Proposal for constructing an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Sims, Michael H.; Podolak, Esther; Mckay, Christopher P.; Thompson, David E.

1990-01-01

Scientific model building can be a time intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We believe that advanced software techniques can facilitate both the model building and model sharing process. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing and using models. The proposed tool will include an interactive intelligent graphical interface and a high level, domain specific, modeling language. As a testbed for this research, we propose development of a software prototype in the domain of planetary atmospheric modeling.

Test Driven Development of Scientific Models

NASA Technical Reports Server (NTRS)

Clune, Thomas L.

2012-01-01

Test-Driven Development (TDD) is a software development process that promises many advantages for developer productivity and has become widely accepted among professional software engineers. As the name suggests, TDD practitioners alternate between writing short automated tests and producing code that passes those tests. Although this overly simplified description will undoubtedly sound prohibitively burdensome to many uninitiated developers, the advent of powerful unit-testing frameworks greatly reduces the effort required to produce and routinely execute suites of tests. By testimony, many developers find TDD to be addicting after only a few days of exposure, and find it unthinkable to return to previous practices. Of course, scientific/technical software differs from other software categories in a number of important respects, but I nonetheless believe that TDD is quite applicable to the development of such software and has the potential to significantly improve programmer productivity and code quality within the scientific community. After a detailed introduction to TDD, I will present the experience within the Software Systems Support Office (SSSO) in applying the technique to various scientific applications. This discussion will emphasize the various direct and indirect benefits as well as some of the difficulties and limitations of the methodology. I will conclude with a brief description of pFUnit, a unit testing framework I co-developed to support test-driven development of parallel Fortran applications.

Lessons Learned through the Development and Publication of AstroImageJ

NASA Astrophysics Data System (ADS)

Collins, Karen

2018-01-01

As lead author of the scientific image processing software package AstroImageJ (AIJ), I will discuss the reasoning behind why we decided to release AIJ to the public, and the lessons we learned related to the development, publication, distribution, and support of AIJ. I will also summarize the AIJ code language selection, code documentation and testing approaches, code distribution, update, and support facilities used, and the code citation and licensing decisions. Since AIJ was initially developed as part of my graduate research and was my first scientific open source software publication, many of my experiences and difficulties encountered may parallel those of others new to scientific software publication. Finally, I will discuss the benefits and disadvantages of releasing scientific software that I now recognize after having AIJ in the public domain for more than five years.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1993-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a testbed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1992-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a test bed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

The Computational Infrastructure for Geodynamics as a Community of Practice

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2016-12-01

Computational Infrastructure for Geodynamics (CIG), geodynamics.org, originated in 2005 out of community recognition that the efforts of individual or small groups of researchers to develop scientifically-sound software is impossible to sustain, duplicates effort, and makes it difficult for scientists to adopt state-of-the art computational methods that promote new discovery. As a community of practice, participants in CIG share an interest in computational modeling in geodynamics and work together on open source software to build the capacity to support complex, extensible, scalable, interoperable, reliable, and reusable software in an effort to increase the return on investment in scientific software development and increase the quality of the resulting software. The group interacts regularly to learn from each other and better their practices formally through webinar series, workshops, and tutorials and informally through listservs and hackathons. Over the past decade, we have learned that successful scientific software development requires at a minimum: collaboration between domain-expert researchers, software developers and computational scientists; clearly identified and committed lead developer(s); well-defined scientific and computational goals that are regularly evaluated and updated; well-defined benchmarks and testing throughout development; attention throughout development to usability and extensibility; understanding and evaluation of the complexity of dependent libraries; and managed user expectations through education, training, and support. CIG's code donation standards provide the basis for recently formalized best practices in software development (geodynamics.org/cig/dev/best-practices/). Best practices include use of version control; widely used, open source software libraries; extensive test suites; portable configuration and build systems; extensive documentation internal and external to the code; and structured, human readable input formats.

Software Reuse Methods to Improve Technological Infrastructure for e-Science

NASA Technical Reports Server (NTRS)

Marshall, James J.; Downs, Robert R.; Mattmann, Chris A.

2011-01-01

Social computing has the potential to contribute to scientific research. Ongoing developments in information and communications technology improve capabilities for enabling scientific research, including research fostered by social computing capabilities. The recent emergence of e-Science practices has demonstrated the benefits from improvements in the technological infrastructure, or cyber-infrastructure, that has been developed to support science. Cloud computing is one example of this e-Science trend. Our own work in the area of software reuse offers methods that can be used to improve new technological development, including cloud computing capabilities, to support scientific research practices. In this paper, we focus on software reuse and its potential to contribute to the development and evaluation of information systems and related services designed to support new capabilities for conducting scientific research.

Cultural and Technological Issues and Solutions for Geodynamics Software Citation

NASA Astrophysics Data System (ADS)

Heien, E. M.; Hwang, L.; Fish, A. E.; Smith, M.; Dumit, J.; Kellogg, L. H.

2014-12-01

Computational software and custom-written codes play a key role in scientific research and teaching, providing tools to perform data analysis and forward modeling through numerical computation. However, development of these codes is often hampered by the fact that there is no well-defined way for the authors to receive credit or professional recognition for their work through the standard methods of scientific publication and subsequent citation of the work. This in turn may discourage researchers from publishing their codes or making them easier for other scientists to use. We investigate the issues involved in citing software in a scientific context, and introduce features that should be components of a citation infrastructure, particularly oriented towards the codes and scientific culture in the area of geodynamics research. The codes used in geodynamics are primarily specialized numerical modeling codes for continuum mechanics problems; they may be developed by individual researchers, teams of researchers, geophysicists in collaboration with computational scientists and applied mathematicians, or by coordinated community efforts such as the Computational Infrastructure for Geodynamics. Some but not all geodynamics codes are open-source. These characteristics are common to many areas of geophysical software development and use. We provide background on the problem of software citation and discuss some of the barriers preventing adoption of such citations, including social/cultural barriers, insufficient technological support infrastructure, and an overall lack of agreement about what a software citation should consist of. We suggest solutions in an initial effort to create a system to support citation of software and promotion of scientific software development.

Adopting Open Source Software to Address Software Risks during the Scientific Data Life Cycle

NASA Astrophysics Data System (ADS)

Vinay, S.; Downs, R. R.

2012-12-01

Software enables the creation, management, storage, distribution, discovery, and use of scientific data throughout the data lifecycle. However, the capabilities offered by software also present risks for the stewardship of scientific data, since future access to digital data is dependent on the use of software. From operating systems to applications for analyzing data, the dependence of data on software presents challenges for the stewardship of scientific data. Adopting open source software provides opportunities to address some of the proprietary risks of data dependence on software. For example, in some cases, open source software can be deployed to avoid licensing restrictions for using, modifying, and transferring proprietary software. The availability of the source code of open source software also enables the inclusion of modifications, which may be contributed by various community members who are addressing similar issues. Likewise, an active community that is maintaining open source software can be a valuable source of help, providing an opportunity to collaborate to address common issues facing adopters. As part of the effort to meet the challenges of software dependence for scientific data stewardship, risks from software dependence have been identified that exist during various times of the data lifecycle. The identification of these risks should enable the development of plans for mitigating software dependencies, where applicable, using open source software, and to improve understanding of software dependency risks for scientific data and how they can be reduced during the data life cycle.

Building the Scientific Modeling Assistant: An interactive environment for specialized software design

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1991-01-01

The construction of scientific software models is an integral part of doing science, both within NASA and within the scientific community at large. Typically, model-building is a time-intensive and painstaking process, involving the design of very large, complex computer programs. Despite the considerable expenditure of resources involved, completed scientific models cannot easily be distributed and shared with the larger scientific community due to the low-level, idiosyncratic nature of the implemented code. To address this problem, we have initiated a research project aimed at constructing a software tool called the Scientific Modeling Assistant. This tool provides automated assistance to the scientist in developing, using, and sharing software models. We describe the Scientific Modeling Assistant, and also touch on some human-machine interaction issues relevant to building a successful tool of this type.

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

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

Gaenko, Alexander; Windus, Theresa L.; Sosonkina, Masha

2012-10-19

The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecularmore » systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods.« less

Software and the Scientist: Coding and Citation Practices in Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, Lorraine; Fish, Allison; Soito, Laura; Smith, MacKenzie; Kellogg, Louise H.

2017-11-01

In geodynamics as in other scientific areas, computation has become a core component of research, complementing field observation, laboratory analysis, experiment, and theory. Computational tools for data analysis, mapping, visualization, modeling, and simulation are essential for all aspects of the scientific workflow. Specialized scientific software is often developed by geodynamicists for their own use, and this effort represents a distinctive intellectual contribution. Drawing on a geodynamics community that focuses on developing and disseminating scientific software, we assess the current practices of software development and attribution, as well as attitudes about the need and best practices for software citation. We analyzed publications by participants in the Computational Infrastructure for Geodynamics and conducted mixed method surveys of the solid earth geophysics community. From this we learned that coding skills are typically learned informally. Participants considered good code as trusted, reusable, readable, and not overly complex and considered a good coder as one that participates in the community in an open and reasonable manor contributing to both long- and short-term community projects. Participants strongly supported citing software reflected by the high rate a software package was named in the literature and the high rate of citations in the references. However, lacking are clear instructions from developers on how to cite and education of users on what to cite. In addition, citations did not always lead to discoverability of the resource. A unique identifier to the software package itself, community education, and citation tools would contribute to better attribution practices.

Built To Last: Using Iterative Development Models for Sustainable Scientific Software Development

NASA Astrophysics Data System (ADS)

Jasiak, M. E.; Truslove, I.; Savoie, M.

2013-12-01

In scientific research, software development exists fundamentally for the results they create. The core research must take focus. It seems natural to researchers, driven by grant deadlines, that every dollar invested in software development should be used to push the boundaries of problem solving. This system of values is frequently misaligned with those of the software being created in a sustainable fashion; short-term optimizations create longer-term sustainability issues. The National Snow and Ice Data Center (NSIDC) has taken bold cultural steps in using agile and lean development and management methodologies to help its researchers meet critical deadlines, while building in the necessary support structure for the code to live far beyond its original milestones. Agile and lean software development and methodologies including Scrum, Kanban, Continuous Delivery and Test-Driven Development have seen widespread adoption within NSIDC. This focus on development methods is combined with an emphasis on explaining to researchers why these methods produce more desirable results for everyone, as well as promoting developers interacting with researchers. This presentation will describe NSIDC's current scientific software development model, how this addresses the short-term versus sustainability dichotomy, the lessons learned and successes realized by transitioning to this agile and lean-influenced model, and the current challenges faced by the organization.

Cooperative Work and Sustainable Scientific Software Practices in R

NASA Astrophysics Data System (ADS)

Weber, N.

