Modern morphometric studies use non-linear image registration to compare anatomies and perform group analysis. Recently, log-Euclidean approaches have contributed to promote the use of such computational anatomy tools by permitting simple computations of statistics on a rather large class of invertible spatial transformations. In this work, we propose a non-linear registration algorithm perfectly fit for log-Euclidean statistics on diffeomorphisms. Our algorithm works completely in the log-domain, i.e. it uses a stationary velocity field. This implies that we guarantee the invertibility of the deformation and have access to the true inverse transformation. This also means that our output can be directly used for log-Euclidean statistics without relying on the heavy computation of the log of the spatial transformation. As it is often desirable, our algorithm is symmetric with respect to the order of the input images. Furthermore, we use an alternate optimization approach related to Thirion's demons algorithm to provide a fast non-linear registration algorithm. First results show that our algorithm outperforms both the demons algorithm and the recently proposed diffeomorphic demons algorithm in terms of accuracy of the transformation while remaining computationally efficient.

Computer-assisted total hip arthroplasty: coding the next generation of navigation systems for orthopedic surgery.

PubMed

Renkawitz, Tobias; Tingart, Markus; Grifka, Joachim; Sendtner, Ernst; Kalteis, Thomas

2009-09-01

This article outlines the scientific basis and a state-of-the-art application of computer-assisted orthopedic surgery in total hip arthroplasty (THA) and provides a future perspective on this technology. Computer-assisted orthopedic surgery in primary THA has the potential to couple 3D simulations with real-time evaluations of surgical performance, which has brought these developments from the research laboratory all the way to clinical use. Nonimage- or imageless-based navigation systems without the need for additional pre- or intra-operative image acquisition have stood the test to significantly reduce the variability in positioning the acetabular component and have shown precise measurement of leg length and offset changes during THA. More recently, computer-assisted orthopedic surgery systems have opened a new frontier for accurate surgical practice in minimally invasive, tissue-preserving THA. The future generation of imageless navigation systems will switch from simple measurement tasks to real navigation tools. These software algorithms will consider the cup and stem as components of a coupled biomechanical system, navigating the orthopedic surgeon to find an optimized complementary component orientation rather than target values intraoperatively, and are expected to have a high impact on clinical practice and postoperative functionality in modern THA.

Ancient Egypt and radiology, a future for the past!

NASA Astrophysics Data System (ADS)

Van Tiggelen, R.

2004-11-01

X-rays, discovered by W.K. Röntgen was a scientific bombshell and was received with extraordinary interest by scientist in all disciplines, including Egyptology: the first radiological essay was already made in Germany 3 months after Röntgens discovery. Since then, radiological examinations of mummies are used to detect frauds, to appreciate sex and age, and possible cause of death. As non-destructive tool it can reveal the nature of materials, presence of jewellery and amulets. The paper gives a brief history of major milestones in Belgium and abroad. More modern technology such as axial computed tomography and image colouring will allow better representations and reveal up to now undiscovered funerary artefacts.

Development of expert systems for analyzing electronic documents

NASA Astrophysics Data System (ADS)

Abeer Yassin, Al-Azzawi; Shidlovskiy, S.; Jamal, A. A.

2018-05-01

The paper analyses a Database Management System (DBMS). Expert systems, Databases, and database technology have become an essential component of everyday life in the modern society. As databases are widely used in every organization with a computer system, data resource control and data management are very important [1]. DBMS is the most significant tool developed to serve multiple users in a database environment consisting of programs that enable users to create and maintain a database. This paper focuses on development of a database management system for General Directorate for education of Diyala in Iraq (GDED) using Clips, java Net-beans and Alfresco and system components, which were previously developed in Tomsk State University at the Faculty of Innovative Technology.

Computational overlay metrology with adaptive data analytics

NASA Astrophysics Data System (ADS)

Schmitt-Weaver, Emil; Subramony, Venky; Ullah, Zakir; Matsunobu, Masazumi; Somasundaram, Ravin; Thomas, Joel; Zhang, Linmiao; Thul, Klaus; Bhattacharyya, Kaustuve; Goossens, Ronald; Lambregts, Cees; Tel, Wim; de Ruiter, Chris

2017-03-01

With photolithography as the fundamental patterning step in the modern nanofabrication process, every wafer within a semiconductor fab will pass through a lithographic apparatus multiple times. With more than 20,000 sensors producing more than 700GB of data per day across multiple subsystems, the combination of a light source and lithographic apparatus provide a massive amount of information for data analytics. This paper outlines how data analysis tools and techniques that extend insight into data that traditionally had been considered unmanageably large, known as adaptive analytics, can be used to show how data collected before the wafer is exposed can be used to detect small process dependent wafer-towafer changes in overlay.

National Toxicology Program

MedlinePlus

... develops and applies tools of modern toxicology and molecular biology to identify substances in the environment that may ... application of new technologies for modern toxicology and molecular biology. A world leader in toxicology research, NTP has ...

Computational toxicology: Its essential role in reducing drug attrition.

PubMed

Naven, R T; Louise-May, S

2015-12-01

Predictive toxicology plays a critical role in reducing the failure rate of new drugs in pharmaceutical research and development. Despite recent gains in our understanding of drug-induced toxicity, however, it is urgent that the utility and limitations of our current predictive tools be determined in order to identify gaps in our understanding of mechanistic and chemical toxicology. Using recently published computational regression analyses of in vitro and in vivo toxicology data, it will be demonstrated that significant gaps remain in early safety screening paradigms. More strategic analyses of these data sets will allow for a better understanding of their domain of applicability and help identify those compounds that cause significant in vivo toxicity but which are currently mis-predicted by in silico and in vitro models. These 'outliers' and falsely predicted compounds are metaphorical lighthouses that shine light on existing toxicological knowledge gaps, and it is essential that these compounds are investigated if attrition is to be reduced significantly in the future. As such, the modern computational toxicologist is more productively engaged in understanding these gaps and driving investigative toxicology towards addressing them. © The Author(s) 2015.

Multicore Architecture-aware Scientific Applications

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

Srinivasa, Avinash

Modern high performance systems are becoming increasingly complex and powerful due to advancements in processor and memory architecture. In order to keep up with this increasing complexity, applications have to be augmented with certain capabilities to fully exploit such systems. These may be at the application level, such as static or dynamic adaptations or at the system level, like having strategies in place to override some of the default operating system polices, the main objective being to improve computational performance of the application. The current work proposes two such capabilites with respect to multi-threaded scientific applications, in particular a largemore » scale physics application computing ab-initio nuclear structure. The first involves using a middleware tool to invoke dynamic adaptations in the application, so as to be able to adjust to the changing computational resource availability at run-time. The second involves a strategy for effective placement of data in main memory, to optimize memory access latencies and bandwidth. These capabilties when included were found to have a significant impact on the application performance, resulting in average speedups of as much as two to four times.« less

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

NASA Astrophysics Data System (ADS)

Shadid, J. N.; Smith, T. M.; Cyr, E. C.; Wildey, T. M.; Pawlowski, R. P.

2016-09-01

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. In this respect the understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In this study we report on initial efforts to apply integrated adjoint-based computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier-Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. Initial results are presented that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.

SNAVA-A real-time multi-FPGA multi-model spiking neural network simulation architecture.

PubMed

Sripad, Athul; Sanchez, Giovanny; Zapata, Mireya; Pirrone, Vito; Dorta, Taho; Cambria, Salvatore; Marti, Albert; Krishnamourthy, Karthikeyan; Madrenas, Jordi

2018-01-01

Spiking Neural Networks (SNN) for Versatile Applications (SNAVA) simulation platform is a scalable and programmable parallel architecture that supports real-time, large-scale, multi-model SNN computation. This parallel architecture is implemented in modern Field-Programmable Gate Arrays (FPGAs) devices to provide high performance execution and flexibility to support large-scale SNN models. Flexibility is defined in terms of programmability, which allows easy synapse and neuron implementation. This has been achieved by using a special-purpose Processing Elements (PEs) for computing SNNs, and analyzing and customizing the instruction set according to the processing needs to achieve maximum performance with minimum resources. The parallel architecture is interfaced with customized Graphical User Interfaces (GUIs) to configure the SNN's connectivity, to compile the neuron-synapse model and to monitor SNN's activity. Our contribution intends to provide a tool that allows to prototype SNNs faster than on CPU/GPU architectures but significantly cheaper than fabricating a customized neuromorphic chip. This could be potentially valuable to the computational neuroscience and neuromorphic engineering communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

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

Shadid, J.N., E-mail: jnshadi@sandia.gov; Department of Mathematics and Statistics, University of New Mexico; Smith, T.M.

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. In this respect the understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In this study we report on initial efforts tomore » apply integrated adjoint-based computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier–Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. Initial results are presented that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.« less

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

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

Shadid, J. N.; Smith, T. M.; Cyr, E. C.

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. The understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In our study we report on initial efforts to apply integrated adjoint-basedmore » computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier–Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. We present the initial results that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.« less

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

DOE PAGES

Shadid, J. N.; Smith, T. M.; Cyr, E. C.; ...

2016-05-20

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. The understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In our study we report on initial efforts to apply integrated adjoint-basedmore » computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier–Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. We present the initial results that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.« less

Improving robustness and computational efficiency using modern C++

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

Paterno, M.; Kowalkowski, J.; Green, C.

2014-01-01

For nearly two decades, the C++ programming language has been the dominant programming language for experimental HEP. The publication of ISO/IEC 14882:2011, the current version of the international standard for the C++ programming language, makes available a variety of language and library facilities for improving the robustness, expressiveness, and computational efficiency of C++ code. However, much of the C++ written by the experimental HEP community does not take advantage of the features of the language to obtain these benefits, either due to lack of familiarity with these features or concern that these features must somehow be computationally inefficient. In thismore » paper, we address some of the features of modern C+-+, and show how they can be used to make programs that are both robust and computationally efficient. We compare and contrast simple yet realistic examples of some common implementation patterns in C, currently-typical C++, and modern C++, and show (when necessary, down to the level of generated assembly language code) the quality of the executable code produced by recent C++ compilers, with the aim of allowing the HEP community to make informed decisions on the costs and benefits of the use of modern C++.« less

The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication.

NASA Astrophysics Data System (ADS)

Ragan-Kelley, M.; Perez, F.; Granger, B.; Kluyver, T.; Ivanov, P.; Frederic, J.; Bussonnier, M.

2014-12-01

IPython has provided terminal-based tools for interactive computing in Python since 2001. The notebook document format and multi-process architecture introduced in 2011 have expanded the applicable scope of IPython into teaching, presenting, and sharing computational work, in addition to interactive exploration. The new architecture also allows users to work in any language, with implementations in Python, R, Julia, Haskell, and several other languages. The language agnostic parts of IPython have been renamed to Jupyter, to better capture the notion that a cross-language design can encapsulate commonalities present in computational research regardless of the programming language being used. This architecture offers components like the web-based Notebook interface, that supports rich documents that combine code and computational results with text narratives, mathematics, images, video and any media that a modern browser can display. This interface can be used not only in research, but also for publication and education, as notebooks can be converted to a variety of output formats, including HTML and PDF. Recent developments in the Jupyter project include a multi-user environment for hosting notebooks for a class or research group, a live collaboration notebook via Google Docs, and better support for languages other than Python.

On the Emergence of Modern Humans

ERIC Educational Resources Information Center

Amati, Daniele; Shallice, Tim

2007-01-01

The emergence of modern humans with their extraordinary cognitive capacities is ascribed to a novel type of cognitive computational process (sustained non-routine multi-level operations) required for abstract projectuality, held to be the common denominator of the cognitive capacities specific to modern humans. A brain operation (latching) that…

Three-dimensional radiation dosimetry using polymer gel and solid radiochromic polymer: From basics to clinical applications

PubMed Central

Watanabe, Yoichi; Warmington, Leighton; Gopishankar, N

2017-01-01

Accurate dose measurement tools are needed to evaluate the radiation dose delivered to patients by using modern and sophisticated radiation therapy techniques. However, the adequate tools which enable us to directly measure the dose distributions in three-dimensional (3D) space are not commonly available. One such 3D dose measurement device is the polymer-based dosimeter, which changes the material property in response to radiation. These are available in the gel form as polymer gel dosimeter (PGD) and ferrous gel dosimeter (FGD) and in the solid form as solid plastic dosimeter (SPD). Those are made of a continuous uniform medium which polymerizes upon irradiation. Hence, the intrinsic spatial resolution of those dosimeters is very high, and it is only limited by the method by which one converts the dose information recorded by the medium to the absorbed dose. The current standard methods of the dose quantification are magnetic resonance imaging, optical computed tomography, and X-ray computed tomography. In particular, magnetic resonance imaging is well established as a method for obtaining clinically relevant dosimetric data by PGD and FGD. Despite the likely possibility of doing 3D dosimetry by PGD, FGD or SPD, the tools are still lacking wider usages for clinical applications. In this review article, we summarize the current status of PGD, FGD, and SPD and discuss the issue faced by these for wider acceptance in radiation oncology clinic and propose some directions for future development. PMID:28396725

Modernization of the Cassini Ground System

NASA Technical Reports Server (NTRS)

Razo, Gus; Fujii, Tammy J.

2014-01-01

The Cassini Spacecraft and its ground system have been operational for over 16 years. Modernization presents several challenges due to the personnel, processes, and tools already invested and embedded into the current ground system structure. Every mission's ground system has its own unique complexities and challenges, involving various organizational units. As any mission from its inception to its execution, schedules are always tight. This forces GDS engineers to implement a working ground system that is not necessarily fully optimized. Ground system challenges increase as technology evolves and cyber threats become more sophisticated. Cassini's main challenges were due to its ground system existing before many security requirements were levied on the multi-mission tools and networks. This caused a domino effect on Cassini GDS tools that relied on outdated technological features. In the aerospace industry reliable and established technology is preferred over innovative yet less proven technology. Loss of data for a spacecraft mission can be catastrophic; therefore, there is a reluctance to make changes and updates to the ground system. Nevertheless, all missions and associated teams face the need to modernize their processes and tools. Systems development methods from well-known system analysis and design principles can be applied to many missions' ground systems. Modernization should always be considered, but should be done in such a way that it does not affect flexibility nor interfere with established practices. Cassini has accomplished a secure and efficient ground data system through periodic updates. The obstacles faced while performing the modernization of the Cassini ground system will be outlined, as well as the advantages and challenges that were encountered.

Through Kazan ASPERA to Modern Projects

NASA Astrophysics Data System (ADS)

Gusev, Alexander; Kitiashvili, Irina; Petrova, Natasha

Now the European Union form the Sixth Framework Programme. One of its the objects of the EU Programme is opening national researches and training programmes. The Russian PhD students and young astronomers have business and financial difficulties in access to modern databases and astronomical projects and so they has not been included in European overview of priorities. Modern requirements to the organization of observant projects on powerful telescopes assumes painstaking scientific computer preparation of the application. A rigid competition for observation time assume preliminary computer modeling of target object for success of the application. Kazan AstroGeoPhysics Partnership

The Problems of Contemporary Education Socio-Cultural Dimension of Military Education in Modern Russia

ERIC Educational Resources Information Center

Abramov, Alexsandr P.; Chuikov, Oleg E.; Gavrikov, Fedor A.; Ludwig, Sergey D.

2017-01-01

The article reveals the essence of the sociocultural approach as a universal tool which allows considering the process of modernization of cadet education in modern Russia in the complex determining its conditions and factors. The basic mechanisms of functioning of cadet education system are the processes that form the equilibrium diad…

Oscillatory Threshold Logic

PubMed Central

Borresen, Jon; Lynch, Stephen

2012-01-01

In the 1940s, the first generation of modern computers used vacuum tube oscillators as their principle components, however, with the development of the transistor, such oscillator based computers quickly became obsolete. As the demand for faster and lower power computers continues, transistors are themselves approaching their theoretical limit and emerging technologies must eventually supersede them. With the development of optical oscillators and Josephson junction technology, we are again presented with the possibility of using oscillators as the basic components of computers, and it is possible that the next generation of computers will be composed almost entirely of oscillatory devices. Here, we demonstrate how coupled threshold oscillators may be used to perform binary logic in a manner entirely consistent with modern computer architectures. We describe a variety of computational circuitry and demonstrate working oscillator models of both computation and memory. PMID:23173034

Untangling the complexity of blood coagulation network: use of computational modelling in pharmacology and diagnostics.

PubMed

Shibeko, Alexey M; Panteleev, Mikhail A

2016-05-01

Blood coagulation is a complex biochemical network that plays critical roles in haemostasis (a physiological process that stops bleeding on injury) and thrombosis (pathological vessel occlusion). Both up- and down-regulation of coagulation remain a major challenge for modern medicine, with the ultimate goal to correct haemostasis without causing thrombosis and vice versa. Mathematical/computational modelling is potentially an important tool for understanding blood coagulation disorders and their treatment. It can save a huge amount of time and resources, and provide a valuable alternative or supplement when clinical studies are limited, or not ethical, or technically impossible. This article reviews contemporary state of the art in the modelling of blood coagulation for practical purposes: to reveal the molecular basis of a disease, to understand mechanisms of drug action, to predict pharmacodynamics and drug-drug interactions, to suggest potential drug targets or to improve quality of diagnostics. Different model types and designs used for this are discussed. Functional mechanisms of procoagulant bypassing agents and investigations of coagulation inhibitors were the two particularly popular applications of computational modelling that gave non-trivial results. Yet, like any other tool, modelling has its limitations, mainly determined by insufficient knowledge of the system, uncertainty and unreliability of complex models. We show how to some extent this can be overcome and discuss what can be expected from the mathematical modelling of coagulation in not-so-far future. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

A browser-based event display for the CMS experiment at the LHC

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

Hategan, M.; McCauley, T.; Nguyen, P.