2013-12-01

Most scientific software projects are dependent on the work of many diverse people, institutions and organizations. Incentivizing these actors to cooperatively develop software that is both reliable, and sustainable is complicated by the fact that the reward structures of these various actors greatly differ: research scientists want results from a software or model run in order to publish papers, produce new data, or test a hypothesis; software engineers and research centers want compilable, well documented code that is refactorable, reusable and reproducible in future research scenarios. While much research has been done on incentives and motivations for participating in open source software projects or cyberinfrastrcture development, little work has been done on what motivates or incentivizes developers to maintain scientific software projects beyond their original application. This poster will present early results of research into the incentives and motivation for cooperative scientific software development. In particular, this work focuses on motivations for the maintenance and repair of libraries on the software platform R. Our work here uses a sample of R packages that were created by research centers, or are specific to earth, environmental and climate science applications. We first mined 'check' logs from the Comprehensive R Archive Network (CRAN) to determine the amount of time a package has existed, the number of versions it has gone through over this time, the number of releases, and finally the contact information for each official package 'maintainer'. We then sent a survey to each official maintainer, asking them questions about what role they played in developing the original package, and what their motivations were for sustaining the project over time. We will present early results from this mining and our survey of R maintainers.

Software Attribution for Geoscience Applications in the Computational Infrastructure for Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, L.; Dumit, J.; Fish, A.; Soito, L.; Kellogg, L. H.; Smith, M.

2015-12-01

Scientific software is largely developed by individual scientists and represents a significant intellectual contribution to the field. As the scientific culture and funding agencies move towards an expectation that software be open-source, there is a corresponding need for mechanisms to cite software, both to provide credit and recognition to developers, and to aid in discoverability of software and scientific reproducibility. We assess the geodynamic modeling community's current citation practices by examining more than 300 predominantly self-reported publications utilizing scientific software in the past 5 years that is available through the Computational Infrastructure for Geodynamics (CIG). Preliminary results indicate that authors cite and attribute software either through citing (in rank order) peer-reviewed scientific publications, a user's manual, and/or a paper describing the software code. Attributions maybe found directly in the text, in acknowledgements, in figure captions, or in footnotes. What is considered citable varies widely. Citations predominantly lack software version numbers or persistent identifiers to find the software package. Versioning may be implied through reference to a versioned user manual. Authors sometimes report code features used and whether they have modified the code. As an open-source community, CIG requests that researchers contribute their modifications to the repository. However, such modifications may not be contributed back to a repository code branch, decreasing the chances of discoverability and reproducibility. Survey results through CIG's Software Attribution for Geoscience Applications (SAGA) project suggest that lack of knowledge, tools, and workflows to cite codes are barriers to effectively implement the emerging citation norms. Generated on-demand attributions on software landing pages and a prototype extensible plug-in to automatically generate attributions in codes are the first steps towards reproducibility.

Scientific Software - the role of best practices and recommendations

NASA Astrophysics Data System (ADS)

Fritzsch, Bernadette; Bernstein, Erik; Castell, Wolfgang zu; Diesmann, Markus; Haas, Holger; Hammitzsch, Martin; Konrad, Uwe; Lähnemann, David; McHardy, Alice; Pampel, Heinz; Scheliga, Kaja; Schreiber, Andreas; Steglich, Dirk

2017-04-01

In Geosciences - like in most other communities - scientific work strongly depends on software. For big data analysis, existing (closed or open source) program packages are often mixed with newly developed codes. Different versions of software components and varying configurations can influence the result of data analysis. This often makes reproducibility of results and reuse of codes very difficult. Policies for publication and documentation of used and newly developed software, along with best practices, can help tackle this problem. Within the Helmholtz Association a Task Group "Access to and Re-use of scientific software" was implemented by the Open Science Working Group in 2016. The aim of the Task Group is to foster the discussion about scientific software in the Open Science context and to formulate recommendations for the production and publication of scientific software, ensuring open access to it. As a first step, a workshop gathered interested scientists from institutions across Germany. The workshop brought together various existing initiatives from different scientific communities to analyse current problems, share established best practices and come up with possible solutions. The subjects in the working groups covered a broad range of themes, including technical infrastructures, standards and quality assurance, citation of software and reproducibility. Initial recommendations are presented and discussed in the talk. They are the foundation for further discussions in the Helmholtz Association and the Priority Initiative "Digital Information" of the Alliance of Science Organisations in Germany. The talk aims to inform about the activities and to link with other initiatives on the national or international level.

Report on Automated Semantic Analysis of Scientific and Engineering Codes

NASA Technical Reports Server (NTRS)

Stewart. Maark E. M.; Follen, Greg (Technical Monitor)

2001-01-01

The loss of the Mars Climate Orbiter due to a software error reveals what insiders know: software development is difficult and risky because, in part, current practices do not readily handle the complex details of software. Yet, for scientific software development the MCO mishap represents the tip of the iceberg; few errors are so public, and many errors are avoided with a combination of expertise, care, and testing during development and modification. Further, this effort consumes valuable time and resources even when hardware costs and execution time continually decrease. Software development could use better tools! This lack of tools has motivated the semantic analysis work explained in this report. However, this work has a distinguishing emphasis; the tool focuses on automated recognition of the fundamental mathematical and physical meaning of scientific code. Further, its comprehension is measured by quantitatively evaluating overall recognition with practical codes. This emphasis is necessary if software errors-like the MCO error-are to be quickly and inexpensively avoided in the future. This report evaluates the progress made with this problem. It presents recommendations, describes the approach, the tool's status, the challenges, related research, and a development strategy.

Sustaining Open Source Communities through Hackathons - An Example from the ASPECT Community

NASA Astrophysics Data System (ADS)

Heister, T.; Hwang, L.; Bangerth, W.; Kellogg, L. H.

2016-12-01

The ecosystem surrounding a successful scientific open source software package combines both social and technical aspects. Much thought has been given to the technology side of writing sustainable software for large infrastructure projects and software libraries, but less about building the human capacity to perpetuate scientific software used in computational modeling. One effective format for building capacity is regular multi-day hackathons. Scientific hackathons bring together a group of science domain users and scientific software contributors to make progress on a specific software package. Innovation comes through the chance to work with established and new collaborations. Especially in the domain sciences with small communities, hackathons give geographically distributed scientists an opportunity to connect face-to-face. They foster lively discussions amongst scientists with different expertise, promote new collaborations, and increase transparency in both the technical and scientific aspects of code development. ASPECT is an open source, parallel, extensible finite element code to simulate thermal convection, that began development in 2011 under the Computational Infrastructure for Geodynamics. ASPECT hackathons for the past 3 years have grown the number of authors to >50, training new code maintainers in the process. Hackathons begin with leaders establishing project-specific conventions for development, demonstrating the workflow for code contributions, and reviewing relevant technical skills. Each hackathon expands the developer community. Over 20 scientists add >6,000 lines of code during the >1 week event. Participants grow comfortable contributing to the repository and over half continue to contribute afterwards. A high return rate of participants ensures continuity and stability of the group as well as mentoring for novice members. We hope to build other software communities on this model, but anticipate each to bring their own unique challenges.

Requirements Engineering in Building Climate Science Software

NASA Astrophysics Data System (ADS)

Batcheller, Archer L.

Software has an important role in supporting scientific work. This dissertation studies teams that build scientific software, focusing on the way that they determine what the software should do. These requirements engineering processes are investigated through three case studies of climate science software projects. The Earth System Modeling Framework assists modeling applications, the Earth System Grid distributes data via a web portal, and the NCAR (National Center for Atmospheric Research) Command Language is used to convert, analyze and visualize data. Document analysis, observation, and interviews were used to investigate the requirements-related work. The first research question is about how and why stakeholders engage in a project, and what they do for the project. Two key findings arise. First, user counts are a vital measure of project success, which makes adoption important and makes counting tricky and political. Second, despite the importance of quantities of users, a few particular "power users" develop a relationship with the software developers and play a special role in providing feedback to the software team and integrating the system into user practice. The second research question focuses on how project objectives are articulated and how they are put into practice. The team seeks to both build a software system according to product requirements but also to conduct their work according to process requirements such as user support. Support provides essential communication between users and developers that assists with refining and identifying requirements for the software. It also helps users to learn and apply the software to their real needs. User support is a vital activity for scientific software teams aspiring to create infrastructure. The third research question is about how change in scientific practice and knowledge leads to changes in the software, and vice versa. The "thickness" of a layer of software infrastructure impacts whether the software team or users have control and responsibility for making changes in response to new scientific ideas. Thick infrastructure provides more functionality for users, but gives them less control of it. The stability of infrastructure trades off against the responsiveness that the infrastructure can have to user needs.

Final Technical Report - Center for Technology for Advanced Scientific Component Software (TASCS)

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

Sussman, Alan

2014-10-21

This is a final technical report for the University of Maryland work in the SciDAC Center for Technology for Advanced Scientific Component Software (TASCS). The Maryland work focused on software tools for coupling parallel software components built using the Common Component Architecture (CCA) APIs. Those tools are based on the Maryland InterComm software framework that has been used in multiple computational science applications to build large-scale simulations of complex physical systems that employ multiple separately developed codes.

Systems aspects of COBE science data compression

NASA Technical Reports Server (NTRS)

Freedman, I.; Boggess, E.; Seiler, E.

1993-01-01

A general approach to compression of diverse data from large scientific projects has been developed and this paper addresses the appropriate system and scientific constraints together with the algorithm development and test strategy. This framework has been implemented for the COsmic Background Explorer spacecraft (COBE) by retrofitting the existing VAS-based data management system with high-performance compression software permitting random access to the data. Algorithms which incorporate scientific knowledge and consume relatively few system resources are preferred over ad hoc methods. COBE exceeded its planned storage by a large and growing factor and the retrieval of data significantly affects the processing, delaying the availability of data for scientific usage and software test. Embedded compression software is planned to make the project tractable by reducing the data storage volume to an acceptable level during normal processing.

Project management in the development of scientific software

NASA Astrophysics Data System (ADS)

Platz, Jochen

1986-08-01

This contribution is a rough outline of a comprehensive project management model for the development of software for scientific applications. The model was tested in the unique environment of the Siemens AG Corporate Research and Technology Division. Its focal points are the structuring of project content - the so-called phase organization, the project organization and the planning model used, and its particular applicability to innovative projects. The outline focuses largely on actual project management aspects rather than associated software engineering measures.

Open Source Software Development and Lotka's Law: Bibliometric Patterns in Programming.

ERIC Educational Resources Information Center

Newby, Gregory B.; Greenberg, Jane; Jones, Paul

2003-01-01

Applies Lotka's Law to metadata on open source software development. Authoring patterns found in software development productivity are found to be comparable to prior studies of Lotka's Law for scientific and scholarly publishing, and offer promise in predicting aggregate behavior of open source developers. (Author/LRW)

The SCEC Broadband Platform: Open-Source Software for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Goulet, C.; Silva, F.; Maechling, P. J.; Callaghan, S.; Jordan, T. H.

2015-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100Hz) ground motions for earthquakes at regional scales. The BBP scientific software modules implement kinematic rupture generation, low and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, seismogram ground motion amplitude calculations, and goodness of fit measurements. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground motion seismograms, using multiple alternative ground motion simulation methods, and software utilities that can generate plots, charts, and maps. The BBP has been developed over the last five years in a collaborative scientific, engineering, and software development project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The SCEC BBP software released in 2015 can be compiled and run on recent Linux systems with GNU compilers. It includes 5 simulation methods, 7 simulation regions covering California, Japan, and Eastern North America, the ability to compare simulation results against GMPEs, updated ground motion simulation methods, and a simplified command line user interface.

The personal receiving document management and the realization of email function in OAS

NASA Astrophysics Data System (ADS)

Li, Biqing; Li, Zhao

2017-05-01

This software is an independent software system, suitable for small and medium enterprises, contains personal office, scientific research project management and system management functions, independently run in relevant environment, and to solve practical needs. This software is an independent software system, using the current popular B/S (browser/server) structure and ASP.NET technology development, using the Windows 7 operating system, Microsoft SQL Server2005 Visual2008 and database as a development platform, suitable for small and medium enterprises, contains personal office, scientific research project management and system management functions, independently run in relevant environment, and to solve practical needs.

Continuous integration and quality control for scientific software

NASA Astrophysics Data System (ADS)

Neidhardt, A.; Ettl, M.; Brisken, W.; Dassing, R.

2013-08-01

Modern software has to be stable, portable, fast and reliable. This is going to be also more and more important for scientific software. But this requires a sophisticated way to inspect, check and evaluate the quality of source code with a suitable, automated infrastructure. A centralized server with a software repository and a version control system is one essential part, to manage the code basis and to control the different development versions. While each project can be compiled separately, the whole code basis can also be compiled with one central “Makefile”. This is used to create automated, nightly builds. Additionally all sources are inspected automatically with static code analysis and inspection tools, which check well-none error situations, memory and resource leaks, performance issues, or style issues. In combination with an automatic documentation generator it is possible to create the developer documentation directly from the code and the inline comments. All reports and generated information are presented as HTML page on a Web server. Because this environment increased the stability and quality of the software of the Geodetic Observatory Wettzell tremendously, it is now also available for scientific communities. One regular customer is already the developer group of the DiFX software correlator project.

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...

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.

Enhancing Environmental HPC Applications: The EnCompAS approach

NASA Astrophysics Data System (ADS)

Frank, Anton; Donners, John; Pursula, Antti; Seinstra, Frank; Kranzlmüller, Dieter

2015-04-01

Many HPC applications in geoscience are of very high scientific quality and highly optimized for supercomputers. However, some of these codes lack the uptake by other adjacent scientific communities or industry due to deficiencies in usability, quality, and availability. Since enhancing software by, e.g., adding a graphical user interface, respecting data standards, setting up a support structure, or writing an extensive documentation is not of direct and immediate scientific relevance, most developers are not willing to invest any additional effort in these issues. Furthermore, if scientists, who are not directly involved in the development of some scientific software, could make benefit from additional features or interfaces, respective requests are often turned down due to the lack of time and resources. On the other hand, such enhancements are crucial for the sustainability of the scientific assets as well as the widespread or even worldwide distribution of European environmental software. Closely collaborating with environmental scientists the national supercomputing and eScience centres in Helsinki, Amsterdam, and Munich have identified that an enhancement of HPC and data analysis software must be provided as a service to the scientists developing such software. Therefore, first steps have been taken to establish respective services at these centres. In this talk we will present the already existing and envisioned service portfolio, some first success stories, and the approach to harmonize the current status aiming to turn this local effort into a pan-European service offering for environmental science.

Test Driven Development of Scientific Models

NASA Technical Reports Server (NTRS)

Clune, Thomas L.

2014-01-01

Test-Driven Development (TDD), a software development process that promises many advantages for developer productivity and software reliability, has become widely accepted among professional software engineers. As the name suggests, TDD practitioners alternate between writing short automated tests and producing code that passes those tests. Although this overly simplified description will undoubtedly sound prohibitively burdensome to many uninitiated developers, the advent of powerful unit-testing frameworks greatly reduces the effort required to produce and routinely execute suites of tests. By testimony, many developers find TDD to be addicting after only a few days of exposure, and find it unthinkable to return to previous practices.After a brief overview of the TDD process and my experience in applying the methodology for development activities at Goddard, I will delve more deeply into some of the challenges that are posed by numerical and scientific software as well as tools and implementation approaches that should address those challenges.

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

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

Kostadin, Damevski

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

The SCEC/UseIT Intern Program: Creating Open-Source Visualization Software Using Diverse Resources

NASA Astrophysics Data System (ADS)

Francoeur, H.; Callaghan, S.; Perry, S.; Jordan, T.

2004-12-01

The Southern California Earthquake Center undergraduate IT intern program (SCEC UseIT) conducts IT research to benefit collaborative earth science research. Through this program, interns have developed real-time, interactive, 3D visualization software using open-source tools. Dubbed LA3D, a distribution of this software is now in use by the seismic community. LA3D enables the user to interactively view Southern California datasets and models of importance to earthquake scientists, such as faults, earthquakes, fault blocks, digital elevation models, and seismic hazard maps. LA3D is now being extended to support visualizations anywhere on the planet. The new software, called SCEC-VIDEO (Virtual Interactive Display of Earth Objects), makes use of a modular, plugin-based software architecture which supports easy development and integration of new data sets. Currently SCEC-VIDEO is in beta testing, with a full open-source release slated for the future. Both LA3D and SCEC-VIDEO were developed using a wide variety of software technologies. These, which included relational databases, web services, software management technologies, and 3-D graphics in Java, were necessary to integrate the heterogeneous array of data sources which comprise our software. Currently the interns are working to integrate new technologies and larger data sets to increase software functionality and value. In addition, both LA3D and SCEC-VIDEO allow the user to script and create movies. Thus program interns with computer science backgrounds have been writing software while interns with other interests, such as cinema, geology, and education, have been making movies that have proved of great use in scientific talks, media interviews, and education. Thus, SCEC UseIT incorporates a wide variety of scientific and human resources to create products of value to the scientific and outreach communities. The program plans to continue with its interdisciplinary approach, increasing the relevance of the software and expanding its use in the scientific community.

HashDist: Reproducible, Relocatable, Customizable, Cross-Platform Software Stacks for Open Hydrological Science

NASA Astrophysics Data System (ADS)

Ahmadia, A. J.; Kees, C. E.

2014-12-01

Developing scientific software is a continuous balance between not reinventing the wheel and getting fragile codes to interoperate with one another. Binary software distributions such as Anaconda provide a robust starting point for many scientific software packages, but this solution alone is insufficient for many scientific software developers. HashDist provides a critical component of the development workflow, enabling highly customizable, source-driven, and reproducible builds for scientific software stacks, available from both the IPython Notebook and the command line. To address these issues, the Coastal and Hydraulics Laboratory at the US Army Engineer Research and Development Center has funded the development of HashDist in collaboration with Simula Research Laboratories and the University of Texas at Austin. HashDist is motivated by a functional approach to package build management, and features intelligent caching of sources and builds, parametrized build specifications, and the ability to interoperate with system compilers and packages. HashDist enables the easy specification of "software stacks", which allow both the novice user to install a default environment and the advanced user to configure every aspect of their build in a modular fashion. As an advanced feature, HashDist builds can be made relocatable, allowing the easy redistribution of binaries on all three major operating systems as well as cloud, and supercomputing platforms. As a final benefit, all HashDist builds are reproducible, with a build hash specifying exactly how each component of the software stack was installed. This talk discusses the role of HashDist in the hydrological sciences, including its use by the Coastal and Hydraulics Laboratory in the development and deployment of the Proteus Toolkit as well as the Rapid Operational Access and Maneuver Support project. We demonstrate HashDist in action, and show how it can effectively support development, deployment, teaching, and reproducibility for scientists working in the hydrological sciences. The HashDist documentation is available from: http://hashdist.readthedocs.org/en/latest/ HashDist is currently hosted at: https://github.com/hashdist/hashdist

Managing Scientific Software Complexity with Bocca and CCA

DOE PAGES

Allan, Benjamin A.; Norris, Boyana; Elwasif, Wael R.; ...

2008-01-01

In high-performance scientific software development, the emphasis is often on short time to first solution. Even when the development of new components mostly reuses existing components or libraries and only small amounts of new code must be created, dealing with the component glue code and software build processes to obtain complete applications is still tedious and error-prone. Component-based software meant to reduce complexity at the application level increases complexity to the extent that the user must learn and remember the interfaces and conventions of the component model itself. To address these needs, we introduce Bocca, the first tool to enablemore » application developers to perform rapid component prototyping while maintaining robust software-engineering practices suitable to HPC environments. Bocca provides project management and a comprehensive build environment for creating and managing applications composed of Common Component Architecture components. Of critical importance for high-performance computing (HPC) applications, Bocca is designed to operate in a language-agnostic way, simultaneously handling components written in any of the languages commonly used in scientific applications: C, C++, Fortran, Python and Java. Bocca automates the tasks related to the component glue code, freeing the user to focus on the scientific aspects of the application. Bocca embraces the philosophy pioneered by Ruby on Rails for web applications: start with something that works, and evolve it to the user's purpose.« less

OntoSoft: A Software Registry for Geosciences

NASA Astrophysics Data System (ADS)

Garijo, D.; Gil, Y.

2017-12-01

The goal of the EarthCube OntoSoft project is to enable the creation of an ecosystem for software stewardship in geosciences that will empower scientists to manage their software as valuable scientific assets. By sharing software metadata in OntoSoft, scientists enable broader access to that software by other scientists, software professionals, students, and decision makers. Our work to date includes: 1) an ontology for describing scientific software metadata, 2) a distributed scientific software repository that contains more than 750 entries that can be searched and compared across metadata fields, 3) an intelligent user interface that guides scientists to publish software and allows them to crowdsource its corresponding metadata. We have also developed a training program where scientists learn to describe and cite software in their papers in addition to data and provenance, and we are using OntoSoft to show them the benefits of publishing their software metadata. This training program is part of a Geoscience Papers of the Future Initiative, where scientists are reflecting on their current practices, benefits and effort for sharing software and data. This journal paper can be submitted to a Special Section of the AGU Earth and Space Science Journal.

Technology-driven dietary assessment: a software developer’s perspective

PubMed Central

Buday, Richard; Tapia, Ramsey; Maze, Gary R.

2015-01-01

Dietary researchers need new software to improve nutrition data collection and analysis, but creating information technology is difficult. Software development projects may be unsuccessful due to inadequate understanding of needs, management problems, technology barriers or legal hurdles. Cost overruns and schedule delays are common. Barriers facing scientific researchers developing software include workflow, cost, schedule, and team issues. Different methods of software development and the role that intellectual property rights play are discussed. A dietary researcher must carefully consider multiple issues to maximize the likelihood of success when creating new software. PMID:22591224

Characterizing the scientific potential of satellite sensors. [San Francisco, California

NASA Technical Reports Server (NTRS)

1984-01-01

Eleven thematic mapper (TM) radiometric calibration programs were tested and evaluated in support of the task to characterize the potential of LANDSAT TM digital imagery for scientific investigations in the Earth sciences and terrestrial physics. Three software errors related to integer overflow, divide by zero, and nonexist file group were found and solved. Raw, calibrated, and corrected image groups that were created and stored on the Barker2 disk are enumerated. Black and white pixel print files were created for various subscenes of a San Francisco scene (ID 40392-18152). The development of linear regression software is discussed. The output of the software and its function are described. Future work in TM radiometric calibration, image processing, and software development is outlined.