2012-01-01

The line between native and web applications is becoming increasingly blurred as modern web browsers are becoming powerful platforms on which applications can be run. Such applications are trivial to install and are readily extensible and easy to use. In an educational setting, web applications permit a way to deploy deploy tools in a highly-restrictive computing environment. The I2U2 collaboration has developed a browser-based event display for viewing events in data collected and released to the public by the CMS experiment at the LHC. The application itself reads a JSON event format and uses the JavaScript 3D rendering engine pre3d.more » The only requirement is a modern browser using HTML5 canvas. The event display has been used by thousands of high school students in the context of programs organized by I2U2, QuarkNet, and IPPOG. This browser-based approach to display of events can have broader usage and impact for experts and public alike.« less

Current applications of molecular imaging and luminescence-based techniques in traditional Chinese medicine.

PubMed

Li, Jinhui; Wan, Haitong; Zhang, Hong; Tian, Mei

2011-09-01

Traditional Chinese medicine (TCM), which is fundamentally different from Western medicine, has been widely investigated using various approaches. Cellular- or molecular-based imaging has been used to investigate and illuminate the various challenges identified and progress made using therapeutic methods in TCM. Insight into the processes of TCM at the cellular and molecular changes and the ability to image these processes will enhance our understanding of various diseases of TCM and will provide new tools to diagnose and treat patients. Various TCM therapies including herbs and formulations, acupuncture and moxibustion, massage, Gua Sha, and diet therapy have been analyzed using positron emission tomography, single photon emission computed tomography, functional magnetic resonance imaging and ultrasound and optical imaging. These imaging tools have kept pace with developments in molecular biology, nuclear medicine, and computer technology. We provide an overview of recent developments in demystifying ancient knowledge - like the power of energy flow and blood flow meridians, and serial naturopathies - which are essential to visually and vividly recognize the body using modern technology. In TCM, treatment can be individualized in a holistic or systematic view that is consistent with molecular imaging technologies. Future studies might include using molecular imaging in conjunction with TCM to easily diagnose or monitor patients naturally and noninvasively. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision.

PubMed

Wiewiórka, Marek S; Messina, Antonio; Pacholewska, Alicja; Maffioletti, Sergio; Gawrysiak, Piotr; Okoniewski, Michał J

2014-09-15

Many time-consuming analyses of next -: generation sequencing data can be addressed with modern cloud computing. The Apache Hadoop-based solutions have become popular in genomics BECAUSE OF: their scalability in a cloud infrastructure. So far, most of these tools have been used for batch data processing rather than interactive data querying. The SparkSeq software has been created to take advantage of a new MapReduce framework, Apache Spark, for next-generation sequencing data. SparkSeq is a general-purpose, flexible and easily extendable library for genomic cloud computing. It can be used to build genomic analysis pipelines in Scala and run them in an interactive way. SparkSeq opens up the possibility of customized ad hoc secondary analyses and iterative machine learning algorithms. This article demonstrates its scalability and overall fast performance by running the analyses of sequencing datasets. Tests of SparkSeq also prove that the use of cache and HDFS block size can be tuned for the optimal performance on multiple worker nodes. Available under open source Apache 2.0 license: https://bitbucket.org/mwiewiorka/sparkseq/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

SOURCE EXPLORER: Towards Web Browser Based Tools for Astronomical Source Visualization and Analysis

NASA Astrophysics Data System (ADS)

Young, M. D.; Hayashi, S.; Gopu, A.

2014-05-01

As a new generation of large format, high-resolution imagers come online (ODI, DECAM, LSST, etc.) we are faced with the daunting prospect of astronomical images containing upwards of hundreds of thousands of identifiable sources. Visualizing and interacting with such large datasets using traditional astronomical tools appears to be unfeasible, and a new approach is required. We present here a method for the display and analysis of arbitrarily large source datasets using dynamically scaling levels of detail, enabling scientists to rapidly move from large-scale spatial overviews down to the level of individual sources and everything in-between. Based on the recognized standards of HTML5+JavaScript, we enable observers and archival users to interact with their images and sources from any modern computer without having to install specialized software. We demonstrate the ability to produce large-scale source lists from the images themselves, as well as overlaying data from publicly available source ( 2MASS, GALEX, SDSS, etc.) or user provided source lists. A high-availability cluster of computational nodes allows us to produce these source maps on demand and customized based on user input. User-generated source lists and maps are persistent across sessions and are available for further plotting, analysis, refinement, and culling.

EIAGRID: In-field optimization of seismic data acquisition by real-time subsurface imaging using a remote GRID computing environment.

NASA Astrophysics Data System (ADS)

Heilmann, B. Z.; Vallenilla Ferrara, A. M.

2009-04-01

The constant growth of contaminated sites, the unsustainable use of natural resources, and, last but not least, the hydrological risk related to extreme meteorological events and increased climate variability are major environmental issues of today. Finding solutions for these complex problems requires an integrated cross-disciplinary approach, providing a unified basis for environmental science and engineering. In computer science, grid computing is emerging worldwide as a formidable tool allowing distributed computation and data management with administratively-distant resources. Utilizing these modern High Performance Computing (HPC) technologies, the GRIDA3 project bundles several applications from different fields of geoscience aiming to support decision making for reasonable and responsible land use and resource management. In this abstract we present a geophysical application called EIAGRID that uses grid computing facilities to perform real-time subsurface imaging by on-the-fly processing of seismic field data and fast optimization of the processing workflow. Even though, seismic reflection profiling has a broad application range spanning from shallow targets in a few meters depth to targets in a depth of several kilometers, it is primarily used by the hydrocarbon industry and hardly for environmental purposes. The complexity of data acquisition and processing poses severe problems for environmental and geotechnical engineering: Professional seismic processing software is expensive to buy and demands large experience from the user. In-field processing equipment needed for real-time data Quality Control (QC) and immediate optimization of the acquisition parameters is often not available for this kind of studies. As a result, the data quality will be suboptimal. In the worst case, a crucial parameter such as receiver spacing, maximum offset, or recording time turns out later to be inappropriate and the complete acquisition campaign has to be repeated. The EIAGRID portal provides an innovative solution to this problem combining state-of-the-art data processing methods and modern remote grid computing technology. In field-processing equipment is substituted by remote access to high performance grid computing facilities. The latter can be ubiquitously controlled by a user-friendly web-browser interface accessed from the field by any mobile computer using wireless data transmission technology such as UMTS (Universal Mobile Telecommunications System) or HSUPA/HSDPA (High-Speed Uplink/Downlink Packet Access). The complexity of data-manipulation and processing and thus also the time demanding user interaction is minimized by a data-driven, and highly automated velocity analysis and imaging approach based on the Common-Reflection-Surface (CRS) stack. Furthermore, the huge computing power provided by the grid deployment allows parallel testing of alternative processing sequences and parameter settings, a feature which considerably reduces the turn-around times. A shared data storage using georeferencing tools and data grid technology is under current development. It will allow to publish already accomplished projects, making results, processing workflows and parameter settings available in a transparent and reproducible way. Creating a unified database shared by all users will facilitate complex studies and enable the use of data-crossing techniques to incorporate results of other environmental applications hosted on the GRIDA3 portal.

Evaluating Modern Defenses Against Control Flow Hijacking

DTIC Science & Technology

2015-09-01

unsound and could introduce false negatives (opening up another possible set of attacks). CFG Construction using DSA We next evaluate the precision of CFG...Evaluating Modern Defenses Against Control Flow Hijacking by Ulziibayar Otgonbaatar Submitted to the Department of Electrical Engineering and...Computer Science in partial fulfillment of the requirements for the degree of Master of Science in Computer Science and Engineering at the MASSACHUSETTS

Translations on Eastern Europe, Scientific Affairs, Number 542.

DTIC Science & Technology

1977-04-18

transplanting human tissue has not as yet been given a final juridical approval like euthanasia, artificial insemination , abortion, birth control, and others...and data teleprocessing. This computer may also be used as a satellite computer for complex systems. The IZOT 310 has a large instruction...a well-known truth that modern science is using the most modern and leading technical facilities—from bathyscaphes to satellites , from gigantic

Resiliency in Future Cyber Combat

DTIC Science & Technology

2016-04-04

including the Internet , telecommunications networks, computer systems, and embed- ded processors and controllers.”6 One important point emerging from the...definition is that while the Internet is part of cyberspace, it is not all of cyberspace. Any computer processor capable of communicating with a...central proces- sor on a modern car are all part of cyberspace, although only some of them are routinely connected to the Internet . Most modern

Analysis of the knowledge and opinions of students and qualified dentists regarding the use of computers.

PubMed

Castelló Castañeda, Coral; Ríos Santos, Jose Vicente; Bullón, Pedro

2008-01-01

Dentists are currently required to make multiple diagnoses and treatment decisions every day and the information necessary to achieve this satisfactorily doubles in volume every five years. Knowledge therefore rapidly becomes out of date, so that it is often impossible to remember established information and assimilate new concepts. This may result in a significant lack of knowledge in the future, which would jeopardize the success of treatments. To remedy this situation and to prevent it, we nowadays have access to modern computing systems, with an extensive data base, which helps us to retain the information necessary for daily practice and access it instantaneously. The objectives of this study are therefore to determine how widespread the use of computing is in this environment and to determine the opinion of students and qualified dentists as regards its use in Dentistry. 90 people were chosen to take part in the study, divided into the following groups (students) (newly qualified dentists) (experts). It has been demonstrated that a high percentage (93.30%) use a computer, but that their level of computing knowledge is predominantly moderate. The place where a computer is used most is the home, which suggests that the majority own a computer. Analysis of the results obtained for evaluation of computers in teaching showed that the participants thought that it saved a great deal of time and had great potential for providing an image (in terms of marketing) and they considered it a very innovative and stimulating tool.

DTIC (Defense Technical Information Center) Model Action Plan for Incorporating DGIS (DOD Gateway Information System) Capabilities.

DTIC Science & Technology

1986-05-01

Information System (DGIS) is being developed to provide the DD crmjnj t with a modern tool to access diverse dtabaiees and extract information products...this community with a modern tool for accessing these databases and extracting information products from them. Since the Defense Technical Information...adjunct to DROLS xesults. The study , thereor. centerd around obtaining background information inside the unit on that unit’s users who request DROLS

Applying Dataflow Architecture and Visualization Tools to In Vitro Pharmacology Data Automation.

PubMed

Pechter, David; Xu, Serena; Kurtz, Marc; Williams, Steven; Sonatore, Lisa; Villafania, Artjohn; Agrawal, Sony

2016-12-01

The pace and complexity of modern drug discovery places ever-increasing demands on scientists for data analysis and interpretation. Data flow programming and modern visualization tools address these demands directly. Three different requirements-one for allosteric modulator analysis, one for a specialized clotting analysis, and one for enzyme global progress curve analysis-are reviewed, and their execution in a combined data flow/visualization environment is outlined. © 2016 Society for Laboratory Automation and Screening.

ESIF 2016: Modernizing Our Grid and Energy System

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

Van Becelaere, Kimberly

This 2016 annual report highlights work conducted at the Energy Systems Integration Facility (ESIF) in FY 2016, including grid modernization, high-performance computing and visualization, and INTEGRATE projects.

Computer Technology: State of the Art.

ERIC Educational Resources Information Center

Withington, Frederic G.

1981-01-01

Describes the nature of modern general-purpose computer systems, including hardware, semiconductor electronics, microprocessors, computer architecture, input output technology, and system control programs. Seven suggested readings are cited. (FM)

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.

cuSwift --- a suite of numerical integration methods for modelling planetary systems implemented in C/CUDA

NASA Astrophysics Data System (ADS)

Hellmich, S.; Mottola, S.; Hahn, G.; Kührt, E.; Hlawitschka, M.

2014-07-01

Simulations of dynamical processes in planetary systems represent an important tool for studying the orbital evolution of the systems [1--3]. Using modern numerical integration methods, it is possible to model systems containing many thousands of objects over timescales of several hundred million years. However, in general, supercomputers are needed to get reasonable simulation results in acceptable execution times [3]. To exploit the ever-growing computation power of Graphics Processing Units (GPUs) in modern desktop computers, we implemented cuSwift, a library of numerical integration methods for studying long-term dynamical processes in planetary systems. cuSwift can be seen as a re-implementation of the famous SWIFT integrator package written by Hal Levison and Martin Duncan. cuSwift is written in C/CUDA and contains different integration methods for various purposes. So far, we have implemented three algorithms: a 15th-order Radau integrator [4], the Wisdom-Holman Mapping (WHM) integrator [5], and the Regularized Mixed Variable Symplectic (RMVS) Method [6]. These algorithms treat only the planets as mutually gravitationally interacting bodies whereas asteroids and comets (or other minor bodies of interest) are treated as massless test particles which are gravitationally influenced by the massive bodies but do not affect each other or the massive bodies. The main focus of this work is on the symplectic methods (WHM and RMVS) which use a larger time step and thus are capable of integrating many particles over a large time span. As an additional feature, we implemented the non-gravitational Yarkovsky effect as described by M. Brož [7]. With cuSwift, we show that the use of modern GPUs makes it possible to speed up these methods by more than one order of magnitude compared to the single-core CPU implementation, thereby enabling modest workstation computers to perform long-term dynamical simulations. We use these methods to study the influence of the Yarkovsky effect on resonant asteroids. We present first results and compare them with integrations done with the original algorithms implemented in SWIFT in order to assess the numerical precision of cuSwift and to demonstrate the speed-up we achieved using the GPU.

Seismic Window Selection and Misfit Measurements for Global Adjoint Tomography

NASA Astrophysics Data System (ADS)

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

2013-12-01

Global Adjoint Tomography requires fast parallel processing of large datasets. After obtaing the preprocessed observed and synthetic seismograms, we use the open source software packages FLEXWIN (Maggi et al. 2007) to select time windows and MEASURE_ADJ to make measurements. These measurements define adjoint sources for data assimilation. Previous versions of these tools work on a pair of SAC files---observed and synthetic seismic data for the same component and station, and loop over all seismic records associated with one earthquake. Given the large number of stations and earthquakes, the frequent read and write operations create severe I/O bottlenecks on modern computing platforms. We present new versions of these tools utilizing a new seismic data format, namely the Adaptive Seismic Data Format(ASDF). This new format shows superior scalability for applications on high-performance computers and accommodates various types of data, including earthquake, industry and seismic interferometry datasets. ASDF also provides user-friendly APIs, which can be easily integrated into the adjoint tomography workflow and combined with other data processing tools. In addition to solving the I/O bottleneck, we are making several improvements to these tools. For example, FLEXWIN is tuned to select windows for different types of earthquakes. To capture their distinct features, we categorize earthquakes by their depths and frequency bands. Moreover, instead of only picking phases between the first P arrival and the surface-wave arrivals, our aim is to select and assimilate many other later prominent phases in adjoint tomography. For example, in the body-wave band (17 s - 60 s), we include SKS, sSKS and their multiple, while in the surface-wave band (60 s - 120 s) we incorporate major-arc surface waves.

COMBINE*: An integrated opto-mechanical tool for laser performance modeling

NASA Astrophysics Data System (ADS)

Rehak, M.; Di Nicola, J. M.

2015-02-01

Accurate modeling of thermal, mechanical and optical processes is important for achieving reliable, high-performance high energy lasers such as those at the National Ignition Facility [1] (NIF). The need for this capability is even more critical for high average power, high repetition rate applications. Modeling the effects of stresses and temperature fields on optical properties allows for optimal design of optical components and more generally of the architecture of the laser system itself. Stresses change the indices of refractions and induce inhomogeneities and anisotropy. We present a modern, integrated analysis tool that efficiently produces reliable results that are used in our laser propagation tools such as VBL [5]. COMBINE is built on and supplants the existing legacy tools developed for the previous generations of lasers at LLNL but also uses commercially available mechanical finite element codes ANSYS or COMSOL (including computational fluid dynamics). The COMBINE code computes birefringence and wave front distortions due to mechanical stresses on lenses and slabs of arbitrary geometry. The stresses calculated typically originate from mounting support, vacuum load, gravity, heat absorption and/or attending cooling. Of particular importance are the depolarization and detuning effects of nonlinear crystals due to thermal loading. Results are given in the form of Jones matrices, depolarization maps and wave front distributions. An incremental evaluation of Jones matrices and ray propagation in a 3D mesh with a stress and temperature field is performed. Wavefront and depolarization maps are available at the optical aperture and at slices within the optical element. The suite is validated, user friendly, supported, documented and amenable to collaborative development. * COMBINE stands for Code for Opto-Mechanical Birefringence Integrated Numerical Evaluations.

Development of an Adaptable Display and Diagnostic System for the Evaluation of Tropical Cyclone Forecasts

NASA Astrophysics Data System (ADS)

Kucera, P. A.; Burek, T.; Halley-Gotway, J.

2015-12-01

NCAR's Joint Numerical Testbed Program (JNTP) focuses on the evaluation of experimental forecasts of tropical cyclones (TCs) with the goal of developing new research tools and diagnostic evaluation methods that can be transitioned to operations. Recent activities include the development of new TC forecast verification methods and the development of an adaptable TC display and diagnostic system. The next generation display and diagnostic system is being developed to support evaluation needs of the U.S. National Hurricane Center (NHC) and broader TC research community. The new hurricane display and diagnostic capabilities allow forecasters and research scientists to more deeply examine the performance of operational and experimental models. The system is built upon modern and flexible technology that includes OpenLayers Mapping tools that are platform independent. The forecast track and intensity along with associated observed track information are stored in an efficient MySQL database. The system provides easy-to-use interactive display system, and provides diagnostic tools to examine forecast track stratified by intensity. Consensus forecasts can be computed and displayed interactively. The system is designed to display information for both real-time and for historical TC cyclones. The display configurations are easily adaptable to meet the needs of the end-user preferences. Ongoing enhancements include improving capabilities for stratification and evaluation of historical best tracks, development and implementation of additional methods to stratify and compute consensus hurricane track and intensity forecasts, and improved graphical display tools. The display is also being enhanced to incorporate gridded forecast, satellite, and sea surface temperature fields. The presentation will provide an overview of the display and diagnostic system development and demonstration of the current capabilities.

A WebGL Tool for Visualizing the Topology of the Sun's Coronal Magnetic Field

NASA Astrophysics Data System (ADS)

Duffy, A.; Cheung, C.; DeRosa, M. L.