IEEE Computer Society/Software Engineering Institute Software Process Achievement (SPA) Award 2009

DTIC Science & Technology

2011-03-01

capabilities to our GDM. We also introduced software as a service ( SaaS ) as part our technology solutions and have further enhanced our ability to...model PROSPER Infosys production support methodology Q&P quality and productivity R&D research and development SaaS software as a service ... Software Development Life Cycle (SDLC) 23 Table 10: Scientific Estimation Coverage by Service Line 27 CMU/SEI-2011-TR-008 | vi CMU/SEI-2011

A toolbox and a record for scientific model development

NASA Technical Reports Server (NTRS)

Ellman, Thomas

1994-01-01

Scientific computation can benefit from software tools that facilitate construction of computational models, control the application of models, and aid in revising models to handle new situations. Existing environments for scientific programming provide only limited means of handling these tasks. This paper describes a two pronged approach for handling these tasks: (1) designing a 'Model Development Toolbox' that includes a basic set of model constructing operations; and (2) designing a 'Model Development Record' that is automatically generated during model construction. The record is subsequently exploited by tools that control the application of scientific models and revise models to handle new situations. Our two pronged approach is motivated by our belief that the model development toolbox and record should be highly interdependent. In particular, a suitable model development record can be constructed only when models are developed using a well defined set of operations. We expect this research to facilitate rapid development of new scientific computational models, to help ensure appropriate use of such models and to facilitate sharing of such models among working computational scientists. We are testing this approach by extending SIGMA, and existing knowledge-based scientific software design tool.

Agile methods in biomedical software development: a multi-site experience report.

PubMed

Kane, David W; Hohman, Moses M; Cerami, Ethan G; McCormick, Michael W; Kuhlmman, Karl F; Byrd, Jeff A

2006-05-30

Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods. We have found that agile methods are well suited to the exploratory and iterative nature of scientific inquiry. They provide a robust framework for reproducing scientific results and for developing clinical support systems. The agile development approach also provides a model for collaboration between software engineers and researchers. We present our experience using agile methodologies in projects at six different biomedical software development organizations. The organizations include academic, commercial and government development teams, and included both bioinformatics and clinical support applications. We found that agile practices were a match for the needs of our biomedical projects and contributed to the success of our organizations. We found that the agile development approach was a good fit for our organizations, and that these practices should be applicable and valuable to other biomedical software development efforts. Although we found differences in how agile methods were used, we were also able to identify a set of core practices that were common to all of the groups, and that could be a focus for others seeking to adopt these methods.

Agile methods in biomedical software development: a multi-site experience report

PubMed Central

Kane, David W; Hohman, Moses M; Cerami, Ethan G; McCormick, Michael W; Kuhlmman, Karl F; Byrd, Jeff A

2006-01-01

Background Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods. Results We have found that agile methods are well suited to the exploratory and iterative nature of scientific inquiry. They provide a robust framework for reproducing scientific results and for developing clinical support systems. The agile development approach also provides a model for collaboration between software engineers and researchers. We present our experience using agile methodologies in projects at six different biomedical software development organizations. The organizations include academic, commercial and government development teams, and included both bioinformatics and clinical support applications. We found that agile practices were a match for the needs of our biomedical projects and contributed to the success of our organizations. Conclusion We found that the agile development approach was a good fit for our organizations, and that these practices should be applicable and valuable to other biomedical software development efforts. Although we found differences in how agile methods were used, we were also able to identify a set of core practices that were common to all of the groups, and that could be a focus for others seeking to adopt these methods. PMID:16734914

ISEES: an institute for sustainable software to accelerate environmental science

NASA Astrophysics Data System (ADS)

Jones, M. B.; Schildhauer, M.; Fox, P. A.

2013-12-01

Software is essential to the full science lifecycle, spanning data acquisition, processing, quality assessment, data integration, analysis, modeling, and visualization. Software runs our meteorological sensor systems, our data loggers, and our ocean gliders. Every aspect of science is impacted by, and improved by, software. Scientific advances ranging from modeling climate change to the sequencing of the human genome have been rendered possible in the last few decades due to the massive improvements in the capabilities of computers to process data through software. This pivotal role of software in science is broadly acknowledged, while simultaneously being systematically undervalued through minimal investments in maintenance and innovation. As a community, we need to embrace the creation, use, and maintenance of software within science, and address problems such as code complexity, openness,reproducibility, and accessibility. We also need to fully develop new skills and practices in software engineering as a core competency in our earth science disciplines, starting with undergraduate and graduate education and extending into university and agency professional positions. The Institute for Sustainable Earth and Environmental Software (ISEES) is being envisioned as a community-driven activity that can facilitate and galvanize activites around scientific software in an analogous way to synthesis centers such as NCEAS and NESCent that have stimulated massive advances in ecology and evolution. We will describe the results of six workshops (Science Drivers, Software Lifecycles, Software Components, Workforce Development and Training, Sustainability and Governance, and Community Engagement) that have been held in 2013 to envision such an institute. We will present community recommendations from these workshops and our strategic vision for how ISEES will address the technical issues in the software lifecycle, sustainability of the whole software ecosystem, and the critical issue of computational training for the scientific community. Process for envisioning ISEES.

The Structure of the Library Market for Scientific Journals: The Case of Chemistry.

ERIC Educational Resources Information Center

Bensman, Stephen J.

1996-01-01

An analysis of price and scientific value of chemistry journals concluded that scientific value does not play a role in the pricing of scientific journals and that consequently little relationship exists between scientific value and the prices charged libraries for journals. Describes a software package, Serials Evaluator, being developed at…

Tracking Clouds with low cost GNSS chips aided by the Arduino platform

NASA Astrophysics Data System (ADS)

Hameed, Saji; Realini, Eugenio; Ishida, Shinya

2016-04-01

The Global Navigation Satellite System (GNSS) is a constellation of satellites that is used to provide geo-positioning services. Besides this application, the GNSS system is important for a wide range of scientific and civilian applications. For example, GNSS systems are routinely used in civilian applications such as surveying and scientific applications such as the study of crustal deformation. Another important scientific application of GNSS system is in meteorological research. Here it is mainly used to determine the total water vapour content of the troposphere, hereafter Precipitable Water Vapor (PWV). However, both GNSS receivers and software have prohibitively high price due to a variety of reasons. To overcome this somewhat artificial barrier we are exploring the use of low-cost GNSS receivers along with open source GNSS software for scientific research, in particular for GNSS meteorology research. To achieve this aim, we have developed a custom Arduino compatible data logging board that is able to operate together with a specific low-cost single frequency GNSS receiver chip from NVS Technologies AG. We have also developed an open-source software bundle that includes a new Arduino core for the Atmel324p chip, which is the main processor used in our custom logger. We have also developed software code that enables data collection, logging and parsing of the GNSS data stream. Additionally we have comprehensively evaluated the low power characteristics of the GNSS receiver and logger boards. Currently we are exploring the use of several openly source or free to use for research software to map GNSS delays to PWV. These include the open source goGPS (http://www.gogps-project.org/) and gLAB (http://gage.upc.edu/gLAB) and the openly available GAMIT software from Massachusetts Institute of Technology (MIT). We note that all the firmware and software developed as part of this project is available on an open source license.

Four simple recommendations to encourage best practices in research software

PubMed Central

Jiménez, Rafael C.; Kuzak, Mateusz; Alhamdoosh, Monther; Barker, Michelle; Batut, Bérénice; Borg, Mikael; Capella-Gutierrez, Salvador; Chue Hong, Neil; Cook, Martin; Corpas, Manuel; Flannery, Madison; Garcia, Leyla; Gelpí, Josep Ll.; Gladman, Simon; Goble, Carole; González Ferreiro, Montserrat; Gonzalez-Beltran, Alejandra; Griffin, Philippa C.; Grüning, Björn; Hagberg, Jonas; Holub, Petr; Hooft, Rob; Ison, Jon; Katz, Daniel S.; Leskošek, Brane; López Gómez, Federico; Oliveira, Luis J.; Mellor, David; Mosbergen, Rowland; Mulder, Nicola; Perez-Riverol, Yasset; Pergl, Robert; Pichler, Horst; Pope, Bernard; Sanz, Ferran; Schneider, Maria V.; Stodden, Victoria; Suchecki, Radosław; Svobodová Vařeková, Radka; Talvik, Harry-Anton; Todorov, Ilian; Treloar, Andrew; Tyagi, Sonika; van Gompel, Maarten; Vaughan, Daniel; Via, Allegra; Wang, Xiaochuan; Watson-Haigh, Nathan S.; Crouch, Steve

2017-01-01

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations. PMID:28751965

Four simple recommendations to encourage best practices in research software.

PubMed

Jiménez, Rafael C; Kuzak, Mateusz; Alhamdoosh, Monther; Barker, Michelle; Batut, Bérénice; Borg, Mikael; Capella-Gutierrez, Salvador; Chue Hong, Neil; Cook, Martin; Corpas, Manuel; Flannery, Madison; Garcia, Leyla; Gelpí, Josep Ll; Gladman, Simon; Goble, Carole; González Ferreiro, Montserrat; Gonzalez-Beltran, Alejandra; Griffin, Philippa C; Grüning, Björn; Hagberg, Jonas; Holub, Petr; Hooft, Rob; Ison, Jon; Katz, Daniel S; Leskošek, Brane; López Gómez, Federico; Oliveira, Luis J; Mellor, David; Mosbergen, Rowland; Mulder, Nicola; Perez-Riverol, Yasset; Pergl, Robert; Pichler, Horst; Pope, Bernard; Sanz, Ferran; Schneider, Maria V; Stodden, Victoria; Suchecki, Radosław; Svobodová Vařeková, Radka; Talvik, Harry-Anton; Todorov, Ilian; Treloar, Andrew; Tyagi, Sonika; van Gompel, Maarten; Vaughan, Daniel; Via, Allegra; Wang, Xiaochuan; Watson-Haigh, Nathan S; Crouch, Steve

2017-01-01

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

NASA Astrophysics Data System (ADS)

Katz, Daniel S.; Choi, Sou-Cheng T.; Niemeyer, Kyle E.; Hetherington, James; Löffler, Frank; Gunter, Dan; Idaszak, Ray; Brandt, Steven R.; Miller, Mark A.; Gesing, Sandra; Jones, Nick D.; Weber, Nic; Marru, Suresh; Allen, Gabrielle; Penzenstadler, Birgit; Venters, Colin C.; Davis, Ethan; Hwang, Lorraine; Todorov, Ilian; Patra, Abani; de Val-Borro, Miguel

2016-02-01

This report records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3). The report includes a description of the keynote presentation of the workshop, which served as an overview of sustainable scientific software. It also summarizes a set of lightning talks in which speakers highlighted to-the-point lessons and challenges pertaining to sustaining scientific software. The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to funding scientific software; constructing useful common metrics for crediting software stakeholders; identifying principles for sustainable software engineering design; reaching out to research software organizations around the world; and building communities for software sustainability. For each group, we include a point of contact and a landing page that can be used by those who want to join that group's future activities. The main challenge left by the workshop is to see if the groups will execute these activities that they have scheduled, and how the WSSSPE community can encourage this to happen.

Singularity: Scientific containers for mobility of compute.

PubMed

Kurtzer, Gregory M; Sochat, Vanessa; Bauer, Michael W

2017-01-01

Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science.

Singularity: Scientific containers for mobility of compute

PubMed Central

Kurtzer, Gregory M.; Bauer, Michael W.

2017-01-01

Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science. PMID:28494014

Fostering successful scientific software communities

NASA Astrophysics Data System (ADS)

Bangerth, W.; Heister, T.; Hwang, L.; Kellogg, L. H.

2016-12-01

Developing sustainable open source software packages for the sciences appears at first to be primarily a technical challenge: How can one create stable and robust algorithms, appropriate software designs, sufficient documentation, quality assurance strategies such as continuous integration and test suites, or backward compatibility approaches that yield high-quality software usable not only by the authors, but also the broader community of scientists? However, our experience from almost two decades of leading the development of the deal.II software library (http://www.dealii.org, a widely-used finite element package) and the ASPECT code (http://aspect.dealii.org, used to simulate convection in the Earth's mantle) has taught us that technical aspects are not the most difficult ones in scientific open source software. Rather, it is the social challenge of building and maintaining a community of users and developers interested in answering questions on user forums, contributing code, and jointly finding solutions to common technical and non-technical challenges. These problems are posed in an environment where project leaders typically have no resources to reward the majority of contributors, where very few people are specifically paid for the work they do on the project, and with frequent turnover of contributors as project members rotate into and out of jobs. In particular, much software work is done by graduate students who may become fluent enough in a software only a year or two before they leave academia. We will discuss strategies we have found do and do not work in maintaining and growing communities around the scientific software projects we lead. Specifically, we will discuss the management style necessary to keep contributors engaged, ways to give credit where credit is due, and structuring documentation to decrease reliance on forums and thereby allow user communities to grow without straining those who answer questions.

A systematic approach to the Planck LFI end-to-end test and its application to the DPC Level 1 pipeline

NASA Astrophysics Data System (ADS)

Frailis, M.; Maris, M.; Zacchei, A.; Morisset, N.; Rohlfs, R.; Meharga, M.; Binko, P.; Türler, M.; Galeotta, S.; Gasparo, F.; Franceschi, E.; Butler, R. C.; D'Arcangelo, O.; Fogliani, S.; Gregorio, A.; Lowe, S. R.; Maggio, G.; Malaspina, M.; Mandolesi, N.; Manzato, P.; Pasian, F.; Perrotta, F.; Sandri, M.; Terenzi, L.; Tomasi, M.; Zonca, A.

2009-12-01

The Level 1 of the Planck LFI Data Processing Centre (DPC) is devoted to the handling of the scientific and housekeeping telemetry. It is a critical component of the Planck ground segment which has to strictly commit to the project schedule to be ready for the launch and flight operations. In order to guarantee the quality necessary to achieve the objectives of the Planck mission, the design and development of the Level 1 software has followed the ESA Software Engineering Standards. A fundamental step in the software life cycle is the Verification and Validation of the software. The purpose of this work is to show an example of procedures, test development and analysis successfully applied to a key software project of an ESA mission. We present the end-to-end validation tests performed on the Level 1 of the LFI-DPC, by detailing the methods used and the results obtained. Different approaches have been used to test the scientific and housekeeping data processing. Scientific data processing has been tested by injecting signals with known properties directly into the acquisition electronics, in order to generate a test dataset of real telemetry data and reproduce as much as possible nominal conditions. For the HK telemetry processing, validation software have been developed to inject known parameter values into a set of real housekeeping packets and perform a comparison with the corresponding timelines generated by the Level 1. With the proposed validation and verification procedure, where the on-board and ground processing are viewed as a single pipeline, we demonstrated that the scientific and housekeeping processing of the Planck-LFI raw data is correct and meets the project requirements.

The State of Software for Evolutionary Biology.

PubMed

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-05-01

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development.

A toolbox and record for scientific models

NASA Technical Reports Server (NTRS)

Ellman, Thomas

1994-01-01

Computational science presents a host of challenges for the field of knowledge-based software design. Scientific computation models are difficult to construct. Models constructed by one scientist are easily misapplied by other scientists to problems for which they are not well-suited. Finally, models constructed by one scientist are difficult for others to modify or extend to handle new types of problems. Construction of scientific models actually involves much more than the mechanics of building a single computational model. In the course of developing a model, a scientist will often test a candidate model against experimental data or against a priori expectations. Test results often lead to revisions of the model and a consequent need for additional testing. During a single model development session, a scientist typically examines a whole series of alternative models, each using different simplifying assumptions or modeling techniques. A useful scientific software design tool must support these aspects of the model development process as well. In particular, it should propose and carry out tests of candidate models. It should analyze test results and identify models and parts of models that must be changed. It should determine what types of changes can potentially cure a given negative test result. It should organize candidate models, test data, and test results into a coherent record of the development process. Finally, it should exploit the development record for two purposes: (1) automatically determining the applicability of a scientific model to a given problem; (2) supporting revision of a scientific model to handle a new type of problem. Existing knowledge-based software design tools must be extended in order to provide these facilities.

Modern software approaches applied to a Hydrological model: the GEOtop Open-Source Software Project

NASA Astrophysics Data System (ADS)

Cozzini, Stefano; Endrizzi, Stefano; Cordano, Emanuele; Bertoldi, Giacomo; Dall'Amico, Matteo

2017-04-01

The GEOtop hydrological scientific package is an integrated hydrological model that simulates the heat and water budgets at and below the soil surface. It describes the three-dimensional water flow in the soil and the energy exchange with the atmosphere, considering the radiative and turbulent fluxes. Furthermore, it reproduces the highly non-linear interactions between the water and energy balance during soil freezing and thawing, and simulates the temporal evolution of snow cover, soil temperature and moisture. The core components of the package were presented in the 2.0 version (Endrizzi et al, 2014), which was released as Free Software Open-source project. However, despite the high scientific quality of the project, a modern software engineering approach was still missing. Such weakness hindered its scientific potential and its use both as a standalone package and, more importantly, in an integrate way with other hydrological software tools. In this contribution we present our recent software re-engineering efforts to create a robust and stable scientific software package open to the hydrological community, easily usable by researchers and experts, and interoperable with other packages. The activity takes as a starting point the 2.0 version, scientifically tested and published. This version, together with several test cases based on recent published or available GEOtop applications (Cordano and Rigon, 2013, WRR, Kollet et al, 2016, WRR) provides the baseline code and a certain number of referenced results as benchmark. Comparison and scientific validation can then be performed for each software re-engineering activity performed on the package. To keep track of any single change the package is published on its own github repository geotopmodel.github.io/geotop/ under GPL v3.0 license. A Continuous Integration mechanism by means of Travis-CI has been enabled on the github repository on master and main development branches. The usage of CMake configuration tool and the suite of tests (easily manageable by means of ctest tools) greatly reduces the burden of the installation and allows us to enhance portability on different compilers and Operating system platforms. The package was also complemented by several software tools which provide web-based visualization of results based on R plugins, in particular "shiny" (Chang at al, 2016), "geotopbricks" and "geotopOptim2" (Cordano et al, 2016) packages, which allow rapid and efficient scientific validation of new examples and tests. The software re-engineering activities are still under development. However, our first results are promising enough to eventually reach a robust and stable software project that manages in a flexible way a complex state-of-the-art hydrological model like GEOtop and integrates it into wider workflows.

Constraints and Opportunities in GCM Model Development

NASA Technical Reports Server (NTRS)

Schmidt, Gavin; Clune, Thomas

2010-01-01

Over the past 30 years climate models have evolved from relatively simple representations of a few atmospheric processes to complex multi-disciplinary system models which incorporate physics from bottom of the ocean to the mesopause and are used for seasonal to multi-million year timescales. Computer infrastructure over that period has gone from punchcard mainframes to modern parallel clusters. Constraints of working within an ever evolving research code mean that most software changes must be incremental so as not to disrupt scientific throughput. Unfortunately, programming methodologies have generally not kept pace with these challenges, and existing implementations now present a heavy and growing burden on further model development as well as limiting flexibility and reliability. Opportunely, advances in software engineering from other disciplines (e.g. the commercial software industry) as well as new generations of powerful development tools can be incorporated by the model developers to incrementally and systematically improve underlying implementations and reverse the long term trend of increasing development overhead. However, these methodologies cannot be applied blindly, but rather must be carefully tailored to the unique characteristics of scientific software development. We will discuss the need for close integration of software engineers and climate scientists to find the optimal processes for climate modeling.

The GenABEL Project for statistical genomics.

PubMed

Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

Developing sustainable software solutions for bioinformatics by the “ Butterfly” paradigm

PubMed Central

Ahmed, Zeeshan; Zeeshan, Saman; Dandekar, Thomas

2014-01-01

Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (“ Butterfly” paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions. PMID:25383181

Gendermetrics.NET: a novel software for analyzing the gender representation in scientific authoring.

PubMed

Bendels, Michael H K; Brüggmann, Dörthe; Schöffel, Norman; Groneberg, David A

2016-01-01

Imbalances in female career promotion are believed to be strong in the field of academic science. A primary parameter to analyze gender inequalities is the gender authoring in scientific publications. Since the presently available data on gender distribution is largely limited to underpowered studies, we here develop a new approach to analyze authors' genders in large bibliometric databases. A SQL-Server based multiuser software suite was developed that serves as an integrative tool for analyzing bibliometric data with a special emphasis on gender and topographical analysis. The presented system allows seamless integration, inspection, modification, evaluation and visualization of bibliometric data. By providing an adaptive and almost fully automatic integration and analysis process, the inter-individual variability of analysis is kept at a low level. Depending on the scientific question, the system enables the user to perform a scientometric analysis including its visualization within a short period of time. In summary, a new software suite for analyzing gender representations in scientific articles was established. The system is suitable for the comparative analysis of scientific structures on the level of continents, countries, cities, city regions, institutions, research fields and journals.

Scaling Watershed Models: Modern Approaches to Science Computation with MapReduce, Parallelization, and Cloud Optimization

EPA Science Inventory

Environmental models are products of the computer architecture and software tools available at the time of development. Scientifically sound algorithms may persist in their original state even as system architectures and software development approaches evolve and progress. Dating...

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

DOE PAGES

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

2008-01-01

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

ObsPy: Establishing and maintaining an open-source community package

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Barsch, R.

2017-12-01

Python's ecosystem evolved into one of the most powerful and productive research environment across disciplines. ObsPy (https://obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology, Integrated access to the largest data centers, web services, and real-time data streams, A powerful signal processing toolbox tuned to the specific needs of seismologists, and Utility functionality like travel time calculations, geodetic functions, and data visualizations. ObsPy has been in constant unfunded development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. By now around 70 people directly contributed code to ObsPy and we aim to make it a self-sustaining community project.This contributions focusses on several meta aspects of open-source software in science, in particular how we experienced them. During the panel we would like to discuss obvious questions like long-term sustainability with very limited to no funding, insufficient computer science training in many sciences, and gaining hard scientific credits for software development, but also the following questions: How to best deal with the fact that a lot of scientific software is very specialized thus usually solves a complex problem but at the same time can only ever reach a limited pool of developers and users by virtue of it being so specialized? Therefore the "many eyes on the code" approach to develop and improve open-source software only applies in a limited fashion. An initial publication for a significant new scientific software package is fairly straightforward. How to on-board and motivate potential new contributors when they can no longer be lured by a potential co-authorship? When is spending significant time and effort on reusable scientific open-source development a reasonable choice for young researchers? The effort to go from purpose tailored code for a single application resulting in a scientific publication is significantly less compared to generalising and engineering it well enough so it can be used by others.