2012-12-01

We present a web-based, topology-viewing tool that allows users to visualize the geometry and topology of the Sun's 3D coronal magnetic field in an interactive manner. The tool is implemented using, open-source, mature, modern web technologies including WebGL, jQuery, HTML 5, and CSS 3, which are compatible with nearly all modern web browsers. As opposed to the traditional method of visualization, which involves the downloading and setup of various software packages-proprietary and otherwise-the tool presents a clean interface that allows the user to easily load and manipulate the model, while also offering great power to choose which topological features are displayed. The tool accepts data encoded in the JSON open format that has libraries available for nearly every major programming language, making it simple to generate the data.

Parallel algorithm for solving Kepler’s equation on Graphics Processing Units: Application to analysis of Doppler exoplanet searches

NASA Astrophysics Data System (ADS)

Ford, Eric B.

2009-05-01

We present the results of a highly parallel Kepler equation solver using the Graphics Processing Unit (GPU) on a commercial nVidia GeForce 280GTX and the "Compute Unified Device Architecture" (CUDA) programming environment. We apply this to evaluate a goodness-of-fit statistic (e.g., χ2) for Doppler observations of stars potentially harboring multiple planetary companions (assuming negligible planet-planet interactions). Given the high-dimensionality of the model parameter space (at least five dimensions per planet), a global search is extremely computationally demanding. We expect that the underlying Kepler solver and model evaluator will be combined with a wide variety of more sophisticated algorithms to provide efficient global search, parameter estimation, model comparison, and adaptive experimental design for radial velocity and/or astrometric planet searches. We tested multiple implementations using single precision, double precision, pairs of single precision, and mixed precision arithmetic. We find that the vast majority of computations can be performed using single precision arithmetic, with selective use of compensated summation for increased precision. However, standard single precision is not adequate for calculating the mean anomaly from the time of observation and orbital period when evaluating the goodness-of-fit for real planetary systems and observational data sets. Using all double precision, our GPU code outperforms a similar code using a modern CPU by a factor of over 60. Using mixed precision, our GPU code provides a speed-up factor of over 600, when evaluating nsys > 1024 models planetary systems each containing npl = 4 planets and assuming nobs = 256 observations of each system. We conclude that modern GPUs also offer a powerful tool for repeatedly evaluating Kepler's equation and a goodness-of-fit statistic for orbital models when presented with a large parameter space.

Reliability based design optimization: Formulations and methodologies

NASA Astrophysics Data System (ADS)

Agarwal, Harish

Modern products ranging from simple components to complex systems should be designed to be optimal and reliable. The challenge of modern engineering is to ensure that manufacturing costs are reduced and design cycle times are minimized while achieving requirements for performance and reliability. If the market for the product is competitive, improved quality and reliability can generate very strong competitive advantages. Simulation based design plays an important role in designing almost any kind of automotive, aerospace, and consumer products under these competitive conditions. Single discipline simulations used for analysis are being coupled together to create complex coupled simulation tools. This investigation focuses on the development of efficient and robust methodologies for reliability based design optimization in a simulation based design environment. Original contributions of this research are the development of a novel efficient and robust unilevel methodology for reliability based design optimization, the development of an innovative decoupled reliability based design optimization methodology, the application of homotopy techniques in unilevel reliability based design optimization methodology, and the development of a new framework for reliability based design optimization under epistemic uncertainty. The unilevel methodology for reliability based design optimization is shown to be mathematically equivalent to the traditional nested formulation. Numerical test problems show that the unilevel methodology can reduce computational cost by at least 50% as compared to the nested approach. The decoupled reliability based design optimization methodology is an approximate technique to obtain consistent reliable designs at lesser computational expense. Test problems show that the methodology is computationally efficient compared to the nested approach. A framework for performing reliability based design optimization under epistemic uncertainty is also developed. A trust region managed sequential approximate optimization methodology is employed for this purpose. Results from numerical test studies indicate that the methodology can be used for performing design optimization under severe uncertainty.

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

Yang, Y M; Bush, K; Han, B

Purpose: Accurate and fast dose calculation is a prerequisite of precision radiation therapy in modern photon and particle therapy. While Monte Carlo (MC) dose calculation provides high dosimetric accuracy, the drastically increased computational time hinders its routine use. Deterministic dose calculation methods are fast, but problematic in the presence of tissue density inhomogeneity. We leverage the useful features of deterministic methods and MC to develop a hybrid dose calculation platform with autonomous utilization of MC and deterministic calculation depending on the local geometry, for optimal accuracy and speed. Methods: Our platform utilizes a Geant4 based “localized Monte Carlo” (LMC) methodmore » that isolates MC dose calculations only to volumes that have potential for dosimetric inaccuracy. In our approach, additional structures are created encompassing heterogeneous volumes. Deterministic methods calculate dose and energy fluence up to the volume surfaces, where the energy fluence distribution is sampled into discrete histories and transported using MC. Histories exiting the volume are converted back into energy fluence, and transported deterministically. By matching boundary conditions at both interfaces, deterministic dose calculation account for dose perturbations “downstream” of localized heterogeneities. Hybrid dose calculation was performed for water and anthropomorphic phantoms. Results: We achieved <1% agreement between deterministic and MC calculations in the water benchmark for photon and proton beams, and dose differences of 2%–15% could be observed in heterogeneous phantoms. The saving in computational time (a factor ∼4–7 compared to a full Monte Carlo dose calculation) was found to be approximately proportional to the volume of the heterogeneous region. Conclusion: Our hybrid dose calculation approach takes advantage of the computational efficiency of deterministic method and accuracy of MC, providing a practical tool for high performance dose calculation in modern RT. The approach is generalizable to all modalities where heterogeneities play a large role, notably particle therapy.« less

The Helicopter Antenna Radiation Prediction Code (HARP)

NASA Technical Reports Server (NTRS)

Klevenow, F. T.; Lynch, B. G.; Newman, E. H.; Rojas, R. G.; Scheick, J. T.; Shamansky, H. T.; Sze, K. Y.

1990-01-01

The first nine months effort in the development of a user oriented computer code, referred to as the HARP code, for analyzing the radiation from helicopter antennas is described. The HARP code uses modern computer graphics to aid in the description and display of the helicopter geometry. At low frequencies the helicopter is modeled by polygonal plates, and the method of moments is used to compute the desired patterns. At high frequencies the helicopter is modeled by a composite ellipsoid and flat plates, and computations are made using the geometrical theory of diffraction. The HARP code will provide a user friendly interface, employing modern computer graphics, to aid the user to describe the helicopter geometry, select the method of computation, construct the desired high or low frequency model, and display the results.

Virtual anthropology: useful radiological tools for age assessment in clinical forensic medicine and thanatology.

PubMed

Dedouit, Fabrice; Saint-Martin, Pauline; Mokrane, Fatima-Zohra; Savall, Frédéric; Rousseau, Hervé; Crubézy, Eric; Rougé, Daniel; Telmon, Norbert

2015-09-01

Virtual anthropology consists of the introduction of modern slice imaging to biological and forensic anthropology. Thanks to this non-invasive scientific revolution, some classifications and staging systems, first based on dry bone analysis, can be applied to cadavers with no need for specific preparation, as well as to living persons. Estimation of bone and dental age is one of the possibilities offered by radiology. Biological age can be estimated in clinical forensic medicine as well as in living persons. Virtual anthropology may also help the forensic pathologist to estimate a deceased person's age at death, which together with sex, geographical origin and stature, is one of the important features determining a biological profile used in reconstructive identification. For this forensic purpose, the radiological tools used are multislice computed tomography and, more recently, X-ray free imaging techniques such as magnetic resonance imaging and ultrasound investigations. We present and discuss the value of these investigations for age estimation in anthropology.

Management information system of medical equipment using mobile devices

NASA Astrophysics Data System (ADS)

Núñez, C.; Castro, D.

2011-09-01

The large numbers of technologies currently incorporated into mobile devices transform them into excellent tools for capture and to manage the information, because of the increasing computing power and storage that allow to add many miscellaneous applications. In order to obtain benefits of these technologies, in the biomedical engineering field, it was developed a mobile information system for medical equipment management. The central platform for the system it's a mobile phone, which by a connection with a web server, it's capable to send and receive information relative to any medical equipment. Decoding a type of barcodes, known as QR-Codes, the management process is simplified and improved. These barcodes identified the medical equipments in a database, when these codes are photographed and decoded with the mobile device, you can access to relevant information about the medical equipment in question. This Project in it's actual state is a basic support tool for the maintenance of medical equipment. It is also a modern alternative, competitive and economic in the actual market.

Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

NASA Astrophysics Data System (ADS)

Hošek, Petr; Spiwok, Vojtěch

2016-01-01

Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.

The Human Face as a Dynamic Tool for Social Communication.

PubMed

Jack, Rachael E; Schyns, Philippe G

2015-07-20

As a highly social species, humans frequently exchange social information to support almost all facets of life. One of the richest and most powerful tools in social communication is the face, from which observers can quickly and easily make a number of inferences - about identity, gender, sex, age, race, ethnicity, sexual orientation, physical health, attractiveness, emotional state, personality traits, pain or physical pleasure, deception, and even social status. With the advent of the digital economy, increasing globalization and cultural integration, understanding precisely which face information supports social communication and which produces misunderstanding is central to the evolving needs of modern society (for example, in the design of socially interactive digital avatars and companion robots). Doing so is challenging, however, because the face can be thought of as comprising a high-dimensional, dynamic information space, and this impacts cognitive science and neuroimaging, and their broader applications in the digital economy. New opportunities to address this challenge are arising from the development of new methods and technologies, coupled with the emergence of a modern scientific culture that embraces cross-disciplinary approaches. Here, we briefly review one such approach that combines state-of-the-art computer graphics, psychophysics and vision science, cultural psychology and social cognition, and highlight the main knowledge advances it has generated. In the light of current developments, we provide a vision of the future directions in the field of human facial communication within and across cultures. Copyright © 2015 Elsevier Ltd. All rights reserved.

The EarthKAM project: creating space imaging tools for teaching and learning

NASA Astrophysics Data System (ADS)

Dodson, Holly; Levin, Paula; Ride, Sally; Souviney, Randall

2000-07-01

The EarthKAM Project is a NASA-supported partnership of secondary and university students with Earth Science and educational researchers. This report describes an ongoing series of activities that more effectively integrate Earth images into classroom instruction. In this project, students select and analyze images of the Earth taken during Shuttle flights and use the tools of modern science (computers, data analysis tools and the Internet) to disseminate the images and results of their research. A related study, the Visualizing Earth Project, explores in greater detail the cognitive aspects of image processing and the educational potential of visualizations in science teaching and learning. The content and organization of the EarthKAM datasystem of images and metadata are also described. An associated project is linking this datasystem of images with the Getty Thesaurus of Geographic Names, which will allow users to access a wide range of geographic and political information for the regions shown in EarthKAM images. Another project will provide tools for automated feature extraction from EarthKAM images. In order to make EarthKAM resources available to a larger number of schools, the next important goal is to create an integrated datasystem that combines iterative resource validation and publication, with multimedia management of instructional materials.

Computational methods in preformulation study for pharmaceutical solid dosage forms of therapeutic proteins

NASA Astrophysics Data System (ADS)

Majee, Sutapa Biswas; Biswas, Gopa Roy

2017-06-01

Design and delivery of protein-based biopharmaceuticals needs detailed planning and strict monitoring of intermediate processing steps, storage conditions and container-closure system to ensure a stable, elegant and biopharmaceutically acceptable dosage form. Selection of manufacturing process variables and conditions along with packaging specifications can be achieved through properly designed preformulation study protocol for the formulation. Thermodynamic stability and biological activity of therapeutic proteins depend on folding-unfolding and three-dimensional packing dynamics of amino acid network in the protein molecule. Lack of favourable environment may cause protein aggregation with loss in activity and even fatal immunological reaction. Although lyophilization can enhance the stability of protein-based formulations in the solid state, it can induce protein unfolding leading to thermodynamic instability. Formulation stabilizers such as preservatives can also result in aggregation of therapeutic proteins. Modern instrumental techniques in conjunction with computational tools enable rapid and accurate prediction of amino acid sequence, thermodynamic parameters associated with protein folding and detection of aggregation "hot-spots." Globular proteins pose a challenge during investigations on their aggregation propensity. Biobetter therapeutic monoclonal antibodies with enhanced stability, solubility and reduced immunogenic potential can be designed through mutation of aggregation-prone zones. The objective of the present review article is to focus on the various analytical methods and computational approaches used in the study of thermodynamic stability and aggregation tendency of therapeutic proteins, with an aim to develop optimal and marketable formulation. Knowledge of protein dynamics through application of computational tools will provide the essential inputs and relevant information for successful and meaningful completion of preformulation studies on solid dosage forms of therapeutic proteins.

Molecular structure input on the web.

PubMed

Ertl, Peter

2010-02-02

A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

TauFactor: An open-source application for calculating tortuosity factors from tomographic data

NASA Astrophysics Data System (ADS)

Cooper, S. J.; Bertei, A.; Shearing, P. R.; Kilner, J. A.; Brandon, N. P.

TauFactor is a MatLab application for efficiently calculating the tortuosity factor, as well as volume fractions, surface areas and triple phase boundary densities, from image based microstructural data. The tortuosity factor quantifies the apparent decrease in diffusive transport resulting from convolutions of the flow paths through porous media. TauFactor was originally developed to improve the understanding of electrode microstructures for batteries and fuel cells; however, the tortuosity factor has been of interest to a wide range of disciplines for over a century, including geoscience, biology and optics. It is still common practice to use correlations, such as that developed by Bruggeman, to approximate the tortuosity factor, but in recent years the increasing availability of 3D imaging techniques has spurred interest in calculating this quantity more directly. This tool provides a fast and accurate computational platform applicable to the big datasets (>108 voxels) typical of modern tomography, without requiring high computational power.

Current Developments in Machine Learning Techniques in Biological Data Mining.

PubMed

Dumancas, Gerard G; Adrianto, Indra; Bello, Ghalib; Dozmorov, Mikhail

2017-01-01

This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under Bioinformatics and Biology Insights aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques. Machine learning methods in particular, a subfield of computer science, have evolved as an indispensable tool applied to a wide spectrum of bioinformatics applications. Thus, it is broadly used to investigate the underlying mechanisms leading to a specific disease, as well as the biomarker discovery process. With a growth in this specific area of science comes the need to access up-to-date, high-quality scholarly articles that will leverage the knowledge of scientists and researchers in the various applications of machine learning techniques in mining biological data.

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research.

PubMed

Yaniv, Ziv; Lowekamp, Bradley C; Johnson, Hans J; Beare, Richard

2018-06-01

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks .

The Computational Ecologist’s Toolbox

EPA Science Inventory

Computational ecology, nestled in the broader field of data science, is an interdisciplinary field that attempts to improve our understanding of complex ecological systems through the use of modern computational methods. Computational ecology is based on a union of competence in...

Dimensioning appropriate technical and economic parameters of elements in urban distribution power nets based on discrete fast marching method

NASA Astrophysics Data System (ADS)

Afanasyev, A. P.; Bazhenov, R. I.; Luchaninov, D. V.

2018-05-01

The main purpose of the research is to develop techniques for defining the best technical and economic trajectories of cables in urban power systems. The proposed algorithms of calculation of the routes for laying cables take into consideration topological, technical and economic features of the cabling. The discrete option of an algorithm Fast marching method is applied as a calculating tool. It has certain advantages compared to other approaches. In particular, this algorithm is cost-effective to compute, therefore, it is not iterative. Trajectories of received laying cables are considered as optimal ones from the point of view of technical and economic criteria. They correspond to the present rules of modern urban development.

Virtual probing system for medical volume data

NASA Astrophysics Data System (ADS)

Xiao, Yongfei; Fu, Yili; Wang, Shuguo

2007-12-01

Because of the huge computation in 3D medical data visualization, looking into its inner data interactively is always a problem to be resolved. In this paper, we present a novel approach to explore 3D medical dataset in real time by utilizing a 3D widget to manipulate the scanning plane. With the help of the 3D texture property in modern graphics card, a virtual scanning probe is used to explore oblique clipping plane of medical volume data in real time. A 3D model of the medical dataset is also rendered to illustrate the relationship between the scanning-plane image and the other tissues in medical data. It will be a valuable tool in anatomy education and understanding of medical images in the medical research.

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

Germain, Shawn

Nuclear Power Plant (NPP) refueling outages create some of the most challenging activities the utilities face in both tracking and coordinating thousands of activities in a short period of time. Other challenges, including nuclear safety concerns arising from atypical system configurations and resource allocation issues, can create delays and schedule overruns, driving up outage costs. Today the majority of the outage communication is done using processes that do not take advantage of advances in modern technologies that enable enhanced communication, collaboration and information sharing. Some of the common practices include: runners that deliver paper-based requests for approval, radios, telephones, desktopmore » computers, daily schedule printouts, and static whiteboards that are used to display information. Many gains have been made to reduce the challenges facing outage coordinators; however; new opportunities can be realized by utilizing modern technological advancements in communication and information tools that can enhance the collective situational awareness of plant personnel leading to improved decision-making. Ongoing research as part of the Light Water Reactor Sustainability Program (LWRS) has been targeting NPP outage improvement. As part of this research, various applications of collaborative software have been demonstrated through pilot project utility partnerships. Collaboration software can be utilized as part of the larger concept of Computer-Supported Cooperative Work (CSCW). Collaborative software can be used for emergent issue resolution, Outage Control Center (OCC) displays, and schedule monitoring. Use of collaboration software enables outage staff and subject matter experts (SMEs) to view and update critical outage information from any location on site or off.« less

The prevalence of encoded digital trace evidence in the nonfile space of computer media(,) (.).