Integrated System for Autonomous Science

NASA Technical Reports Server (NTRS)

Chien, Steve; Sherwood, Robert; Tran, Daniel; Cichy, Benjamin; Davies, Ashley; Castano, Rebecca; Rabideau, Gregg; Frye, Stuart; Trout, Bruce; Shulman, Seth;

Software Carpentry In The Hydrological Sciences

NASA Astrophysics Data System (ADS)

Ahmadia, A. J.; Kees, C. E.

2014-12-01

Scientists are spending an increasing amount of time building and using hydrology software. However, most scientists are never taught how to do this efficiently. As a result, many are unaware of tools and practices that would allow them to write more reliable and maintainable code with less effort. As hydrology models increase in capability and enter use by a growing number of scientists and their communities, it is important that the scientific software development practices scale up to meet the challenges posed by increasing software complexity, lengthening software lifecycles, a growing number of stakeholders and contributers, and a broadened developer base that extends from application domains to high performance computing centers. Many of these challenges in complexity, lifecycles, and developer base have been successfully met by the open source community, and there are many lessons to be learned from their experiences and practices. Additionally, there is much wisdom to be found in the results of research studies conducted on software engineering itself. Software Carpentry aims to bridge the gap between the current state of software development and these known best practices for scientific software development, with a focus on hands-on exercises and practical advice. In 2014, Software Carpentry workshops targeting earth/environmental sciences and hydrological modeling have been organized and run at the Massachusetts Institute of Technology, the US Army Corps of Engineers, the Community Surface Dynamics Modeling System Annual Meeting, and the Earth Science Information Partners Summer Meeting. In this presentation, we will share some of the successes in teaching this material, as well as discuss and present instructional material specific to hydrological modeling.

Blended Training on Scientific Software: A Study on How Scientific Data Are Generated

ERIC Educational Resources Information Center

Skordaki, Efrosyni-Maria; Bainbridge, Susan

2018-01-01

This paper presents the results of a research study on scientific software training in blended learning environments. The investigation focused on training approaches followed by scientific software users whose goal is the reliable application of such software. A key issue in current literature is the requirement for a theory-substantiated…

Computational Infrastructure for Geodynamics (CIG)

NASA Astrophysics Data System (ADS)

Gurnis, M.; Kellogg, L. H.; Bloxham, J.; Hager, B. H.; Spiegelman, M.; Willett, S.; Wysession, M. E.; Aivazis, M.

2004-12-01

Solid earth geophysicists have a long tradition of writing scientific software to address a wide range of problems. In particular, computer simulations came into wide use in geophysics during the decade after the plate tectonic revolution. Solution schemes and numerical algorithms that developed in other areas of science, most notably engineering, fluid mechanics, and physics, were adapted with considerable success to geophysics. This software has largely been the product of individual efforts and although this approach has proven successful, its strength for solving problems of interest is now starting to show its limitations as we try to share codes and algorithms or when we want to recombine codes in novel ways to produce new science. With funding from the NSF, the US community has embarked on a Computational Infrastructure for Geodynamics (CIG) that will develop, support, and disseminate community-accessible software for the greater geodynamics community from model developers to end-users. The software is being developed for problems involving mantle and core dynamics, crustal and earthquake dynamics, magma migration, seismology, and other related topics. With a high level of community participation, CIG is leveraging state-of-the-art scientific computing into a suite of open-source tools and codes. The infrastructure that we are now starting to develop will consist of: (a) a coordinated effort to develop reusable, well-documented and open-source geodynamics software; (b) the basic building blocks - an infrastructure layer - of software by which state-of-the-art modeling codes can be quickly assembled; (c) extension of existing software frameworks to interlink multiple codes and data through a superstructure layer; (d) strategic partnerships with the larger world of computational science and geoinformatics; and (e) specialized training and workshops for both the geodynamics and broader Earth science communities. The CIG initiative has already started to leverage and develop long-term strategic partnerships with open source development efforts within the larger thrusts of scientific computing and geoinformatics. These strategic partnerships are essential as the frontier has moved into multi-scale and multi-physics problems in which many investigators now want to use simulation software for data interpretation, data assimilation, and hypothesis testing.

Improving Reuse in Software Development for the Life Sciences

ERIC Educational Resources Information Center

Iannotti, Nicholas V.

2013-01-01

The last several years have seen unprecedented advancements in the application of technology to the life sciences, particularly in the area of data generation. Novel scientific insights are now often driven primarily by software development supporting new multidisciplinary and increasingly multifaceted data analysis. However, despite the…

The need for scientific software engineering in the pharmaceutical industry

NASA Astrophysics Data System (ADS)

Luty, Brock; Rose, Peter W.

2017-03-01

Scientific software engineering is a distinct discipline from both computational chemistry project support and research informatics. A scientific software engineer not only has a deep understanding of the science of drug discovery but also the desire, skills and time to apply good software engineering practices. A good team of scientific software engineers can create a software foundation that is maintainable, validated and robust. If done correctly, this foundation enable the organization to investigate new and novel computational ideas with a very high level of efficiency.

The need for scientific software engineering in the pharmaceutical industry.

PubMed

Luty, Brock; Rose, Peter W

2017-03-01

Scientific software engineering is a distinct discipline from both computational chemistry project support and research informatics. A scientific software engineer not only has a deep understanding of the science of drug discovery but also the desire, skills and time to apply good software engineering practices. A good team of scientific software engineers can create a software foundation that is maintainable, validated and robust. If done correctly, this foundation enable the organization to investigate new and novel computational ideas with a very high level of efficiency.

A Call for Bioimaging Software Usability

PubMed Central

Carpenter, Anne E.; Kamentsky, Lee; Eliceiri, Kevin W.

2013-01-01

Bioimaging software developed in a research setting often fails to be widely used by the scientific community. We suggest that, to maximize both the public’s and researchers’ investments, usability should be a more highly valued goal. We describe specific characteristics of usability towards which bioimaging software projects should aim. PMID:22743771

The State of Software for Evolutionary Biology

PubMed Central

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-01-01

Abstract With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development. PMID:29385525

The SCEC Broadband Platform: A Collaborative Open-Source Software Package for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Maechling, P. J.; Goulet, C.; Somerville, P.; Jordan, T. H.

2013-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform is a collaborative software development project involving SCEC researchers, graduate students, and the SCEC Community Modeling Environment. The SCEC Broadband Platform is open-source scientific software that can generate broadband (0-100Hz) ground motions for earthquakes, integrating complex scientific modules that implement rupture generation, low and high-frequency seismogram synthesis, non-linear site effects calculation, and visualization into a software system that supports easy on-demand computation of seismograms. The Broadband Platform operates in two primary modes: validation simulations and scenario simulations. In validation mode, the Broadband Platform runs earthquake rupture and wave propagation modeling software to calculate seismograms of a historical earthquake for which observed strong ground motion data is available. Also in validation mode, the Broadband Platform calculates a number of goodness of fit measurements that quantify how well the model-based broadband seismograms match the observed seismograms for a certain event. Based on these results, the Platform can be used to tune and validate different numerical modeling techniques. During the past year, we have modified the software to enable the addition of a large number of historical events, and we are now adding validation simulation inputs and observational data for 23 historical events covering the Eastern and Western United States, Japan, Taiwan, Turkey, and Italy. In scenario mode, the Broadband Platform can run simulations for hypothetical (scenario) earthquakes. In this mode, users input an earthquake description, a list of station names and locations, and a 1D velocity model for their region of interest, and the Broadband Platform software then calculates ground motions for the specified stations. By establishing an interface between scientific modules with a common set of input and output files, the Broadband Platform facilitates the addition of new scientific methods, which are written by earth scientists in a number of languages such as C, C++, Fortran, and Python. The Broadband Platform's modular design also supports the reuse of existing software modules as building blocks to create new scientific methods. Additionally, the Platform implements a wrapper around each scientific module, converting input and output files to and from the specific formats required (or produced) by individual scientific codes. Working in close collaboration with scientists and research engineers, the SCEC software development group continues to add new capabilities to the Broadband Platform and to release new versions as open-source scientific software distributions that can be compiled and run on many Linux computer systems. Our latest release includes the addition of 3 new simulation methods and several new data products, such as map and distance-based goodness of fit plots. Finally, as the number and complexity of scenarios simulated using the Broadband Platform increase, we have added batching utilities to substantially improve support for running large-scale simulations on computing clusters.

Software Carpentry and the Hydrological Sciences

NASA Astrophysics Data System (ADS)

Ahmadia, A. J.; Kees, C. E.; Farthing, M. W.

2013-12-01

Scientists are spending an increasing amount of time building and using hydrology software. However, most scientists are never taught how to do this efficiently. As a result, many are unaware of tools and practices that would allow them to write more reliable and maintainable code with less effort. As hydrology models increase in capability and enter use by a growing number of scientists and their communities, it is important that the scientific software development practices scale up to meet the challenges posed by increasing software complexity, lengthening software lifecycles, a growing number of stakeholders and contributers, and a broadened developer base that extends from application domains to high performance computing centers. Many of these challenges in complexity, lifecycles, and developer base have been successfully met by the open source community, and there are many lessons to be learned from their experiences and practices. Additionally, there is much wisdom to be found in the results of research studies conducted on software engineering itself. Software Carpentry aims to bridge the gap between the current state of software development and these known best practices for scientific software development, with a focus on hands-on exercises and practical advice based on the following principles: 1. Write programs for people, not computers. 2. Automate repetitive tasks 3. Use the computer to record history 4. Make incremental changes 5. Use version control 6. Don't repeat yourself (or others) 7. Plan for mistakes 8. Optimize software only after it works 9. Document design and purpose, not mechanics 10. Collaborate We discuss how these best practices, arising from solid foundations in research and experience, have been shown to help improve scientist's productivity and the reliability of their software.

Instrument control software requirement specification for Extremely Large Telescopes

NASA Astrophysics Data System (ADS)

Young, Peter J.; Kiekebusch, Mario J.; Chiozzi, Gianluca

2010-07-01

Engineers in several observatories are now designing the next generation of optical telescopes, the Extremely Large Telescopes (ELT). These are very complex machines that will host sophisticated astronomical instruments to be used for a wide range of scientific studies. In order to carry out scientific observations, a software infrastructure is required to orchestrate the control of the multiple subsystems and functions. This paper will focus on describing the considerations, strategies and main issues related to the definition and analysis of the software requirements for the ELT's Instrument Control System using modern development processes and modelling tools like SysML.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific biomedical problems. Many of these tools are designed and developed by biomedical scientists independently or with the support of computer experts and often made freely available for the benefit of scientific community. The current trends for customized biomedical software tools are highlighted in this short review.

The GenABEL Project for statistical genomics

PubMed Central

Karssen, Lennart C.; van Duijn, Cornelia M.; Aulchenko, Yurii S.

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

Software Engineering Support of the Third Round of Scientific Grand Challenge Investigations: An Earth Modeling System Software Framework Strawman Design that Integrates Cactus and UCLA/UCB Distributed Data Broker

NASA Technical Reports Server (NTRS)

Talbot, Bryan; Zhou, Shu-Jia; Higgins, Glenn

2002-01-01

One of the most significant challenges in large-scale climate modeling, as well as in high-performance computing in other scientific fields, is that of effectively integrating many software models from multiple contributors. A software framework facilitates the integration task. both in the development and runtime stages of the simulation. Effective software frameworks reduce the programming burden for the investigators, freeing them to focus more on the science and less on the parallel communication implementation, while maintaining high performance across numerous supercomputer and workstation architectures. This document proposes a strawman framework design for the climate community based on the integration of Cactus, from the relativistic physics community, and UCLA/UCB Distributed Data Broker (DDB) from the climate community. This design is the result of an extensive survey of climate models and frameworks in the climate community as well as frameworks from many other scientific communities. The design addresses fundamental development and runtime needs using Cactus, a framework with interfaces for FORTRAN and C-based languages, and high-performance model communication needs using DDB. This document also specifically explores object-oriented design issues in the context of climate modeling as well as climate modeling issues in terms of object-oriented design.

Open-source framework for documentation of scientific software written on MATLAB-compatible programming languages

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

Numerical simulators for adaptive optics systems have become an essential tool for the research and development of the future advanced astronomical instruments. However, growing software code of the numerical simulator makes it difficult to continue to support the code itself. The problem of adequate documentation of the astronomical software for adaptive optics simulators may complicate the development since the documentation must contain up-to-date schemes and mathematical descriptions implemented in the software code. Although most modern programming environments like MATLAB or Octave have in-built documentation abilities, they are often insufficient for the description of a typical adaptive optics simulator code. This paper describes a general cross-platform framework for the documentation of scientific software using open-source tools such as LATEX, mercurial, Doxygen, and Perl. Using the Perl script that translates M-files MATLAB comments into C-like, one can use Doxygen to generate and update the documentation for the scientific source code. The documentation generated by this framework contains the current code description with mathematical formulas, images, and bibliographical references. A detailed description of the framework components is presented as well as the guidelines for the framework deployment. Examples of the code documentation for the scripts and functions of a MATLAB-based adaptive optics simulator are provided.

Open Marketplace for Simulation Software on the Basis of a Web Platform

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-02-01

The focus in development of a new generation of middleware shifts from the global grid systems to building convenient and efficient web platforms for remote access to individual computing resources. Further line of their development, suggested in this work, is related not only with the quantitative increase in their number and with the expansion of scientific, engineering, and manufacturing areas in which they are used, but also with improved technology for remote deployment of application software on the resources interacting with the web platforms. Currently, the services for providers of application software in the context of scientific-oriented web platforms is not developed enough. The proposed in this work new web platforms of application software market should have all the features of the existing web platforms for submissions of jobs to remote resources plus the provision of specific web services for interaction on market principles between the providers and consumers of application packages. The suggested approach will be approved on the example of simulation applications in the field of nonlinear optics.

Software quality and process improvement in scientific simulation codes

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

Ambrosiano, J.; Webster, R.

1997-11-01

This report contains viewgraphs on the quest to develope better simulation code quality through process modeling and improvement. This study is based on the experience of the authors and interviews with ten subjects chosen from simulation code development teams at LANL. This study is descriptive rather than scientific.

Perspectives on distributed computing : thirty people, four user types, and the distributed computing user experience.

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

Childers, L.; Liming, L.; Foster, I.

2008-10-15

This report summarizes the methodology and results of a user perspectives study conducted by the Community Driven Improvement of Globus Software (CDIGS) project. The purpose of the study was to document the work-related goals and challenges facing today's scientific technology users, to record their perspectives on Globus software and the distributed-computing ecosystem, and to provide recommendations to the Globus community based on the observations. Globus is a set of open source software components intended to provide a framework for collaborative computational science activities. Rather than attempting to characterize all users or potential users of Globus software, our strategy has beenmore » to speak in detail with a small group of individuals in the scientific community whose work appears to be the kind that could benefit from Globus software, learn as much as possible about their work goals and the challenges they face, and describe what we found. The result is a set of statements about specific individuals experiences. We do not claim that these are representative of a potential user community, but we do claim to have found commonalities and differences among the interviewees that may be reflected in the user community as a whole. We present these as a series of hypotheses that can be tested by subsequent studies, and we offer recommendations to Globus developers based on the assumption that these hypotheses are representative. Specifically, we conducted interviews with thirty technology users in the scientific community. We included both people who have used Globus software and those who have not. We made a point of including individuals who represent a variety of roles in scientific projects, for example, scientists, software developers, engineers, and infrastructure providers. The following material is included in this report: (1) A summary of the reported work-related goals, significant issues, and points of satisfaction with the use of Globus software; (2) A method for characterizing users according to their technology interactions, and identification of four user types among the interviewees using the method; (3) Four profiles that highlight points of commonality and diversity in each user type; (4) Recommendations for technology developers and future studies; (5) A description of the interview protocol and overall study methodology; (6) An anonymized list of the interviewees; and (7) Interview writeups and summary data. The interview summaries in Section 3 and transcripts in Appendix D illustrate the value of distributed computing software--and Globus in particular--to scientific enterprises. They also document opportunities to make these tools still more useful both to current users and to new communities. We aim our recommendations at developers who intend their software to be used and reused in many applications. (This kind of software is often referred to as 'middleware.') Our two core recommendations are as follows. First, it is essential for middleware developers to understand and explicitly manage the multiple user products in which their software components are used. We must avoid making assumptions about the commonality of these products and, instead, study and account for their diversity. Second, middleware developers should engage in different ways with different kinds of users. Having identified four general user types in Section 4, we provide specific ideas for how to engage them in Section 5.« less

The SCEC Broadband Platform: Open-Source Software for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Goulet, C. A.; Maechling, P. J.; Callaghan, S.; Jordan, T. H.

2016-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100 Hz) ground motions for earthquakes at regional scales. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The BBP scientific software modules implement kinematic rupture generation, low- and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, several ground motion intensity measure calculations, and various ground motion goodness-of-fit tools. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground-motion seismograms, using multiple alternative ground motion simulation methods, and software utilities to generate tables, plots, and maps. The BBP has been developed over the last five years in a collaborative project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The SCEC BBP software released in 2016 can be compiled and run on recent Linux and Mac OS X systems with GNU compilers. It includes five simulation methods, seven simulation regions covering California, Japan, and Eastern North America, and the ability to compare simulation results against empirical ground motion models (aka GMPEs). The latest version includes updated ground motion simulation methods, a suite of new validation metrics and a simplified command line user interface.

Visualization techniques to aid in the analysis of multi-spectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, Edward W.; Domik, Gitta O.; Ayres, Thomas R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions, and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists.

Automated real-time software development

NASA Technical Reports Server (NTRS)

Jones, Denise R.; Walker, Carrie K.; Turkovich, John J.

1993-01-01

A Computer-Aided Software Engineering (CASE) system has been developed at the Charles Stark Draper Laboratory (CSDL) under the direction of the NASA Langley Research Center. The CSDL CASE tool provides an automated method of generating source code and hard copy documentation from functional application engineering specifications. The goal is to significantly reduce the cost of developing and maintaining real-time scientific and engineering software while increasing system reliability. This paper describes CSDL CASE and discusses demonstrations that used the tool to automatically generate real-time application code.

Harnessing the power of emerging petascale platforms

NASA Astrophysics Data System (ADS)

Mellor-Crummey, John

2007-07-01

As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC-2) program, science teams are tackling problems that require computational simulation and modeling at the petascale. A grand challenge for computer science is to develop software technology that makes it easier to harness the power of these systems to aid scientific discovery. As part of its activities, the SciDAC-2 Center for Scalable Application Development Software (CScADS) is building open source software tools to support efficient scientific computing on the emerging leadership-class platforms. In this paper, we describe two tools for performance analysis and tuning that are being developed as part of CScADS: a tool for analyzing scalability and performance, and a tool for optimizing loop nests for better node performance. We motivate these tools by showing how they apply to S3D, a turbulent combustion code under development at Sandia National Laboratory. For S3D, our node performance analysis tool helped uncover several performance bottlenecks. Using our loop nest optimization tool, we transformed S3D's most costly loop nest to reduce execution time by a factor of 2.94 for a processor working on a 503 domain.

Component Verification and Certification in NASA Missions

NASA Technical Reports Server (NTRS)

Giannakopoulou, Dimitra; Penix, John; Norvig, Peter (Technical Monitor)

2001-01-01

Software development for NASA missions is a particularly challenging task. Missions are extremely ambitious scientifically, have very strict time frames, and must be accomplished with a maximum degree of reliability. Verification technologies must therefore be pushed far beyond their current capabilities. Moreover, reuse and adaptation of software architectures and components must be incorporated in software development within and across missions. This paper discusses NASA applications that we are currently investigating from these perspectives.

The Particle-in-Cell and Kinetic Simulation Software Center

NASA Astrophysics Data System (ADS)

Mori, W. B.; Decyk, V. K.; Tableman, A.; Fonseca, R. A.; Tsung, F. S.; Hu, Q.; Winjum, B. J.; An, W.; Dalichaouch, T. N.; Davidson, A.; Hildebrand, L.; Joglekar, A.; May, J.; Miller, K.; Touati, M.; Xu, X. L.

2017-10-01

The UCLA Particle-in-Cell and Kinetic Simulation Software Center (PICKSC) aims to support an international community of PIC and plasma kinetic software developers, users, and educators; to increase the use of this software for accelerating the rate of scientific discovery; and to be a repository of knowledge and history for PIC. We discuss progress towards making available and documenting illustrative open-source software programs and distinct production programs; developing and comparing different PIC algorithms; coordinating the development of resources for the educational use of kinetic software; and the outcomes of our first sponsored OSIRIS users workshop. We also welcome input and discussion from anyone interested in using or developing kinetic software, in obtaining access to our codes, in collaborating, in sharing their own software, or in commenting on how PICKSC can better serve the DPP community. Supported by NSF under Grant ACI-1339893 and by the UCLA Institute for Digital Research and Education.

Software Reviews: Programs Worth a Second Look.

ERIC Educational Resources Information Center

Classroom Computer Learning, 1989

1989-01-01

Reviews three software programs: (1) "Cartooners"--develops creative arts and animation, grades 1-6, Apple IIGS; (2) "PC Globe+"--social studies, geography, grades 4-12, IBM(384K); (3) "Wood Car Rally"--physical science, scientific method, grades 3-9, Apple II. (MVL)

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

Towards Test Driven Development for Computational Science with pFUnit

NASA Technical Reports Server (NTRS)

Rilee, Michael L.; Clune, Thomas L.