PubMed

Garfinkel, Simson L

2014-09-01

Forensically significant digital trace evidence that is frequently present in sectors of digital media not associated with allocated or deleted files. Modern digital forensic tools generally do not decompress such data unless a specific file with a recognized file type is first identified, potentially resulting in missed evidence. Email addresses are encoded differently for different file formats. As a result, trace evidence can be categorized as Plain in File (PF), Encoded in File (EF), Plain Not in File (PNF), or Encoded Not in File (ENF). The tool bulk_extractor finds all of these formats, but other forensic tools do not. A study of 961 storage devices purchased on the secondary market and shows that 474 contained encoded email addresses that were not in files (ENF). Different encoding formats are the result of different application programs that processed different kinds of digital trace evidence. Specific encoding formats explored include BASE64, GZIP, PDF, HIBER, and ZIP. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Journal of Forensic Sciences published by Wiley Periodicals, Inc. on behalf of American Academy of Forensic Sciences.

Experimenter's laboratory for visualized interactive science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Klemp, Marjorie K.; Lasater, Sally W.; Szczur, Marti R.; Klemp, Joseph B.

1992-01-01

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

Experimenter's laboratory for visualized interactive science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Klemp, Marjorie K.; Lasater, Sally W.; Szczur, Marti R.; Klemp, Joseph B.

1993-01-01

The science activities of the 1990's will require the analysis of complex phenomena and large diverse sets of data. In order to meet these needs, we must take advantage of advanced user interaction techniques: modern user interface tools; visualization capabilities; affordable, high performance graphics workstations; and interoperatable data standards and translator. To meet these needs, we propose to adopt and upgrade several existing tools and systems to create an experimenter's laboratory for visualized interactive science. Intuitive human-computer interaction techniques have already been developed and demonstrated at the University of Colorado. A Transportable Applications Executive (TAE+), developed at GSFC, is a powerful user interface tool for general purpose applications. A 3D visualization package developed by NCAR provides both color-shaded surface displays and volumetric rendering in either index or true color. The Network Common Data Form (NetCDF) data access library developed by Unidata supports creation, access and sharing of scientific data in a form that is self-describing and network transparent. The combination and enhancement of these packages constitutes a powerful experimenter's laboratory capable of meeting key science needs of the 1990's. This proposal encompasses the work required to build and demonstrate this capability.

The Capability Portfolio Analysis Tool (CPAT): A Mixed Integer Linear Programming Formulation for Fleet Modernization Analysis (Version 2.0.2).

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

Waddell, Lucas; Muldoon, Frank; Henry, Stephen Michael

In order to effectively plan the management and modernization of their large and diverse fleets of vehicles, Program Executive Office Ground Combat Systems (PEO GCS) and Program Executive Office Combat Support and Combat Service Support (PEO CS&CSS) commis- sioned the development of a large-scale portfolio planning optimization tool. This software, the Capability Portfolio Analysis Tool (CPAT), creates a detailed schedule that optimally prioritizes the modernization or replacement of vehicles within the fleet - respecting numerous business rules associated with fleet structure, budgets, industrial base, research and testing, etc., while maximizing overall fleet performance through time. This paper contains a thor-more » ough documentation of the terminology, parameters, variables, and constraints that comprise the fleet management mixed integer linear programming (MILP) mathematical formulation. This paper, which is an update to the original CPAT formulation document published in 2015 (SAND2015-3487), covers the formulation of important new CPAT features.« less

How Computer Graphics Work.

ERIC Educational Resources Information Center

Prosise, Jeff

This document presents the principles behind modern computer graphics without straying into the arcane languages of mathematics and computer science. Illustrations accompany the clear, step-by-step explanations that describe how computers draw pictures. The 22 chapters of the book are organized into 5 sections. "Part 1: Computer Graphics in…

Application of Modern Fortran to Spacecraft Trajectory Design and Optimization

NASA Technical Reports Server (NTRS)

Williams, Jacob; Falck, Robert D.; Beekman, Izaak B.

2018-01-01

In this paper, applications of the modern Fortran programming language to the field of spacecraft trajectory optimization and design are examined. Modern object-oriented Fortran has many advantages for scientific programming, although many legacy Fortran aerospace codes have not been upgraded to use the newer standards (or have been rewritten in other languages perceived to be more modern). NASA's Copernicus spacecraft trajectory optimization program, originally a combination of Fortran 77 and Fortran 95, has attempted to keep up with modern standards and makes significant use of the new language features. Various algorithms and methods are presented from trajectory tools such as Copernicus, as well as modern Fortran open source libraries and other projects.

Analysis of Defenses Against Code Reuse Attacks on Modern and New Architectures

DTIC Science & Technology

2015-09-01

soundness or completeness. An incomplete analysis will produce extra edges in the CFG that might allow an attacker to slip through. An unsound analysis...Analysis of Defenses Against Code Reuse Attacks on Modern and New Architectures by Isaac Noah Evans Submitted to the Department of Electrical...Engineering and Computer Science in partial fulfillment of the requirements for the degree of Master of Engineering in Electrical Engineering and Computer

Body metaphors--reading the body in contemporary culture.

PubMed

Skara, Danica

2004-01-01

This paper addresses the linguistic reframing of the human body in contemporary culture. Our aim is to provide a linguistic description of the ways in which the body is represented in modern English language. First, we will try to focus on body metaphors in general. We have collected a sample of 300 words and phrases functioning as body metaphors in modern English language. Reading the symbolism of the body we are witnessing changes in the basic metaphorical structuring of the human body. The results show that new vocabulary binds different fields of knowledge associated with machines and human beings according to a shared textual frame: human as computer and computer as human metaphor. Humans are almost blended with computers and vice versa. This metaphorical use of the human body and its parts reveals not only currents of unconscious though but also the structures of modern society and culture.

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.

Root-cause estimation of ultrasonic scattering signatures within a complex textured titanium

NASA Astrophysics Data System (ADS)

Blackshire, James L.; Na, Jeong K.; Freed, Shaun

2016-02-01

The nondestructive evaluation of polycrystalline materials has been an active area of research for many decades, and continues to be an area of growth in recent years. Titanium alloys in particular have become a critical material system used in modern turbine engine applications, where an evaluation of the local microstructure properties of engine disk/blade components is desired for performance and remaining life assessments. Current NDE methods are often limited to estimating ensemble material properties or detecting localized voids, inclusions, or damage features within a material. Recent advances in computational NDE and material science characterization methods are providing new and unprecedented access to heterogeneous material properties, which permits microstructure-sensing interactions to be studied in detail. In the present research, Integrated Computational Materials Engineering (ICME) methods and tools are being leveraged to gain a comprehensive understanding of root-cause ultrasonic scattering processes occurring within a textured titanium aerospace material. A combination of destructive, nondestructive, and computational methods are combined within the ICME framework to collect, holistically integrate, and study complex ultrasound scattering using realistic 2-dimensional representations of the microstructure properties. Progress towards validating the computational sensing methods are discussed, along with insight into the key scattering processes occurring within the bulk microstructure, and how they manifest in pulse-echo immersion ultrasound measurements.

Federal Aviation Administration : challenges in modernizing the agency

DOT National Transportation Integrated Search

2000-02-01

FAA's efforts to implement initiatives in five key areas-air traffic control modernization, procurement and personnel reform, aviation safety, aviation and computer security, and financial management-have met with limited success. For example, FAA ha...

Preparing Dairy Technologists

ERIC Educational Resources Information Center

Sliva, William R.

1977-01-01

The size of modern dairy plant operations has led to extreme specialization in product manufacturing, milk processing, microbiological analysis, chemical and mathematical computations. Morrisville Agricultural and Technical College, New York, has modernized its curricula to meet these changes. (HD)

[Application of water jet ERBEJET 2 in salivary glands surgery].

PubMed

Gasiński, Mateusz; Modrzejewski, Maciej; Cenda, Paweł; Nazim-Zygadło, Elzbieta; Kozok, Andrzej; Dobosz, Paweł

2009-09-01

Anatomical location of salivary glands requires from surgeon high precision during the operation in this site. Waterjet is one of the modern tools which allows to perform "minimal invasive" operating procedure. This tool helps to separate pathological structures from healthy tissue with a stream of high pressure saline pumped to the operating area via special designed applicators. Stream of fluid is generated by double piston pummp under 1 to 80 bar pressure that can be regulated. This allows to precise remove tumors, spare nerves and vessels in glandular tissue and minimize use of electrocoagulation. Waterjet is a modern tool that can help to improve the safety of patients and comfort of surgeon's work.

Modern CACSD using the Robust-Control Toolbox

NASA Technical Reports Server (NTRS)

Chiang, Richard Y.; Safonov, Michael G.

1989-01-01

The Robust-Control Toolbox is a collection of 40 M-files which extend the capability of PC/PRO-MATLAB to do modern multivariable robust control system design. Included are robust analysis tools like singular values and structured singular values, robust synthesis tools like continuous/discrete H(exp 2)/H infinity synthesis and Linear Quadratic Gaussian Loop Transfer Recovery methods and a variety of robust model reduction tools such as Hankel approximation, balanced truncation and balanced stochastic truncation, etc. The capabilities of the toolbox are described and illustated with examples to show how easily they can be used in practice. Examples include structured singular value analysis, H infinity loop-shaping and large space structure model reduction.

Student Perceived Importance and Correlations of Selected Computer Literacy Course Topics

ERIC Educational Resources Information Center

Ciampa, Mark

2013-01-01

Traditional college-level courses designed to teach computer literacy are in a state of flux. Today's students have high rates of access to computing technology and computer ownership, leading many policy decision makers to conclude that students already are computer literate and thus computer literacy courses are dinosaurs in a modern digital…

Visions of the Future - the Changing Role of Actors in Data-Intensive Science

NASA Astrophysics Data System (ADS)

Schäfer, L.; Klump, J. F.

2013-12-01

Around the world scientific disciplines are increasingly facing the challenge of a burgeoning volume of research data. This data avalanche consists of a stream of information generated from sensors and scientific instruments, digital recordings, social-science surveys or drawn from the World Wide Web. All areas of the scientific economy are affected by this rapid growth in data, from the logging of digs in Archaeology, telescope data with observations of distant galaxies in Astrophysics or data from polls and surveys in the Social Sciences. The challenge for science is not only to process the data through analysis, reduction and visualization, but also to set up infrastructures for provisioning and storing the data. The rise of new technologies and developments also poses new challenges for the actors in the area of research data infrastructures. Libraries, as one of the actors, enable access to digital media and support the publication of research data and its long-term archiving. Digital media and research data, however, introduce new aspects into the libraries' range of activities. How are we to imagine the library of the future? The library as an interface to the computer centers? Will library and computer center fuse into a new service unit? What role will scientific publishers play in future? Currently the traditional form of publication still carry greater weight - articles for conferences and journals. But will this still be the case in future? New forms of publication are already making their presence felt. The tasks of the computer centers may also change. Yesterday their remit was provisioning of rapid hardware, whereas now everything revolves around the topic of data and services. Finally, how about the researchers themselves? Not such a long time ago, Geoscience was not necessarily seen as linked to Computer Science. Nowadays, modern Geoscience relies heavily on IT and its techniques. Thus, in how far will the profile of the modern geoscientist change? This gives rise to the question of what tools are required to locate and pursue the correct course in a networked world. One tool from the area of innovation management is the scenario technique. This poster will outline visions of the future as possible developments of the scientific world in 2020 (or later). The scenarios presented will show possible developments - both positive and negative. It is up then to the actors themselves to define their own position in this context, to rethink it and consider steps that can achieve a positive development for the future.

Verification and Validation Strategy for LWRS Tools

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

Carl M. Stoots; Richard R. Schultz; Hans D. Gougar

2012-09-01

One intension of the Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) program is to create advanced computational tools for safety assessment that enable more accurate representation of a nuclear power plant safety margin. These tools are to be used to study the unique issues posed by lifetime extension and relicensing of the existing operating fleet of nuclear power plants well beyond their first license extension period. The extent to which new computational models / codes such as RELAP-7 can be used for reactor licensing / relicensing activities depends mainly upon the thoroughness with which they have been verifiedmore » and validated (V&V). This document outlines the LWRS program strategy by which RELAP-7 code V&V planning is to be accomplished. From the perspective of developing and applying thermal-hydraulic and reactivity-specific models to reactor systems, the US Nuclear Regulatory Commission (NRC) Regulatory Guide 1.203 gives key guidance to numeric model developers and those tasked with the validation of numeric models. By creating Regulatory Guide 1.203 the NRC defined a framework for development, assessment, and approval of transient and accident analysis methods. As a result, this methodology is very relevant and is recommended as the path forward for RELAP-7 V&V. However, the unique issues posed by lifetime extension will require considerations in addition to those addressed in Regulatory Guide 1.203. Some of these include prioritization of which plants / designs should be studied first, coupling modern supporting experiments to the stringent needs of new high fidelity models / codes, and scaling of aging effects.« less

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

PubMed

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

PubMed Central

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA. PMID:29511354

Experimental Insights into the Cognitive Significance of Early Stone Tools

PubMed Central

Perston, Yinika

2016-01-01

Stone-flaking technology is the most enduring evidence for the evolving cognitive abilities of our early ancestors. Flake-making was mastered by African hominins ~3.3 ma, followed by the appearance of handaxes ~1.75 ma and complex stone reduction strategies by ~1.6 ma. Handaxes are stones flaked on two opposed faces (‘bifacially’), creating a robust, sharp-edged tool, and complex reduction strategies are reflected in strategic prior flaking to prepare or ‘predetermine’ the nature of a later flake removal that served as a tool blank. These technologies are interpreted as major milestones in hominin evolution that reflect the development of higher-order cognitive abilities, and the presence and nature of these technologies are used to track movements of early hominin species or ‘cultures’ in the archaeological record. However, the warranting argument that certain variations in stone tool morphologies are caused by differences in cognitive abilities relies on analogy with technical replications by skilled modern stoneworkers, and this raises the possibility that researchers are projecting modern approaches to technical problems onto our non-modern hominin ancestors. Here we present the results of novel experiments that randomise flake removal and disrupt the modern stoneworker’s inclination to use higher-order reasoning to guide the stone reduction process. Although our protocols prevented goal-directed replication of stone tool types, the experimental assemblage is morphologically standardised and includes handaxe-like ‘protobifaces’ and cores with apparently ‘predetermined’ flake removals. This shows that the geometrical constraints of fracture mechanics can give rise to what appear to be highly-designed stoneworking products and techniques when multiple flakes are removed randomly from a stone core. PMID:27392022

Ubiquitous computing to support co-located clinical teams: using the semiotics of physical objects in system design.

PubMed

Bang, Magnus; Timpka, Toomas

2007-06-01

Co-located teams often use material objects to communicate messages in collaboration. Modern desktop computing systems with abstract graphical user interface (GUIs) fail to support this material dimension of inter-personal communication. The aim of this study is to investigate how tangible user interfaces can be used in computer systems to better support collaborative routines among co-located clinical teams. The semiotics of physical objects used in team collaboration was analyzed from data collected during 1 month of observations at an emergency room. The resulting set of communication patterns was used as a framework when designing an experimental system. Following the principles of augmented reality, physical objects were mapped into a physical user interface with the goal of maintaining the symbolic value of those objects. NOSTOS is an experimental ubiquitous computing environment that takes advantage of interaction devices integrated into the traditional clinical environment, including digital pens, walk-up displays, and a digital desk. The design uses familiar workplace tools to function as user interfaces to the computer in order to exploit established cognitive and collaborative routines. Paper-based tangible user interfaces and digital desks are promising technologies for co-located clinical teams. A key issue that needs to be solved before employing such solutions in practice is associated with limited feedback from the passive paper interfaces.

Modern Electronic Devices: An Increasingly Common Cause of Skin Disorders in Consumers.

PubMed

Corazza, Monica; Minghetti, Sara; Bertoldi, Alberto Maria; Martina, Emanuela; Virgili, Annarosa; Borghi, Alessandro

2016-01-01

: The modern conveniences and enjoyment brought about by electronic devices bring with them some health concerns. In particular, personal electronic devices are responsible for rising cases of several skin disorders, including pressure, friction, contact dermatitis, and other physical dermatitis. The universal use of such devices, either for work or recreational purposes, will probably increase the occurrence of polymorphous skin manifestations over time. It is important for clinicians to consider electronics as potential sources of dermatological ailments, for proper patient management. We performed a literature review on skin disorders associated with the personal use of modern technology, including personal computers and laptops, personal computer accessories, mobile phones, tablets, video games, and consoles.

A diagnostic interface for the ICOsahedral Non-hydrostatic (ICON) modelling framework based on the Modular Earth Submodel System (MESSy v2.50)

NASA Astrophysics Data System (ADS)

Kern, Bastian; Jöckel, Patrick

2016-10-01

Numerical climate and weather models have advanced to finer scales, accompanied by large amounts of output data. The model systems hit the input and output (I/O) bottleneck of modern high-performance computing (HPC) systems. We aim to apply diagnostic methods online during the model simulation instead of applying them as a post-processing step to written output data, to reduce the amount of I/O. To include diagnostic tools into the model system, we implemented a standardised, easy-to-use interface based on the Modular Earth Submodel System (MESSy) into the ICOsahedral Non-hydrostatic (ICON) modelling framework. The integration of the diagnostic interface into the model system is briefly described. Furthermore, we present a prototype implementation of an advanced online diagnostic tool for the aggregation of model data onto a user-defined regular coarse grid. This diagnostic tool will be used to reduce the amount of model output in future simulations. Performance tests of the interface and of two different diagnostic tools show, that the interface itself introduces no overhead in form of additional runtime to the model system. The diagnostic tools, however, have significant impact on the model system's runtime. This overhead strongly depends on the characteristics and implementation of the diagnostic tool. A diagnostic tool with high inter-process communication introduces large overhead, whereas the additional runtime of a diagnostic tool without inter-process communication is low. We briefly describe our efforts to reduce the additional runtime from the diagnostic tools, and present a brief analysis of memory consumption. Future work will focus on optimisation of the memory footprint and the I/O operations of the diagnostic interface.

GEAS Spectroscopy Tools for Authentic Research Investigations in the Classroom

NASA Astrophysics Data System (ADS)

Rector, Travis A.; Vogt, Nicole P.

2018-06-01

Spectroscopy is one of the most powerful tools that astronomers use to study the universe. However relatively few resources are available that enable undergraduates to explore astronomical spectra interactively. We present web-based applications which guide students through the analysis of real spectra of stars, galaxies, and quasars. The tools are written in HTML5 and function in all modern web browsers on computers and tablets. No software needs to be installed nor do any datasets need to be downloaded, enabling students to use the tools in or outside of class (e.g., for online classes).Approachable GUIs allow students to analyze spectra in the same manner as professional astronomers. The stellar spectroscopy tool can fit a continuum with a blackbody and identify spectral features, as well as fit line profiles and determine equivalent widths. The galaxy and AGN tools can also measure redshifts and calcium break strengths. The tools provide access to an archive of hundreds of spectra obtained with the optical telescopes at Kitt Peak National Observatory. It is also possible to load your own spectra or to query the Sloan Digital Sky Survey (SDSS) database.We have also developed curricula to investigate these topics: spectral classification, variable stars, redshift, and AGN classification. We will present the functionality of the tools and describe the associated curriculum. The tools are part of the General Education Astronomy Source (GEAS) project based at New Mexico State University, with support from the National Science Foundation (NSF, AST-0349155) and the National Aeronautics and Space Administration (NASA, NNX09AV36G). Curriculum development was supported by the NSF (DUE-0618849 and DUE-0920293).

An Analytical Study of the Modernism and Contemporary Values in the Developed Communication Skills Books Taught in Grades Third Cycle for Basic Stage

ERIC Educational Resources Information Center

Shaban, Zakariyya Shaban

2015-01-01

This study aimed to investigate arrange of include communication skills text books modernism and contemporary value, and is there experience sequence, and the study tried to determine the orientation behind this concentration. A list of values included 10th modernism and contemporary values. Content analysis was used as a tool in collecting data,…

LTPP Climate Tool [Tech Brief

DOT National Transportation Integrated Search

2017-01-01

This Product Brief describes the Long-Term Pavement Performance (LTPP) Climate Tool (intended for use by infrastructure engineers) that provides convenient access to the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective An...

Efficient development of memory bounded geo-applications to scale on modern supercomputers

NASA Astrophysics Data System (ADS)

Räss, Ludovic; Omlin, Samuel; Licul, Aleksandar; Podladchikov, Yuri; Herman, Frédéric

2016-04-01

Numerical modeling is an actual key tool in the area of geosciences. The current challenge is to solve problems that are multi-physics and for which the length scale and the place of occurrence might not be known in advance. Also, the spatial extend of the investigated domain might strongly vary in size, ranging from millimeters for reactive transport to kilometers for glacier erosion dynamics. An efficient way to proceed is to develop simple but robust algorithms that perform well and scale on modern supercomputers and permit therefore very high-resolution simulations. We propose an efficient approach to solve memory bounded real-world applications on modern supercomputers architectures. We optimize the software to run on our newly acquired state-of-the-art GPU cluster "octopus". Our approach shows promising preliminary results on important geodynamical and geomechanical problematics: we have developed a Stokes solver for glacier flow and a poromechanical solver including complex rheologies for nonlinear waves in stressed rocks porous rocks. We solve the system of partial differential equations on a regular Cartesian grid and use an iterative finite difference scheme with preconditioning of the residuals. The MPI communication happens only locally (point-to-point); this method is known to scale linearly by construction. The "octopus" GPU cluster, which we use for the computations, has been designed to achieve maximal data transfer throughput at minimal hardware cost. It is composed of twenty compute nodes, each hosting four Nvidia Titan X GPU accelerators. These high-density nodes are interconnected with a parallel (dual-rail) FDR InfiniBand network. Our efforts show promising preliminary results for the different physics investigated. The glacier flow solver achieves good accuracy in the relevant benchmarks and the coupled poromechanical solver permits to explain previously unresolvable focused fluid flow as a natural outcome of the porosity setup. In both cases, near peak memory bandwidth transfer is achieved. Our approach allows us to get the best out of the current hardware.

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr.

PubMed

Privé, Florian; Aschard, Hugues; Ziyatdinov, Andrey; Blum, Michael G B

2017-03-30

Genome-wide datasets produced for association studies have dramatically increased in size over the past few years, with modern datasets commonly including millions of variants measured in dozens of thousands of individuals. This increase in data size is a major challenge severely slowing down genomic analyses, leading to some software becoming obsolete and researchers having limited access to diverse analysis tools. Here we present two R packages, bigstatsr and bigsnpr, allowing for the analysis of large scale genomic data to be performed within R. To address large data size, the packages use memory-mapping for accessing data matrices stored on disk instead of in RAM. To perform data pre-processing and data analysis, the packages integrate most of the tools that are commonly used, either through transparent system calls to existing software, or through updated or improved implementation of existing methods. In particular, the packages implement fast and accurate computations of principal component analysis and association studies, functions to remove SNPs in linkage disequilibrium and algorithms to learn polygenic risk scores on millions of SNPs. We illustrate applications of the two R packages by analyzing a case-control genomic dataset for celiac disease, performing an association study and computing Polygenic Risk Scores. Finally, we demonstrate the scalability of the R packages by analyzing a simulated genome-wide dataset including 500,000 individuals and 1 million markers on a single desktop computer. https://privefl.github.io/bigstatsr/ & https://privefl.github.io/bigsnpr/. florian.prive@univ-grenoble-alpes.fr & michael.blum@univ-grenoble-alpes.fr. Supplementary materials are available at Bioinformatics online.

Speeding Up Geophysical Research Using Docker Containers Within Multi-Cloud Environment.

NASA Astrophysics Data System (ADS)

Synytsky, R.; Henadiy, S.; Lobzakov, V.; Kolesnikov, L.; Starovoit, Y. O.

2016-12-01

How useful are the geophysical observations in a scope of minimizing losses from natural disasters today? Does it help to decrease number of human victims during tsunami and earthquake? Unfortunately it's still at early stage these days. It's a big goal and achievement to make such observations more useful by improving early warning and prediction systems with the help of cloud computing. Cloud computing technologies have proved the ability to speed up application development in many areas for 10 years already. Cloud unlocks new opportunities for geoscientists by providing access to modern data processing tools and algorithms including real-time high-performance computing, big data processing, artificial intelligence and others. Emerging lightweight cloud technologies, such as Docker containers, are gaining wide traction in IT due to the fact of faster and more efficient deployment of different applications in a cloud environment. It allows to deploy and manage geophysical applications and systems in minutes across multiple clouds and data centers that becomes of utmost importance for the next generation applications. In this session we'll demonstrate how Docker containers technology within multi-cloud can accelerate the development of applications specifically designed for geophysical researches.

nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.

PubMed

Róg, T; Murzyn, K; Hinsen, K; Kneller, G R

2003-04-15

We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques. The quantities that can be calculated by nMoldyn are the mean-square displacement, the velocity autocorrelation function as well as its Fourier transform (the density of states) and its memory function, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function, and several functions specific to neutron scattering: the coherent and incoherent intermediate scattering functions with their Fourier transforms, the memory function of the coherent scattering function, and the elastic incoherent structure factor. The possibility to compute memory function is a new and powerful feature that allows to relate simulation results to theoretical studies. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 657-667, 2003

Use of a wireless local area network in an orthodontic clinic.

PubMed

Mupparapu, Muralidhar; Binder, Robert E; Cummins, John M

2005-06-01

Radiographic images and other patient records, including medical histories, demographics, and health insurance information, can now be stored digitally and accessed via patient management programs. However, digital image acquisition and diagnosis and treatment planning are independent tasks, and each is time consuming, especially when performed at different computer workstations. Networking or linking the computers in an office enhances access to imaging and treatment planning tools. Access can be further enhanced if the entire network is wireless. Thanks to wireless technology, stand-alone, desk-bound personal computers have been replaced with mobile, hand-held devices that can communicate with each other and the rest of the world via the Internet. As with any emerging technology, some issues should be kept in mind when adapting to the wireless environment. Foremost is network security. Second is the choice of mobile hardware devices that are used by the orthodontist, office staff, and patients. This article details the standards and choices in wireless technology that can be implemented in an orthodontic clinic and suggests how to select suitable mobile hardware for accessing or adding data to a preexisting network. The network security protocols discussed comply with HIPAA regulations and boost the efficiency of a modern orthodontic clinic.

Density functional theory in the solid state

PubMed Central

Hasnip, Philip J.; Refson, Keith; Probert, Matt I. J.; Yates, Jonathan R.; Clark, Stewart J.; Pickard, Chris J.

2014-01-01

Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure–property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program. PMID:24516184

Grid Modernization Laboratory Consortium - Testing and Verification

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

Kroposki, Benjamin; Skare, Paul; Pratt, Rob

This paper highlights some of the unique testing capabilities and projects being performed at several national laboratories as part of the U. S. Department of Energy Grid Modernization Laboratory Consortium. As part of this effort, the Grid Modernization Laboratory Consortium Testing Network isbeing developed to accelerate grid modernization by enablingaccess to a comprehensive testing infrastructure and creating a repository of validated models and simulation tools that will be publicly available. This work is key to accelerating thedevelopment, validation, standardization, adoption, and deployment of new grid technologies to help meet U. S. energy goals.

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks. GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.

Case for a field-programmable gate array multicore hybrid machine for an image-processing application

NASA Astrophysics Data System (ADS)

Rakvic, Ryan N.; Ives, Robert W.; Lira, Javier; Molina, Carlos

2011-01-01

General purpose computer designers have recently begun adding cores to their processors in order to increase performance. For example, Intel has adopted a homogeneous quad-core processor as a base for general purpose computing. PlayStation3 (PS3) game consoles contain a multicore heterogeneous processor known as the Cell, which is designed to perform complex image processing algorithms at a high level. Can modern image-processing algorithms utilize these additional cores? On the other hand, modern advancements in configurable hardware, most notably field-programmable gate arrays (FPGAs) have created an interesting question for general purpose computer designers. Is there a reason to combine FPGAs with multicore processors to create an FPGA multicore hybrid general purpose computer? Iris matching, a repeatedly executed portion of a modern iris-recognition algorithm, is parallelized on an Intel-based homogeneous multicore Xeon system, a heterogeneous multicore Cell system, and an FPGA multicore hybrid system. Surprisingly, the cheaper PS3 slightly outperforms the Intel-based multicore on a core-for-core basis. However, both multicore systems are beaten by the FPGA multicore hybrid system by >50%.

Identification of key ancestors of modern germplasm in a breeding program of maize.

PubMed

Technow, F; Schrag, T A; Schipprack, W; Melchinger, A E

2014-12-01

Probabilities of gene origin computed from the genomic kinships matrix can accurately identify key ancestors of modern germplasms Identifying the key ancestors of modern plant breeding populations can provide valuable insights into the history of a breeding program and provide reference genomes for next generation whole genome sequencing. In an animal breeding context, a method was developed that employs probabilities of gene origin, computed from the pedigree-based additive kinship matrix, for identifying key ancestors. Because reliable and complete pedigree information is often not available in plant breeding, we replaced the additive kinship matrix with the genomic kinship matrix. As a proof-of-concept, we applied this approach to simulated data sets with known ancestries. The relative contribution of the ancestral lines to later generations could be determined with high accuracy, with and without selection. Our method was subsequently used for identifying the key ancestors of the modern Dent germplasm of the public maize breeding program of the University of Hohenheim. We found that the modern germplasm can be traced back to six or seven key ancestors, with one or two of them having a disproportionately large contribution. These results largely corroborated conjectures based on early records of the breeding program. We conclude that probabilities of gene origin computed from the genomic kinships matrix can be used for identifying key ancestors in breeding programs and estimating the proportion of genes contributed by them.

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

PubMed

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

2008-05-28

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

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

PubMed Central

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

2008-01-01

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

SeqWare Query Engine: storing and searching sequence data in the cloud.

PubMed

O'Connor, Brian D; Merriman, Barry; Nelson, Stanley F

2010-12-21

Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net). The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

PubMed

Hardisty, Alex R; Bacall, Finn; Beard, Niall; Balcázar-Vargas, Maria-Paula; Balech, Bachir; Barcza, Zoltán; Bourlat, Sarah J; De Giovanni, Renato; de Jong, Yde; De Leo, Francesca; Dobor, Laura; Donvito, Giacinto; Fellows, Donal; Guerra, Antonio Fernandez; Ferreira, Nuno; Fetyukova, Yuliya; Fosso, Bruno; Giddy, Jonathan; Goble, Carole; Güntsch, Anton; Haines, Robert; Ernst, Vera Hernández; Hettling, Hannes; Hidy, Dóra; Horváth, Ferenc; Ittzés, Dóra; Ittzés, Péter; Jones, Andrew; Kottmann, Renzo; Kulawik, Robert; Leidenberger, Sonja; Lyytikäinen-Saarenmaa, Päivi; Mathew, Cherian; Morrison, Norman; Nenadic, Aleksandra; de la Hidalga, Abraham Nieva; Obst, Matthias; Oostermeijer, Gerard; Paymal, Elisabeth; Pesole, Graziano; Pinto, Salvatore; Poigné, Axel; Fernandez, Francisco Quevedo; Santamaria, Monica; Saarenmaa, Hannu; Sipos, Gergely; Sylla, Karl-Heinz; Tähtinen, Marko; Vicario, Saverio; Vos, Rutger Aldo; Williams, Alan R; Yilmaz, Pelin

2016-10-20

Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

SeqWare Query Engine: storing and searching sequence data in the cloud

PubMed Central

2010-01-01

Background Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. Results In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net). Conclusions The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets. PMID:21210981

The importance of data curation on QSAR Modeling ...

EPA Pesticide Factsheets

During the last few decades many QSAR models and tools have been developed at the US EPA, including the widely used EPISuite. During this period the arsenal of computational capabilities supporting cheminformatics has broadened dramatically with multiple software packages. These modern tools allow for more advanced techniques in terms of chemical structure representation and storage, as well as enabling automated data-mining and standardization approaches to examine and fix data quality issues.This presentation will investigate the impact of data curation on the reliability of QSAR models being developed within the EPA‘s National Center for Computational Toxicology. As part of this work we have attempted to disentangle the influence of the quality versus quantity of data based on the Syracuse PHYSPROP database partly used by EPISuite software. We will review our automated approaches to examining key datasets related to the EPISuite data to validate across chemical structure representations (e.g., mol file and SMILES) and identifiers (chemical names and registry numbers) and approaches to standardize data into QSAR-ready formats prior to modeling procedures. Our efforts to quantify and segregate data into quality categories has allowed us to evaluate the resulting models that can be developed from these data slices and to quantify to what extent efforts developing high-quality datasets have the expected pay-off in terms of predicting performance. The most accur

NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications

PubMed Central

Rautenberg, Philipp L.; Kumaraswamy, Ajayrama; Tejero-Cantero, Alvaro; Doblander, Christoph; Norouzian, Mohammad R.; Kai, Kazuki; Jacobsen, Hans-Arno; Ai, Hiroyuki; Wachtler, Thomas; Ikeno, Hidetoshi

2014-01-01

Neuroscience today deals with a “data deluge” derived from the availability of high-throughput sensors of brain structure and brain activity, and increased computational resources for detailed simulations with complex output. We report here (1) a novel approach to data sharing between collaborating scientists that brings together file system tools and cloud technologies, (2) a service implementing this approach, called NeuronDepot, and (3) an example application of the service to a complex use case in the neurosciences. The main drivers for our approach are to facilitate collaborations with a transparent, automated data flow that shields scientists from having to learn new tools or data structuring paradigms. Using NeuronDepot is simple: one-time data assignment from the originator and cloud based syncing—thus making experimental and modeling data available across the collaboration with minimum overhead. Since data sharing is cloud based, our approach opens up the possibility of using new software developments and hardware scalabitliy which are associated with elastic cloud computing. We provide an implementation that relies on existing synchronization services and is usable from all devices via a reactive web interface. We are motivating our solution by solving the practical problems of the GinJang project, a collaboration of three universities across eight time zones with a complex workflow encompassing data from electrophysiological recordings, imaging, morphological reconstructions, and simulations. PMID:24971059

Reduced-form air quality modeling for community-scale ...

EPA Pesticide Factsheets

Transportation plays an important role in modern society, but its impact on air quality has been shown to have significant adverse effects on public health. Numerous reviews (HEI, CDC, WHO) summarizing findings of hundreds of studies conducted mainly in the last decade, conclude that exposures to traffic emissions near roads are a public health concern. The Community LINE Source Model (C-LINE) is a web-based model designed to inform the community user of local air quality impacts due to roadway vehicles in their region of interest using a simplified modeling approach. Reduced-form air quality modeling is a useful tool for examining what-if scenarios of changes in emissions, such as those due to changes in traffic volume, fleet mix, or vehicle speed. Examining various scenarios of air quality impacts in this way can identify potentially at-risk populations located near roadways, and the effects that a change in traffic activity may have on them. C-LINE computes dispersion of primary mobile source pollutants using meteorological conditions for the region of interest and computes air-quality concentrations corresponding to these selected conditions. C-LINE functionality has been expanded to model emissions from port-related activities (e.g. ships, trucks, cranes, etc.) in a reduced-form modeling system for local-scale near-port air quality analysis. This presentation describes the Community modeling tools C-LINE and C-PORT that are intended to be used by local gove

NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications.

PubMed

Rautenberg, Philipp L; Kumaraswamy, Ajayrama; Tejero-Cantero, Alvaro; Doblander, Christoph; Norouzian, Mohammad R; Kai, Kazuki; Jacobsen, Hans-Arno; Ai, Hiroyuki; Wachtler, Thomas; Ikeno, Hidetoshi

2014-01-01

Neuroscience today deals with a "data deluge" derived from the availability of high-throughput sensors of brain structure and brain activity, and increased computational resources for detailed simulations with complex output. We report here (1) a novel approach to data sharing between collaborating scientists that brings together file system tools and cloud technologies, (2) a service implementing this approach, called NeuronDepot, and (3) an example application of the service to a complex use case in the neurosciences. The main drivers for our approach are to facilitate collaborations with a transparent, automated data flow that shields scientists from having to learn new tools or data structuring paradigms. Using NeuronDepot is simple: one-time data assignment from the originator and cloud based syncing-thus making experimental and modeling data available across the collaboration with minimum overhead. Since data sharing is cloud based, our approach opens up the possibility of using new software developments and hardware scalabitliy which are associated with elastic cloud computing. We provide an implementation that relies on existing synchronization services and is usable from all devices via a reactive web interface. We are motivating our solution by solving the practical problems of the GinJang project, a collaboration of three universities across eight time zones with a complex workflow encompassing data from electrophysiological recordings, imaging, morphological reconstructions, and simulations.

Application of Neutron Tomography in Culture Heritage research.

PubMed

Mongy, T

2014-02-01

Neutron Tomography (NT) investigation of Culture Heritages (CH) is an efficient tool for understanding the culture of ancient civilizations. Neutron imaging (NI) is a-state-of-the-art non-destructive tool in the area of CH and plays an important role in the modern archeology. The NI technology can be widely utilized in the field of elemental analysis. At Egypt Second Research Reactor (ETRR-2), a collimated Neutron Radiography (NR) beam is employed for neutron imaging purposes. A digital CCD camera is utilized for recording the beam attenuation in the sample. This helps for the detection of hidden objects and characterization of material properties. Research activity can be extended to use computer software for quantitative neutron measurement. Development of image processing algorithms can be used to obtain high quality images. In this work, full description of ETRR-2 was introduced with up to date neutron imaging system as well. Tomographic investigation of a clay forged artifact represents CH object was studied by neutron imaging methods in order to obtain some hidden information and highlight some attractive quantitative measurements. Computer software was used for imaging processing and enhancement. Also the Astra Image 3.0 Pro software was employed for high precise measurements and imaging enhancement using advanced algorithms. This work increased the effective utilization of the ETRR-2 Neutron Radiography/Tomography (NR/T) technique in Culture Heritages activities. © 2013 Elsevier Ltd. All rights reserved.

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

PubMed Central

2011-01-01

Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined. PMID:22172142

Data and Workflow Management Challenges in Global Adjoint Tomography

NASA Astrophysics Data System (ADS)

Lei, W.; Ruan, Y.; Smith, J. A.; Modrak, R. T.; Orsvuran, R.; Krischer, L.; Chen, Y.; Balasubramanian, V.; Hill, J.; Turilli, M.; Bozdag, E.; Lefebvre, M. P.; Jha, S.; Tromp, J.

2017-12-01

It is crucial to take the complete physics of wave propagation into account in seismic tomography to further improve the resolution of tomographic images. The adjoint method is an efficient way of incorporating 3D wave simulations in seismic tomography. However, global adjoint tomography is computationally expensive, requiring thousands of wavefield simulations and massive data processing. Through our collaboration with the Oak Ridge National Laboratory (ORNL) computing group and an allocation on Titan, ORNL's GPU-accelerated supercomputer, we are now performing our global inversions by assimilating waveform data from over 1,000 earthquakes. The first challenge we encountered is dealing with the sheer amount of seismic data. Data processing based on conventional data formats and processing tools (such as SAC), which are not designed for parallel systems, becomes our major bottleneck. To facilitate the data processing procedures, we designed the Adaptive Seismic Data Format (ASDF) and developed a set of Python-based processing tools to replace legacy FORTRAN-based software. These tools greatly enhance reproducibility and accountability while taking full advantage of highly parallel system and showing superior scaling on modern computational platforms. The second challenge is that the data processing workflow contains more than 10 sub-procedures, making it delicate to handle and prone to human mistakes. To reduce human intervention as much as possible, we are developing a framework specifically designed for seismic inversion based on the state-of-the art workflow management research, specifically the Ensemble Toolkit (EnTK), in collaboration with the RADICAL team from Rutgers University. Using the initial developments of the EnTK, we are able to utilize the full computing power of the data processing cluster RHEA at ORNL while keeping human interaction to a minimum and greatly reducing the data processing time. Thanks to all the improvements, we are now able to perform iterations fast enough on more than a 1,000 earthquakes dataset. Starting from model GLAD-M15 (Bozdag et al., 2016), an elastic 3D model with a transversely isotropic upper mantle, we have successfully performed 5 iterations. Our goal is to finish 10 iterations, i.e., generating GLAD M25* by the end of this year.

Laboratory Mathematics

ERIC Educational Resources Information Center

de Mestre, Neville

2004-01-01

Computers were invented to help mathematicians perform long and complicated calculations more efficiently. By the time that a computing area became a familiar space in primary and secondary schools, the initial motivation for computer use had been submerged in the many other functions that modern computers now accomplish. Not only the mathematics…

Computing Legacy Software Behavior to Understand Functionality and Security Properties: An IBM/370 Demonstration

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

Linger, Richard C; Pleszkoch, Mark G; Prowell, Stacy J

Organizations maintaining mainframe legacy software can benefit from code modernization and incorporation of security capabilities to address the current threat environment. Oak Ridge National Laboratory is developing the Hyperion system to compute the behavior of software as a means to gain understanding of software functionality and security properties. Computation of functionality is critical to revealing security attributes, which are in fact specialized functional behaviors of software. Oak Ridge is collaborating with MITRE Corporation to conduct a demonstration project to compute behavior of legacy IBM Assembly Language code for a federal agency. The ultimate goal is to understand functionality and securitymore » vulnerabilities as a basis for code modernization. This paper reports on the first phase, to define functional semantics for IBM Assembly instructions and conduct behavior computation experiments.« less

Ptolemy's Britain and Ireland: A New Digital Reconstruction

NASA Astrophysics Data System (ADS)

Abshire, Corey; Durham, Anthony; Gusev, Dmitri A.; Stafeyev, Sergey K.

2018-05-01

In this paper, we expand application of our mathematical methods for translating ancient coordinates from the classical Geography by Claudius Ptolemy into modern coordinates from India and Arabia to Britain and Ireland, historically important islands on the periphery of the ancient Roman Empire. The methods include triangulation and flocking with subsequent Bayesian correction. The results of our work can be conveniently visualized in modern GIS tools, such as ArcGIS, QGIS, and Google Earth. The enhancements we have made include a novel technique for handling tentatively identified points. We compare the precision of reconstruction achieved for Ptolemy's Britain and Ireland with the precisions that we had computed earlier for his India before the Ganges and three provinces of Arabia. We also provide improved validation and comparison amongst the methods applied. We compare our results with the prior work, while utilizing knowledge from such important ancient sources as the Antonine Itinerary, Tabula Peutingeriana, and the Ravenna Cosmography. The new digital reconstruction of Claudius Ptolemy's Britain and Ireland presented in this paper, along with the accompanying linguistic analysis of ancient toponyms, contributes to improvement of understanding of our cultural cartographic heritage by making it easier to study the ancient world using the popular and accessible GIS programs.

An Overview of Cloud Implementation in the Manufacturing Process Life Cycle

NASA Astrophysics Data System (ADS)

Kassim, Noordiana; Yusof, Yusri; Hakim Mohamad, Mahmod Abd; Omar, Abdul Halim; Roslan, Rosfuzah; Aryanie Bahrudin, Ida; Ali, Mohd Hatta Mohamed

2017-08-01

The advancement of information and communication technology (ICT) has changed the structure and functions of various sectors and it has also started to play a significant role in modern manufacturing in terms of computerized machining and cloud manufacturing. It is important for industries to keep up with the current trend of ICT for them to be able survive and be competitive. Cloud manufacturing is an approach that wanted to realize a real-world manufacturing processes that will apply the basic concept from the field of Cloud computing to the manufacturing domain called Cloud-based manufacturing (CBM) or cloud manufacturing (CM). Cloud manufacturing has been recognized as a new paradigm for manufacturing businesses. In cloud manufacturing, manufacturing companies need to support flexible and scalable business processes in the shop floor as well as the software itself. This paper provides an insight or overview on the implementation of cloud manufacturing in the modern manufacturing processes and at the same times analyses the requirements needed regarding process enactment for Cloud manufacturing and at the same time proposing a STEP-NC concept that can function as a tool to support the cloud manufacturing concept.

An Adaptable Seismic Data Format for Modern Scientific Workflows

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

FOREWORD: Focus on Combinatorial Materials Science Focus on Combinatorial Materials Science

NASA Astrophysics Data System (ADS)

Chikyo, Toyohiro

2011-10-01

About 15 years have passed since the introduction of modern combinatorial synthesis and high-throughput techniques for the development of novel inorganic materials; however, similar methods existed before. The most famous was reported in 1970 by Hanak who prepared composition-spread films of metal alloys by sputtering mixed-material targets. Although this method was innovative, it was rarely used because of the large amount of data to be processed. This problem is solved in the modern combinatorial material research, which is strongly related to computer data analysis and robotics. This field is still at the developing stage and may be enriched by new methods. Nevertheless, given the progress in measurement equipment and procedures, we believe the combinatorial approach will become a major and standard tool of materials screening and development. The first article of this journal, published in 2000, was titled 'Combinatorial solid state materials science and technology', and this focus issue aims to reintroduce this topic to the Science and Technology of Advanced Materials audience. It covers recent progress in combinatorial materials research describing new results in catalysis, phosphors, polymers and metal alloys for shape memory materials. Sophisticated high-throughput characterization schemes and innovative synthesis tools are also presented, such as spray deposition using nanoparticles or ion plating. On a technical note, data handling systems are introduced to familiarize researchers with the combinatorial methodology. We hope that through this focus issue a wide audience of materials scientists can learn about recent and future trends in combinatorial materials science and high-throughput experimentation.

Image analysis in modern ophthalmology: from acquisition to computer assisted diagnosis and telemedicine

NASA Astrophysics Data System (ADS)

Marrugo, Andrés G.; Millán, María S.; Cristóbal, Gabriel; Gabarda, Salvador; Sorel, Michal; Sroubek, Filip

2012-06-01

Medical digital imaging has become a key element of modern health care procedures. It provides visual documentation and a permanent record for the patients, and most important the ability to extract information about many diseases. Modern ophthalmology thrives and develops on the advances in digital imaging and computing power. In this work we present an overview of recent image processing techniques proposed by the authors in the area of digital eye fundus photography. Our applications range from retinal image quality assessment to image restoration via blind deconvolution and visualization of structural changes in time between patient visits. All proposed within a framework for improving and assisting the medical practice and the forthcoming scenario of the information chain in telemedicine.

STORM WATER MANAGEMENT MODEL (SWMM) MODERNIZATION

EPA Science Inventory

The U.S. Environmental Protection Agency's Water Supply and Water Resources Division in partnership with the consulting firm of CDM to redevelop and modernize the Storm Water Management Model (SWMM). In the initial phase of this project EPA rewrote SWMM's computational engine usi...

76 FR 10827 - Modernizing the FCC Form 477 Data Program

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-28

... Congress, the Commission, other policy makers, and consumers.'' The Commission designed the program as a... Initiative, designed to modernize and streamline how the Commission collects, uses, and disseminates data. As... burden for filers, for example, in the design of the collection or in tools the Commission can provide...

Top Four Trends in Student Information Systems

ERIC Educational Resources Information Center

Weathers, Robert

2013-01-01

The modern student information systems (SIS) is a powerful administrative tool with robust functionality. As such, it is essential that school and district administrators consider the top trends in modern student information systems before going forward with system upgrades or new purchases. These trends, described herein, are: (1) Support for…

Photogrammetry for documentation of vehicle deformations--a tool in a system for advanced accident data collection.

PubMed

Kullgren, A; Lie, A; Tingvall, C

1994-02-01

Vehicle deformations are important sources for information about the performance of safety systems. Photogrammetry has developed vastly under recent years. In this study modern photogrammetrical methods have been used for vehicle deformation analysis. The study describes the equipment for documentation and recording in the field (semi-metric camera), and a system for photogrammetrical measurements of the images in laboratory environment (personal computer and digitizing tablet). The material used is approximately 500 collected and measured cases. The study shows that the reliability is high and that accuracies around 15mm can be achieved even if the equipment and routines used are relatively simple. The effects of further development using video cameras for data capture and digital images for measurements are discussed.

Echocardiography in the Era of Multimodality Cardiovascular Imaging

PubMed Central

Shah, Benoy Nalin

2013-01-01

Echocardiography remains the most frequently performed cardiac imaging investigation and is an invaluable tool for detailed and accurate evaluation of cardiac structure and function. Echocardiography, nuclear cardiology, cardiac magnetic resonance imaging, and cardiovascular-computed tomography comprise the subspeciality of cardiovascular imaging, and these techniques are often used together for a multimodality, comprehensive assessment of a number of cardiac diseases. This paper provides the general cardiologist and physician with an overview of state-of-the-art modern echocardiography, summarising established indications as well as highlighting advances in stress echocardiography, three-dimensional echocardiography, deformation imaging, and contrast echocardiography. Strengths and limitations of echocardiography are discussed as well as the growing role of real-time three-dimensional echocardiography in the guidance of structural heart interventions in the cardiac catheter laboratory. PMID:23878804

Contribution of Asteroid Generated Tsunami to the Impact Hazard

NASA Technical Reports Server (NTRS)

Morrison, David; Venkatapathy, Ethiraj

2017-01-01

The long-standing uncertainty about the importance of asteroid-generated tsunami was addressed at a workshop in August 2016, co-sponsored by NASA and NOAA. Experts from NASA, NOAA, the DoE tri-labs (LLNL, SNL, and LANL), DHS, FEMA, and academia addressed the hazard of tsunami created by asteroid impacts, focusing primarily on NEAs with diameter less than 250m. Participants jointly identified key issues and shared information for nearly a year to coordinate their results for discussion at the workshop. They used modern computational tools to examine 1) Near-field wave generation by the impact; 2) Long-distance wave propagation; 3) Damage from coastal run-up and inundation, and associated hazard. The workshop resulted in broad consensus that the asteroid impact tsunami threat is not as great as previously thought.

Mathematics and engineering in real life through mathematical competitions

NASA Astrophysics Data System (ADS)

More, M.

2018-02-01

We bring out an experience of organizing mathematical competitions that can be used as a medium to motivate the student and teacher minds in new directions of thinking. This can contribute to fostering research, innovation and provide a hands-on experience of mathematical concepts with the real world. Mathematical competitions can be used to build curiosity and give an understanding of mathematical applications in real life. Participation in the competition has been classified under four broad categories. Student can showcase their findings in various forms of expression like model, poster, soft presentation, animation, live performance, art and poetry. The basic focus of the competition is on using open source computation tools and modern technology, to emphasize the relationship of mathematical concepts with engineering applications in real life.

Airplane numerical simulation for the rapid prototyping process

NASA Astrophysics Data System (ADS)

Roysdon, Paul F.

Airplane Numerical Simulation for the Rapid Prototyping Process is a comprehensive research investigation into the most up-to-date methods for airplane development and design. Uses of modern engineering software tools, like MatLab and Excel, are presented with examples of batch and optimization algorithms which combine the computing power of MatLab with robust aerodynamic tools like XFOIL and AVL. The resulting data is demonstrated in the development and use of a full non-linear six-degrees-of-freedom simulator. The applications for this numerical tool-box vary from un-manned aerial vehicles to first-order analysis of manned aircraft. A Blended-Wing-Body airplane is used for the analysis to demonstrate the flexibility of the code from classic wing-and-tail configurations to less common configurations like the blended-wing-body. This configuration has been shown to have superior aerodynamic performance -- in contrast to their classic wing-and-tube fuselage counterparts -- and have reduced sensitivity to aerodynamic flutter as well as potential for increased engine noise abatement. Of course without a classic tail elevator to damp the nose up pitching moment, and the vertical tail rudder to damp the yaw and possible rolling aerodynamics, the challenges in lateral roll and yaw stability, as well as pitching moment are not insignificant. This thesis work applies the tools necessary to perform the airplane development and optimization on a rapid basis, demonstrating the strength of this tool through examples and comparison of the results to similar airplane performance characteristics published in literature.

Gene Unprediction with Spurio: A tool to identify spurious protein sequences.

PubMed

Höps, Wolfram; Jeffryes, Matt; Bateman, Alex

2018-01-01

We now have access to the sequences of tens of millions of proteins. These protein sequences are essential for modern molecular biology and computational biology. The vast majority of protein sequences are derived from gene prediction tools and have no experimental supporting evidence for their translation.  Despite the increasing accuracy of gene prediction tools there likely exists a large number of spurious protein predictions in the sequence databases.  We have developed the Spurio tool to help identify spurious protein predictions in prokaryotes.  Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. The tblastn matches are used to score the query sequence's likelihood of being a spurious protein prediction using a Gaussian process model. The most informative feature is the appearance of stop codons within the presumed translation of homologous DNA sequences. Benchmarking shows that the Spurio tool is able to distinguish spurious from true proteins. However, transposon proteins are prone to be predicted as spurious because of the frequency of degraded homologs found in the DNA sequence databases. Our initial experiments suggest that less than 1% of the proteins in the UniProtKB sequence database are likely to be spurious and that Spurio is able to identify over 60 times more spurious proteins than the AntiFam resource. The Spurio software and source code is available under an MIT license at the following URL: https://bitbucket.org/bateman-group/spurio.

C 3, A Command-line Catalog Cross-match Tool for Large Astrophysical Catalogs

NASA Astrophysics Data System (ADS)

Riccio, Giuseppe; Brescia, Massimo; Cavuoti, Stefano; Mercurio, Amata; di Giorgio, Anna Maria; Molinari, Sergio

2017-02-01

Modern Astrophysics is based on multi-wavelength data organized into large and heterogeneous catalogs. Hence, the need for efficient, reliable and scalable catalog cross-matching methods plays a crucial role in the era of the petabyte scale. Furthermore, multi-band data have often very different angular resolution, requiring the highest generality of cross-matching features, mainly in terms of region shape and resolution. In this work we present C 3 (Command-line Catalog Cross-match), a multi-platform application designed to efficiently cross-match massive catalogs. It is based on a multi-core parallel processing paradigm and conceived to be executed as a stand-alone command-line process or integrated within any generic data reduction/analysis pipeline, providing the maximum flexibility to the end-user, in terms of portability, parameter configuration, catalog formats, angular resolution, region shapes, coordinate units and cross-matching types. Using real data, extracted from public surveys, we discuss the cross-matching capabilities and computing time efficiency also through a direct comparison with some publicly available tools, chosen among the most used within the community, and representative of different interface paradigms. We verified that the C 3 tool has excellent capabilities to perform an efficient and reliable cross-matching between large data sets. Although the elliptical cross-match and the parametric handling of angular orientation and offset are known concepts in the astrophysical context, their availability in the presented command-line tool makes C 3 competitive in the context of public astronomical tools.

A History of Computer Numerical Control.

ERIC Educational Resources Information Center

Haggen, Gilbert L.

Computer numerical control (CNC) has evolved from the first significant counting method--the abacus. Babbage had perhaps the greatest impact on the development of modern day computers with his analytical engine. Hollerith's functioning machine with punched cards was used in tabulating the 1890 U.S. Census. In order for computers to become a…

Genomics Portals: integrative web-platform for mining genomics data.

PubMed

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

Computational mechanics

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

Raboin, P J

1998-01-01

The Computational Mechanics thrust area is a vital and growing facet of the Mechanical Engineering Department at Lawrence Livermore National Laboratory (LLNL). This work supports the development of computational analysis tools in the areas of structural mechanics and heat transfer. Over 75 analysts depend on thrust area-supported software running on a variety of computing platforms to meet the demands of LLNL programs. Interactions with the Department of Defense (DOD) High Performance Computing and Modernization Program and the Defense Special Weapons Agency are of special importance as they support our ParaDyn project in its development of new parallel capabilities for DYNA3D.more » Working with DOD customers has been invaluable to driving this technology in directions mutually beneficial to the Department of Energy. Other projects associated with the Computational Mechanics thrust area include work with the Partnership for a New Generation Vehicle (PNGV) for ''Springback Predictability'' and with the Federal Aviation Administration (FAA) for the ''Development of Methodologies for Evaluating Containment and Mitigation of Uncontained Engine Debris.'' In this report for FY-97, there are five articles detailing three code development activities and two projects that synthesized new code capabilities with new analytic research in damage/failure and biomechanics. The article this year are: (1) Energy- and Momentum-Conserving Rigid-Body Contact for NIKE3D and DYNA3D; (2) Computational Modeling of Prosthetics: A New Approach to Implant Design; (3) Characterization of Laser-Induced Mechanical Failure Damage of Optical Components; (4) Parallel Algorithm Research for Solid Mechanics Applications Using Finite Element Analysis; and (5) An Accurate One-Step Elasto-Plasticity Algorithm for Shell Elements in DYNA3D.« less

Parallel Computational Protein Design.

PubMed

Zhou, Yichao; Donald, Bruce R; Zeng, Jianyang

2017-01-01

Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process. To address this issue, we extend and add a new module to the OSPREY program that was previously developed in the Donald lab (Gainza et al., Methods Enzymol 523:87, 2013) to implement a GPU-based massively parallel A* algorithm for improving protein design pipeline. By exploiting the modern GPU computational framework and optimizing the computation of the heuristic function for A* search, our new program, called gOSPREY, can provide up to four orders of magnitude speedups in large protein design cases with a small memory overhead comparing to the traditional A* search algorithm implementation, while still guaranteeing the optimality. In addition, gOSPREY can be configured to run in a bounded-memory mode to tackle the problems in which the conformation space is too large and the global optimal solution cannot be computed previously. Furthermore, the GPU-based A* algorithm implemented in the gOSPREY program can be combined with the state-of-the-art rotamer pruning algorithms such as iMinDEE (Gainza et al., PLoS Comput Biol 8:e1002335, 2012) and DEEPer (Hallen et al., Proteins 81:18-39, 2013) to also consider continuous backbone and side-chain flexibility.

2018 Informatics Tool Challenge Winners

Cancer.gov

DCEG announced six winners of the 2018 DCEG Informatics Tool Challenge, a competitive funding program that supports innovation to enhance epidemiological methods, data collection, analysis, and other research using modern technology and informatics. Learn more about the winning innovations.

eHealth in Modern Patient-Caregiver Communication: High Rate of Acceptance Among Physicians for Additional Support of Breast Cancer Patients During Long-Term Therapy.

PubMed

Kirkovits, Thomas; Schinkoethe, Timo; Drewes, Caroline; Gehring, Caroline; Bauerfeind, Ingo; Harbeck, Nadia; Wuerstlein, Rachel

2016-09-19

Lack of adherence and compliance with drug regimens among breast cancer patients represent substantial problems in oral therapies, leading to significant impacts on mortality. Where other systems have failed, electronic health (eHealth) could be a possible solution to improve medication intake, along with the doctor-patient relationship. Initial results from studies concerning new interventions for therapy support are promising, but reports suggest that general acceptance of new treatment support tools is needed among patients and physicians alike. The aim of this study was to investigate the actual use of the Internet and other modern media among physicians involved in breast cancer treatment. Using a standardized questionnaire, actual utilization of new media among physicians was analyzed. Internet-related behaviors in private, as well as in business life, were investigated. Attention was focused on physicians' opinions regarding modern eHealth tools and how patients could be best supported to enhance adherence. A total of 120 physicians, all participating in breast cancer care, completed the questionnaire (median age 41 years). Almost all participants (99.2%, 119/120) used the Internet for general purposes and 98.3% (118/120) used it for medical issues as well. Virtually all medical professionals (99.2%, 119/120) reported that they owned a computer, while more recently invented technologies such as tablets and smartphones were owned by 31.9% (38/119) and 73.1% (87/119), respectively. The Internet was favored by 66.4% (79/119) of the physicians in our survey as a source for patient support; 71.2% (84/118) would also favor modern media for side effect registration. Based on our analysis, the most frequent Internet-utilizing physicians were characterized by age <60, worked in a hospital, and were employed as a junior physician. This study demonstrated a high usage of Internet-related technologies among physicians, indicating that the use of eHealth for advanced and individualized support in breast cancer care is a promising addition to treatment management. Such technologies have the potential to enhance adherence and compliance in therapy among cancer patients. ©Thomas Kirkovits, Timo Schinkoethe, Caroline Drewes, Caroline Gehring, Ingo Bauerfeind, Nadia Harbeck, Rachel Wuerstlein. Originally published in JMIR Cancer (http://cancer.jmir.org), 19.09.2016.

Community Coordinated Modeling Center: A Powerful Resource in Space Science and Space Weather Education

NASA Astrophysics Data System (ADS)

Chulaki, A.; Kuznetsova, M. M.; Rastaetter, L.; MacNeice, P. J.; Shim, J. S.; Pulkkinen, A. A.; Taktakishvili, A.; Mays, M. L.; Mendoza, A. M. M.; Zheng, Y.; Mullinix, R.; Collado-Vega, Y. M.; Maddox, M. M.; Pembroke, A. D.; Wiegand, C.

2015-12-01

Community Coordinated Modeling Center (CCMC) is a NASA affiliated interagency partnership with the primary goal of aiding the transition of modern space science models into space weather forecasting while supporting space science research. Additionally, over the past ten years it has established itself as a global space science education resource supporting undergraduate and graduate education and research, and spreading space weather awareness worldwide. A unique combination of assets, capabilities and close ties to the scientific and educational communities enable this small group to serve as a hub for raising generations of young space scientists and engineers. CCMC resources are publicly available online, providing unprecedented global access to the largest collection of modern space science models (developed by the international research community). CCMC has revolutionized the way simulations are utilized in classrooms settings, student projects, and scientific labs and serves hundreds of educators, students and researchers every year. Another major CCMC asset is an expert space weather prototyping team primarily serving NASA's interplanetary space weather needs. Capitalizing on its unrivaled capabilities and experiences, the team provides in-depth space weather training to students and professionals worldwide, and offers an amazing opportunity for undergraduates to engage in real-time space weather monitoring, analysis, forecasting and research. In-house development of state-of-the-art space weather tools and applications provides exciting opportunities to students majoring in computer science and computer engineering fields to intern with the software engineers at the CCMC while also learning about the space weather from the NASA scientists.

Tools and Their Uses. Rate Training Manual.

ERIC Educational Resources Information Center

Naval Personnel Program Support Activity, Washington, DC.

One of a series of training manuals prepared for enlisted personnel in the Navy and Naval Reserve, this supplementary manual contains data pertinent to a variety of tools necessary to the satisfactory performance of modern technical equipment used by the Navy. It is designed to help the learner identify tools and fastening devices by their correct…

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

Training, age and technological change: difficulties associated with age, the design of tools, and the organization of work.

PubMed

Cau-Bareille, Dominique; Gaudart, Corinne; Delgoulet, Catherine

2012-01-01

This article presents two ergonomic studies carried out when two French administrative bodies modernized their work tools. Our objective was to identify and define the vocational learning of experienced technicians who were required to adopt new working methods to cope with these technological changes. We observed the work activity of technicians of different ages and length of service both before and during training, and also after their return to their work unit during the appropriation phase. These two studies revealed some difficulties that were common to all the technicians and others that were more specific to the older employees. In terms of the design of the training course, we were able to point out some mistaken assumptions about the technicians' original command of the work activity and the computers, which made it difficult for them to adopt new work procedures. The difficulties encountered by the older employees were ultimately found to be more an indication of organizational problems to do with the management of change rather than training problems due to age.

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)

PubMed Central

Weber, Griffin; Mendis, Michael; Gainer, Vivian; Chueh, Henry C; Churchill, Susanne; Kohane, Isaac

2010-01-01

Informatics for Integrating Biology and the Bedside (i2b2) is one of seven projects sponsored by the NIH Roadmap National Centers for Biomedical Computing (http://www.ncbcs.org). Its mission is to provide clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart. i2b2 software may be used by an enterprise's research community to find sets of interesting patients from electronic patient medical record data, while preserving patient privacy through a query tool interface. Project-specific mini-databases (“data marts”) can be created from these sets to make highly detailed data available on these specific patients to the investigators on the i2b2 platform, as reviewed and restricted by the Institutional Review Board. The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software. PMID:20190053

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

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

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

PubMed Central

Sale, Kenneth L.; Simmons, Blake A.; Popelier, Paul L. A.

2017-01-01

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:28857244

New diagnostic tool for robotic psychology and robotherapy studies.

PubMed

Libin, Elena; Libin, Alexander

2003-08-01

Robotic psychology and robotherapy as a new research area employs a systematic approach in studying psycho-physiological, psychological, and social aspects of person-robot communication. An analysis of the mechanisms underlying different forms of computer-mediated behavior requires both an adequate methodology and research tools. In the proposed article we discuss the concept, basic principles, structure, and contents of the newly designed Person-Robot Complex Interactive Scale (PRCIS), proposed for the purpose of investigating psychological specifics and therapeutic potentials of multilevel person-robot interactions. Assuming that human-robot communication has symbolic meaning, each interactive pattern evaluated via the newly developed scale is assigned certain psychological value associated with the person's past life experiences, likes and dislikes, emotional, cognitive, and behavioral traits or states. PRCIS includes (1) assessment of a person's individual style of communication with the robotic creature based on direct observations; (2) the participant's evaluation of his/her new experiences with an interactive robot and evaluation of its features, advantages and disadvantages, as well as past experiences with modern technology; and (3) the instructor's overall evaluation of the session.

Towards ethical decision support and knowledge management in neonatal intensive care.

PubMed

Yang, L; Frize, M; Eng, P; Walker, R; Catley, C

2004-01-01

Recent studies in neonatal medicine, clinical nursing, and cognitive psychology have indicated the need to augment current decision-making practice in neonatal intensive care units with computerized, intelligent decision support systems. Rapid progress in artificial intelligence and knowledge management facilitates the design of collaborative ethical decision-support tools that allow clinicians to provide better support for parents facing inherently difficult choices, such as when to withdraw aggressive treatment. The appropriateness of using computers to support ethical decision-making is critically analyzed through research and literature review. In ethical dilemmas, multiple diverse participants need to communicate and function as a team to select the best treatment plan. In order to do this, physicians require reliable estimations of prognosis, while parents need a highly useable tool to help them assimilate complex medical issues and address their own value system. Our goal is to improve and structuralize the ethical decision-making that has become an inevitable part of modern neonatal care units. The paper contributes to clinical decision support by outlining the needs and basis for ethical decision support and justifying the proposed development efforts.

Neutron Tomography and X-ray Tomography as Tools for the Morphological Investigation of Non-mammalian Synapsids

NASA Astrophysics Data System (ADS)

Laaß, Michael; Schillinger, Burkhard; Werneburg, Ingmar

As having evolved on the stem line of mammals, the taxonomy and phylogeny of therapsids (Synapsida) are of special interest with respect to early mammalian evolution. Due to the fact that in most cases soft tissue of fossil vertebrates is not preserved, species can only be distinguished by diagnosis of morphological features of the skeleton. Moreover, investigations of vertebrate fossils are often obstructed, because internal cranial anatomy is usually hidden and parts of the fossils may be embedded in stone matrix. As a consequence, most species of non-mammalian synapsids were only defined on the basis of external skeletal features. Our investigations on Diictodon skulls (Therapsida, Anomodontia) show that non-destructive methods are very useful to clearly distinguish fossil species. We, therefore, propose using modern non-destructive techniques such as neutron tomography, synchrotron tomography, and micro-computed tomography (μCT) as standard tools for the investigation and virtual reconstruction of fossils and to include features of the internal cranial anatomy into morphological descriptions and phylogenetic analyses of fossil vertebrates.

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

DOE PAGES

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.; ...

2017-08-31

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Ice Accretion Test Results for Three Large-Scale Swept-Wing Models in the NASA Icing Research Tunnel

NASA Technical Reports Server (NTRS)

Broeren, Andy; Potapczuk, Mark; Lee, Sam; Malone, Adam; Paul, Ben; Woodard, Brian

2016-01-01

The design and certification of modern transport airplanes for flight in icing conditions increasing relies on three-dimensional numerical simulation tools for ice accretion prediction. There is currently no publically available, high-quality, ice accretion database upon which to evaluate the performance of icing simulation tools for large-scale swept wings that are representative of modern commercial transport airplanes. The purpose of this presentation is to present the results of a series of icing wind tunnel test campaigns whose aim was to provide an ice accretion database for large-scale, swept wings.

High performance flight computer developed for deep space applications

NASA Technical Reports Server (NTRS)

Bunker, Robert L.

1993-01-01

The development of an advanced space flight computer for real time embedded deep space applications which embodies the lessons learned on Galileo and modern computer technology is described. The requirements are listed and the design implementation that meets those requirements is described. The development of SPACE-16 (Spaceborne Advanced Computing Engine) (where 16 designates the databus width) was initiated to support the MM2 (Marine Mark 2) project. The computer is based on a radiation hardened emulation of a modern 32 bit microprocessor and its family of support devices including a high performance floating point accelerator. Additional custom devices which include a coprocessor to improve input/output capabilities, a memory interface chip, and an additional support chip that provide management of all fault tolerant features, are described. Detailed supporting analyses and rationale which justifies specific design and architectural decisions are provided. The six chip types were designed and fabricated. Testing and evaluation of a brass/board was initiated.

Structures and Boolean Dynamics in Gene Regulatory Networks

NASA Astrophysics Data System (ADS)

Szedlak, Anthony

This dissertation discusses the topological and dynamical properties of GRNs in cancer, and is divided into four main chapters. First, the basic tools of modern complex network theory are introduced. These traditional tools as well as those developed by myself (set efficiency, interset efficiency, and nested communities) are crucial for understanding the intricate topological properties of GRNs, and later chapters recall these concepts. Second, the biology of gene regulation is discussed, and a method for disease-specific GRN reconstruction developed by our collaboration is presented. This complements the traditional exhaustive experimental approach of building GRNs edge-by-edge by quickly inferring the existence of as of yet undiscovered edges using correlations across sets of gene expression data. This method also provides insight into the distribution of common mutations across GRNs. Third, I demonstrate that the structures present in these reconstructed networks are strongly related to the evolutionary histories of their constituent genes. Investigation of how the forces of evolution shaped the topology of GRNs in multicellular organisms by growing outward from a core of ancient, conserved genes can shed light upon the ''reverse evolution'' of normal cells into unicellular-like cancer states. Next, I simulate the dynamics of the GRNs of cancer cells using the Hopfield model, an infinite range spin-glass model designed with the ability to encode Boolean data as attractor states. This attractor-driven approach facilitates the integration of gene expression data into predictive mathematical models. Perturbations representing therapeutic interventions are applied to sets of genes, and the resulting deviations from their attractor states are recorded, suggesting new potential drug targets for experimentation. Finally, I extend the Hopfield model to modular networks, cyclic attractors, and complex attractors, and apply these concepts to simulations of the cell cycle process. Futher development of these and other theoretical and computational tools is necessary to analyze the deluge of experimental data produced by modern and future biological high throughput methods. (Abstract shortened by ProQuest.).

Diffraction scattering computed tomography: a window into the structures of complex nanomaterials

PubMed Central

Birkbak, M. E.; Leemreize, H.; Frølich, S.; Stock, S. R.

2015-01-01

Modern functional nanomaterials and devices are increasingly composed of multiple phases arranged in three dimensions over several length scales. Therefore there is a pressing demand for improved methods for structural characterization of such complex materials. An excellent emerging technique that addresses this problem is diffraction/scattering computed tomography (DSCT). DSCT combines the merits of diffraction and/or small angle scattering with computed tomography to allow imaging the interior of materials based on the diffraction or small angle scattering signals. This allows, e.g., one to distinguish the distributions of polymorphs in complex mixtures. Here we review this technique and give examples of how it can shed light on modern nanoscale materials. PMID:26505175

Organizational Potential of Scientific Work in the System of Neuromanagement by the Example of Higher Education

ERIC Educational Resources Information Center

Nikolaevskaya, Olga

2015-01-01

Neuromanagement of higher education is an effective tool for the development of higher education, professional identification of specialist, increase of the professional authority and prestige of modern scientific and research work. The target point of neuromanagement system is competitiveness of the modern university graduate whose competence…

Architecture as a Diplomatic Tool: A Proposal for the New American Embassy in Baghdad, Iraq

DTIC Science & Technology

2006-04-01

133 William J. R. Curtis, Modern Architecture Since 1900, 3 ed. (New York: Phaidon , 1996) 295-96. 134 Curtis 296. 135 Curtis...Dover, 1986. Curtis, William J. R. Modern Architecture Since 1900. 3d ed. New York: Phaidon , 1996. De Quincy, Quatremère. The True, the Fictive

Sirius PSB: a generic system for analysis of biological sequences.

PubMed

Koh, Chuan Hock; Lin, Sharene; Jedd, Gregory; Wong, Limsoon

2009-12-01

Computational tools are essential components of modern biological research. For example, BLAST searches can be used to identify related proteins based on sequence homology, or when a new genome is sequenced, prediction models can be used to annotate functional sites such as transcription start sites, translation initiation sites and polyadenylation sites and to predict protein localization. Here we present Sirius Prediction Systems Builder (PSB), a new computational tool for sequence analysis, classification and searching. Sirius PSB has four main operations: (1) Building a classifier, (2) Deploying a classifier, (3) Search for proteins similar to query proteins, (4) Preliminary and post-prediction analysis. Sirius PSB supports all these operations via a simple and interactive graphical user interface. Besides being a convenient tool, Sirius PSB has also introduced two novelties in sequence analysis. Firstly, genetic algorithm is used to identify interesting features in the feature space. Secondly, instead of the conventional method of searching for similar proteins via sequence similarity, we introduced searching via features' similarity. To demonstrate the capabilities of Sirius PSB, we have built two prediction models - one for the recognition of Arabidopsis polyadenylation sites and another for the subcellular localization of proteins. Both systems are competitive against current state-of-the-art models based on evaluation of public datasets. More notably, the time and effort required to build each model is greatly reduced with the assistance of Sirius PSB. Furthermore, we show that under certain conditions when BLAST is unable to find related proteins, Sirius PSB can identify functionally related proteins based on their biophysical similarities. Sirius PSB and its related supplements are available at: http://compbio.ddns.comp.nus.edu.sg/~sirius.

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

Tan, Lizhen; Yang, Ying; Tyburska-Puschel, Beata

The mission of the Nuclear Energy Enabling Technologies (NEET) program is to develop crosscutting technologies for nuclear energy applications. Advanced structural materials with superior performance at elevated temperatures are always desired for nuclear reactors, which can improve reactor economics, safety margins, and design flexibility. They benefit not only new reactors, including advanced light water reactors (LWRs) and fast reactors such as sodium-cooled fast reactor (SFR) that is primarily designed for management of high-level wastes, but also life extension of the existing fleet when component exchange is needed. Developing and utilizing the modern materials science tools (experimental, theoretical, and computational tools)more » is an important path to more efficient alloy development and process optimization. Ferritic-martensitic (FM) steels are important structural materials for nuclear reactors due to their advantages over other applicable materials like austenitic stainless steels, notably their resistance to void swelling, low thermal expansion coefficients, and higher thermal conductivity. However, traditional FM steels exhibit a noticeable yield strength reduction at elevated temperatures above ~500°C, which limits their applications in advanced nuclear reactors which target operating temperatures at 650°C or higher. Although oxide-dispersion-strengthened (ODS) ferritic steels have shown excellent high-temperature performance, their extremely high cost, limited size and fabricability of products, as well as the great difficulty with welding and joining, have limited or precluded their commercial applications. Zirconium has shown many benefits to Fe-base alloys such as grain refinement, improved phase stability, and reduced radiation-induced segregation. The ultimate goal of this project is, with the aid of computational modeling tools, to accelerate the development of a new generation of Zr-bearing ferritic alloys to be fabricated using conventional steelmaking practices, which have excellent radiation resistance and enhanced high-temperature creep performance greater than Grade 91.« less

Code Modernization of VPIC

NASA Astrophysics Data System (ADS)

Bird, Robert; Nystrom, David; Albright, Brian

2017-10-01

The ability of scientific simulations to effectively deliver performant computation is increasingly being challenged by successive generations of high-performance computing architectures. Code development to support efficient computation on these modern architectures is both expensive, and highly complex; if it is approached without due care, it may also not be directly transferable between subsequent hardware generations. Previous works have discussed techniques to support the process of adapting a legacy code for modern hardware generations, but despite the breakthroughs in the areas of mini-app development, portable-performance, and cache oblivious algorithms the problem still remains largely unsolved. In this work we demonstrate how a focus on platform agnostic modern code-development can be applied to Particle-in-Cell (PIC) simulations to facilitate effective scientific delivery. This work builds directly on our previous work optimizing VPIC, in which we replaced intrinsic based vectorisation with compile generated auto-vectorization to improve the performance and portability of VPIC. In this work we present the use of a specialized SIMD queue for processing some particle operations, and also preview a GPU capable OpenMP variant of VPIC. Finally we include a lessons learnt. Work performed under the auspices of the U.S. Dept. of Energy by the Los Alamos National Security, LLC Los Alamos National Laboratory under contract DE-AC52-06NA25396 and supported by the LANL LDRD program.

Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.

PubMed

Nowotka, Michał M; Gaulton, Anna; Mendez, David; Bento, A Patricia; Hersey, Anne; Leach, Andrew

2017-08-01

ChEMBL is a manually curated database of bioactivity data on small drug-like molecules, used by drug discovery scientists. Among many access methods, a REST API provides programmatic access, allowing the remote retrieval of ChEMBL data and its integration into other applications. This approach allows scientists to move from a world where they go to the ChEMBL web site to search for relevant data, to one where ChEMBL data can be simply integrated into their everyday tools and work environment. Areas covered: This review highlights some of the audiences who may benefit from using the ChEMBL API, and the goals they can address, through the description of several use cases. The examples cover a team communication tool (Slack), a data analytics platform (KNIME), batch job management software (Luigi) and Rich Internet Applications. Expert opinion: The advent of web technologies, cloud computing and micro services oriented architectures have made REST APIs an essential ingredient of modern software development models. The widespread availability of tools consuming RESTful resources have made them useful for many groups of users. The ChEMBL API is a valuable resource of drug discovery bioactivity data for professional chemists, chemistry students, data scientists, scientific and web developers.

Updates to FuncLab, a Matlab based GUI for handling receiver functions

NASA Astrophysics Data System (ADS)

Porritt, Robert W.; Miller, Meghan S.

2018-02-01

Receiver functions are a versatile tool commonly used in seismic imaging. Depending on how they are processed, they can be used to image discontinuity structure within the crust or mantle or they can be inverted for seismic velocity either directly or jointly with complementary datasets. However, modern studies generally require large datasets which can be challenging to handle; therefore, FuncLab was originally written as an interactive Matlab GUI to assist in handling these large datasets. This software uses a project database to allow interactive trace editing, data visualization, H-κ stacking for crustal thickness and Vp/Vs ratio, and common conversion point stacking while minimizing computational costs. Since its initial release, significant advances have been made in the implementation of web services and changes in the underlying Matlab platform have necessitated a significant revision to the software. Here, we present revisions to the software, including new features such as data downloading via irisFetch.m, receiver function calculations via processRFmatlab, on-the-fly cross-section tools, interface picking, and more. In the descriptions of the tools, we present its application to a test dataset in Michigan, Wisconsin, and neighboring areas following the passage of USArray Transportable Array. The software is made available online at https://robporritt.wordpress.com/software.

Benefits of object-oriented models and ModeliChart: modern tools and methods for the interdisciplinary research on smart biomedical technology.

PubMed

Gesenhues, Jonas; Hein, Marc; Ketelhut, Maike; Habigt, Moriz; Rüschen, Daniel; Mechelinck, Mare; Albin, Thivaharan; Leonhardt, Steffen; Schmitz-Rode, Thomas; Rossaint, Rolf; Autschbach, Rüdiger; Abel, Dirk

2017-04-01

Computational models of biophysical systems generally constitute an essential component in the realization of smart biomedical technological applications. Typically, the development process of such models is characterized by a great extent of collaboration between different interdisciplinary parties. Furthermore, due to the fact that many underlying mechanisms and the necessary degree of abstraction of biophysical system models are unknown beforehand, the steps of the development process of the application are iteratively repeated when the model is refined. This paper presents some methods and tools to facilitate the development process. First, the principle of object-oriented (OO) modeling is presented and the advantages over classical signal-oriented modeling are emphasized. Second, our self-developed simulation tool ModeliChart is presented. ModeliChart was designed specifically for clinical users and allows independently performing in silico studies in real time including intuitive interaction with the model. Furthermore, ModeliChart is capable of interacting with hardware such as sensors and actuators. Finally, it is presented how optimal control methods in combination with OO models can be used to realize clinically motivated control applications. All methods presented are illustrated on an exemplary clinically oriented use case of the artificial perfusion of the systemic circulation.

[Surgical treatment of secondary peritonitis: A continuing problem. German version].

PubMed

van Ruler, O; Boermeester, M A

2016-01-01

Secondary peritonitis remains associated with high mortality and morbidity rates. Treatment of secondary peritonitis is still challenging even in the era of modern medicine. Surgical intervention for source control remains the cornerstone of treatment besides adequate antimicrobial therapy and when necessary intensive medical care measures and resuscitation. A randomized clinical trial showed that relaparotomy on demand (ROD) after initial emergency surgery was the preferred treatment strategy, irrespective of the severity and extent of peritonitis. The effective and safe use of ROD requires intensive monitoring of the patient in a setting where diagnostic tests and decision making about relaparotomy are guaranteed round the clock. The lack of knowledge on timely and adequate patient selection, together with the lack of use of easy but reliable monitoring tools seem to hamper full implementation of ROD. The accuracy of the relaparotomy decision tool is reasonable for prediction of the formation of peritonitis and necessary selection of patients for computed tomography (CT). The value of CT in the early postoperative phase is unclear. Future research and innovative technologies should focus on the additive value of CT after surgical treatment for secondary peritonitis and on the further optimization of bedside prediction tools to enhance adequate patient selection for interventions in a multidisciplinary setting.

Gene editing for cell engineering: trends and applications.

PubMed

Gupta, Sanjeev K; Shukla, Pratyoosh

2017-08-01

Gene editing with all its own advantages in molecular biology applications has made easy manipulation of various production hosts with the discovery and implementation of modern gene editing tools such as Crispr (Clustered regularly interspaced short palindromic repeats), TALENs (Transcription activator-like effector nucleases) and ZFNs (Zinc finger nucleases). With the advent of these modern tools, it is now possible to manipulate the genome of industrial production hosts such as yeast and mammalian cells which allows developing a potential and cost effective recombinant therapeutic protein. These tools also allow single editing to multiple genes for knocking-in or knocking-out of a host genome quickly in an efficient manner. A recent study on "multiplexed" gene editing revolutionized the knock-out and knock-in events of yeast and CHO, mammalian cells genome for metabolic engineering as well as high, stable, and consistent expression of a transgene encoding complex therapeutic protein such as monoclonal antibody. The gene of interest can either be integrated or deleted at single or multiple loci depending on the strategy and production requirement. This review will give a gist of all the modern tools with a brief description and advances in genetic manipulation using three major tools being implemented for the modification of such hosts with the emphasis on the use of Crispr-Cas9 for the "multiplexing gene-editing approach" for genetic manipulation of yeast and CHO mammalian hosts that ultimately leads to a fast track product development with consistent, improved product yield, quality, and thus affordability for a population at large.

Evaluating Application Resilience with XRay

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

Chen, Sui; Bronevetsky, Greg; Li, Bin

2015-05-07

The rising count and shrinking feature size of transistors within modern computers is making them increasingly vulnerable to various types of soft faults. This problem is especially acute in high-performance computing (HPC) systems used for scientific computing, because these systems include many thousands of compute cores and nodes, all of which may be utilized in a single large-scale run. The increasing vulnerability of HPC applications to errors induced by soft faults is motivating extensive work on techniques to make these applications more resiilent to such faults, ranging from generic techniques such as replication or checkpoint/restart to algorithmspecific error detection andmore » tolerance techniques. Effective use of such techniques requires a detailed understanding of how a given application is affected by soft faults to ensure that (i) efforts to improve application resilience are spent in the code regions most vulnerable to faults and (ii) the appropriate resilience technique is applied to each code region. This paper presents XRay, a tool to view the application vulnerability to soft errors, and illustrates how XRay can be used in the context of a representative application. In addition to providing actionable insights into application behavior XRay automatically selects the number of fault injection experiments required to provide an informative view of application behavior, ensuring that the information is statistically well-grounded without performing unnecessary experiments.« less

Computation and analysis of cavitating flow in Francis-class hydraulic turbines

NASA Astrophysics Data System (ADS)

Leonard, Daniel J.

Hydropower is the most proven renewable energy technology, supplying the world with 16% of its electricity. Conventional hydropower generates a vast majority of that percentage. Although a mature technology, hydroelectric generation shows great promise for expansion through new dams and plants in developing hydro countries. Moreover, in developed hydro countries, such as the United States, installing generating units in existing dams and the modern refurbishment of existing plants can greatly expand generating capabilities with little to no further impact on the environment. In addition, modern computational technology and fluid dynamics expertise has led to substantial improvements in modern turbine design and performance. Cavitation has always presented a problem in hydroturbines, causing performance breakdown, erosion, damage, vibration, and noise. While modern turbines are usually designed to be cavitation-free at their best efficiency point, due to the variable demand of the energy market it is fairly common to operate at off-design conditions. Here, cavitation and its deleterious effects are unavoidable, and hence, cavitation is a limiting factor on the design and operation of these turbines. Multiphase Computational Fluid Dynamics (CFD) has been used in recent years to model cavitating flow for a large range of problems, including turbomachinery. However, CFD of cavitating flow in hydroturbines is still in its infancy. This dissertation presents steady-periodic Reynolds-averaged Navier-Stokes simulations of a cavitating Francis-class hydroturbine at model and prototype scales. Computational results of the reduced-scale model and full-scale prototype, undergoing performance breakdown, are compared with empirical model data and prototype performance estimations based on standard industry scalings from the model data. Mesh convergence of the simulations is also displayed. Comparisons are made between the scales to display that cavitation performance breakdown can occur more abruptly in the model than the prototype, due to lack of Froude similitude between the two. When severe cavitation occurs, clear differences are observed in vapor content between the scales. A stage-by-stage performance decomposition is conducted to analyze the losses within individual components of each scale of the machine. As cavitation becomes more severe, the losses in the draft tube account for an increasing amount of the total losses in the machine. More losses occur in the model draft tube as cavitation formation in the prototype draft tube is prevented by the larger hydrostatic pressure gradient across the machine. Additionally, unsteady Detached Eddy Simulations of the fully-coupled cavitating hydroturbine are performed for both scales. Both mesh and temporal convergence studies are provided. The temporal and spectral content of fluctuations in torque and pressure are monitored and compared between single-phase, cavitating, model, and prototype cases. A shallow draft tube induced runner imbalance results in an asymmetric vapor distribution about the runner, leading to more extensive growth and collapse of vapor on any individual blade as it undergoes a revolution. Unique frequency components manifest and persist through the entire machine only when cavitation is present in the hub vortex. Large maximum pressure spikes, which result from vapor collapse, are observed on the blade surfaces in the multiphase simulations, and these may be a potential source of cavitation damage and erosion. Multiphase CFD is shown to be an accurate and effective technique for simulating and analyzing cavitating flow in Francis-class hydraulic turbines. It is recommended that it be used as an industrial tool to supplement model cavitation experiments for all types of hydraulic turbines. Moreover, multiphase CFD can be equally effective as a research tool, to investigate mechanisms of cavitating hydraulic turbines that are not understood, and to uncover unique new phenomena which are currently unknown.

Multimodal system for the planning and guidance of bronchoscopy

NASA Astrophysics Data System (ADS)

Higgins, William E.; Cheirsilp, Ronnarit; Zang, Xiaonan; Byrnes, Patrick

2015-03-01

Many technical innovations in multimodal radiologic imaging and bronchoscopy have emerged recently in the effort against lung cancer. Modern X-ray computed-tomography (CT) scanners provide three-dimensional (3D) high-resolution chest images, positron emission tomography (PET) scanners give complementary molecular imaging data, and new integrated PET/CT scanners combine the strengths of both modalities. State-of-the-art bronchoscopes permit minimally invasive tissue sampling, with vivid endobronchial video enabling navigation deep into the airway-tree periphery, while complementary endobronchial ultrasound (EBUS) reveals local views of anatomical structures outside the airways. In addition, image-guided intervention (IGI) systems have proven their utility for CT-based planning and guidance of bronchoscopy. Unfortunately, no IGI system exists that integrates all sources effectively through the complete lung-cancer staging work flow. This paper presents a prototype of a computer-based multimodal IGI system that strives to fill this need. The system combines a wide range of automatic and semi-automatic image-processing tools for multimodal data fusion and procedure planning. It also provides a flexible graphical user interface for follow-on guidance of bronchoscopy/EBUS. Human-study results demonstrate the system's potential.

Optimizing product life cycle processes in design phase

NASA Astrophysics Data System (ADS)

Faneye, Ola. B.; Anderl, Reiner

2002-02-01

Life cycle concepts do not only serve as basis in assisting product developers understand the dependencies between products and their life cycles, they also help in identifying potential opportunities for improvement in products. Common traditional concepts focus mainly on energy and material flow across life phases, necessitating the availability of metrics derived from a reference product. Knowledge of life cycle processes won from an existing product is directly reused in its redesign. Depending on sales volume nevertheless, the environmental impact before product optimization can be substantial. With modern information technologies today, computer-aided life cycle methodologies can be applied well before product use. On the basis of a virtual prototype, life cycle processes are analyzed and optimized, using simulation techniques. This preventive approach does not only help in minimizing (or even eliminating) environmental burdens caused by product, costs incurred due to changes in real product can also be avoided. The paper highlights the relationship between product and life cycle and presents a computer-based methodology for optimizing the product life cycle during design, as presented by SFB 392: Design for Environment - Methods and Tools at Technical University, Darmstadt.