2014-01-01

Developers working in Computational Science & Engineering (CSE)/High Performance Computing (HPC) must contend with constant change due to advances in computing technology and science. Test Driven Development (TDD) is a methodology that mitigates software development risks due to change at the cost of adding comprehensive and continuous testing to the development process. Testing frameworks tailored for CSE/HPC, like pFUnit, can lower the barriers to such testing, yet CSE software faces unique constraints foreign to the broader software engineering community. Effective testing of numerical software requires a comprehensive suite of oracles, i.e., use cases with known answers, as well as robust estimates for the unavoidable numerical errors associated with implementation with finite-precision arithmetic. At first glance these concerns often seem exceedingly challenging or even insurmountable for real-world scientific applications. However, we argue that this common perception is incorrect and driven by (1) a conflation between model validation and software verification and (2) the general tendency in the scientific community to develop relatively coarse-grained, large procedures that compound numerous algorithmic steps.We believe TDD can be applied routinely to numerical software if developers pursue fine-grained implementations that permit testing, neatly side-stepping concerns about needing nontrivial oracles as well as the accumulation of errors. We present an example of a successful, complex legacy CSE/HPC code whose development process shares some aspects with TDD, which we contrast with current and potential capabilities. A mix of our proposed methodology and framework support should enable everyday use of TDD by CSE-expert developers.

Administrative automation in a scientific environment

NASA Technical Reports Server (NTRS)

Jarrett, J. R.

1984-01-01

Although the scientific personnel at GSFC were advanced in the development and use of hardware and software for scientific applications, resistance to the use of automation or purchase of terminals, software and services, specifically for administrative functions was widespread. The approach used to address problems and constraints and plans for administrative automation within the Space and Earth Sciences Directorate are delineated. Accomplishments thus far include reduction of paperwork and manual efforts; improved communications through telemail and committees; additional support staff; increased awareness at all levels on ergonomic concerns and the need for training; better equipment; improved ADP skills through experience; management commitment; and an overall strategy for automating.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1993-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X DataSlice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1992-01-01

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X Data Slice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

Report: Scientific Software.

ERIC Educational Resources Information Center

Borman, Stuart A.

1985-01-01

Discusses various aspects of scientific software, including evaluation and selection of commercial software products; program exchanges, catalogs, and other information sources; major data analysis packages; statistics and chemometrics software; and artificial intelligence. (JN)

Bioconductor: open software development for computational biology and bioinformatics

PubMed Central

Gentleman, Robert C; Carey, Vincent J; Bates, Douglas M; Bolstad, Ben; Dettling, Marcel; Dudoit, Sandrine; Ellis, Byron; Gautier, Laurent; Ge, Yongchao; Gentry, Jeff; Hornik, Kurt; Hothorn, Torsten; Huber, Wolfgang; Iacus, Stefano; Irizarry, Rafael; Leisch, Friedrich; Li, Cheng; Maechler, Martin; Rossini, Anthony J; Sawitzki, Gunther; Smith, Colin; Smyth, Gordon; Tierney, Luke; Yang, Jean YH; Zhang, Jianhua

2004-01-01

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples. PMID:15461798

What makes computational open source software libraries successful?

NASA Astrophysics Data System (ADS)

Bangerth, Wolfgang; Heister, Timo

2013-01-01

Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.

eSciMart: Web Platform for Scientific Software Marketplace

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-10-01

In this paper we suggest a design of a web marketplace where users of scientific application software and databases, presented in the form of web services, as well as their providers will have presence simultaneously. The model, which will be the basis for the web marketplace is close to the customer-to-customer (C2C) model, which has been successfully used, for example, on the auction sites such as eBay (ebay.com). Unlike the classical model of C2C the suggested marketplace focuses on application software in the form of web services, and standardization of API through which application software will be integrated into the web marketplace. A prototype of such a platform, entitled eSciMart, is currently being developed at SINP MSU.

A toolbox for developing bioinformatics software

PubMed Central

Potrzebowski, Wojciech; Puton, Tomasz; Rother, Magdalena; Wywial, Ewa; Bujnicki, Janusz M.

2012-01-01

Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers. PMID:21803787

Software Issues at the User Interface

DTIC Science & Technology

1991-05-01

successful integration of parallel computers into mainstream scientific computing. Clearly a compiler is the most important software tool available to a...Computer Science University of Colorado Boulder, CO 80309 ABSTRACT We review software issues that are critical to the successful integration of parallel...The development of an optimizing compiler of this quality, addressing communicaton instructions as well as computational instructions is a major

Automated Reuse of Scientific Subroutine Libraries through Deductive Synthesis

NASA Technical Reports Server (NTRS)

Lowry, Michael R.; Pressburger, Thomas; VanBaalen, Jeffrey; Roach, Steven

1997-01-01

Systematic software construction offers the potential of elevating software engineering from an art-form to an engineering discipline. The desired result is more predictable software development leading to better quality and more maintainable software. However, the overhead costs associated with the formalisms, mathematics, and methods of systematic software construction have largely precluded their adoption in real-world software development. In fact, many mainstream software development organizations, such as Microsoft, still maintain a predominantly oral culture for software development projects; which is far removed from a formalism-based culture for software development. An exception is the limited domain of safety-critical software, where the high-assuiance inherent in systematic software construction justifies the additional cost. We believe that systematic software construction will only be adopted by mainstream software development organization when the overhead costs have been greatly reduced. Two approaches to cost mitigation are reuse (amortizing costs over many applications) and automation. For the last four years, NASA Ames has funded the Amphion project, whose objective is to automate software reuse through techniques from systematic software construction. In particular, deductive program synthesis (i.e., program extraction from proofs) is used to derive a composition of software components (e.g., subroutines) that correctly implements a specification. The construction of reuse libraries of software components is the standard software engineering solution for improving software development productivity and quality.

Scientific Computation Application Partnerships in Materials and Chemical Sciences, Charge Transfer and Charge Transport in Photoactivated Systems, Developing Electron-Correlated Methods for Excited State Structure and Dynamics in the NWChem Software Suite

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

Cramer, Christopher J.

Charge transfer and charge transport in photoactivated systems are fundamental processes that underlie solar energy capture, solar energy conversion, and photoactivated catalysis, both organometallic and enzymatic. We developed methods, algorithms, and software tools needed for reliable treatment of the underlying physics for charge transfer and charge transport, an undertaking with broad applicability to the goals of the fundamental-interaction component of the Department of Energy Office of Basic Energy Sciences and the exascale initiative of the Office of Advanced Scientific Computing Research.

The Scientific Filesystem.

PubMed

Sochat, Vanessa

2018-05-01

Here, we present the Scientific Filesystem (SCIF), an organizational format that supports exposure of executables and metadata for discoverability of scientific applications. The format includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within. SCIF makes it easy to expose metadata, multiple environments, installation steps, files, and entry points to render scientific applications consistent, modular, and discoverable. A SCIF can be installed on a traditional host or in a container technology such as Docker or Singularity. We start by reviewing the background and rationale for the SCIF, followed by an overview of the specification and the different levels of internal modules ("apps") that the organizational format affords. Finally, we demonstrate that SCIF is useful by implementing and discussing several use cases that improve user interaction and understanding of scientific applications. SCIF is released along with a client and integration in the Singularity 2.4 software to quickly install and interact with SCIF. When used inside of a reproducible container, a SCIF is a recipe for reproducibility and introspection of the functions and users that it serves. We use SCIF to evaluate container software, provide metrics, serve scientific workflows, and execute a primary function under different contexts. To encourage collaboration and sharing of applications, we developed tools along with an open source, version-controlled, tested, and programmatically accessible web infrastructure. SCIF and associated resources are available at https://sci-f.github.io. The ease of using SCIF, especially in the context of containers, offers promise for scientists' work to be self-documenting and programatically parseable for maximum reproducibility. SCIF opens up an abstraction from underlying programming languages and packaging logic to work with scientific applications, opening up new opportunities for scientific software development.

Anomalies as a Catalyst for Middle School Students' Knowledge Construction and Scientific Reasoning during Science Inquiry.

ERIC Educational Resources Information Center

Echevarria, Marissa

2003-01-01

Knowledge construction and scientific reasoning were examined during a unit in genetics, in which anomalies were used as a catalyst for student learning. Students used genetics simulation software to develop hypotheses and run tests of fruit fly crosses to develop mental models of simple dominance trait transmission. Instruction was intended to…

Artificial intelligence support for scientific model-building

NASA Technical Reports Server (NTRS)

Keller, Richard M.

1992-01-01

Scientific model-building can be a time-intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientific development team to understand. We believe that artificial intelligence techniques can facilitate both the model-building and model-sharing process. In this paper, we overview our effort to build a scientific modeling software tool that aids the scientist in developing and using models. This tool includes an interactive intelligent graphical interface, a high-level domain specific modeling language, a library of physics equations and experimental datasets, and a suite of data display facilities.

Visualization techniques to aid in the analysis of multispectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, E. W.; Domik, Gitta O.; Ayres, T. R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists. Twenty-one examples of the use of visualization for astrophysical data are included with this report. Sixteen publications related to efforts performed during or initiated through work on this project are listed at the end of this report.

Enhancing GIS Capabilities for High Resolution Earth Science Grids

NASA Astrophysics Data System (ADS)

Koziol, B. W.; Oehmke, R.; Li, P.; O'Kuinghttons, R.; Theurich, G.; DeLuca, C.

2017-12-01

Applications for high performance GIS will continue to increase as Earth system models pursue more realistic representations of Earth system processes. Finer spatial resolution model input and output, unstructured or irregular modeling grids, data assimilation, and regional coordinate systems present novel challenges for GIS frameworks operating in the Earth system modeling domain. This presentation provides an overview of two GIS-driven applications that combine high performance software with big geospatial datasets to produce value-added tools for the modeling and geoscientific community. First, a large-scale interpolation experiment using National Hydrography Dataset (NHD) catchments, a high resolution rectilinear CONUS grid, and the Earth System Modeling Framework's (ESMF) conservative interpolation capability will be described. ESMF is a parallel, high-performance software toolkit that provides capabilities (e.g. interpolation) for building and coupling Earth science applications. ESMF is developed primarily by the NOAA Environmental Software Infrastructure and Interoperability (NESII) group. The purpose of this experiment was to test and demonstrate the utility of high performance scientific software in traditional GIS domains. Special attention will be paid to the nuanced requirements for dealing with high resolution, unstructured grids in scientific data formats. Second, a chunked interpolation application using ESMF and OpenClimateGIS (OCGIS) will demonstrate how spatial subsetting can virtually remove computing resource ceilings for very high spatial resolution interpolation operations. OCGIS is a NESII-developed Python software package designed for the geospatial manipulation of high-dimensional scientific datasets. An overview of the data processing workflow, why a chunked approach is required, and how the application could be adapted to meet operational requirements will be discussed here. In addition, we'll provide a general overview of OCGIS's parallel subsetting capabilities including challenges in the design and implementation of a scientific data subsetter.

Test Driven Development of a Parameterized Ice Sheet Component

NASA Astrophysics Data System (ADS)

Clune, T.

2011-12-01

Test driven development (TDD) is a software development methodology that offers many advantages over traditional approaches including reduced development and maintenance costs, improved reliability, and superior design quality. Although TDD is widely accepted in many software communities, the suitability to scientific software is largely undemonstrated and warrants a degree of skepticism. Indeed, numerical algorithms pose several challenges to unit testing in general, and TDD in particular. Among these challenges are the need to have simple, non-redundant closed-form expressions to compare against the results obtained from the implementation as well as realistic error estimates. The necessity for serial and parallel performance raises additional concerns for many scientific applicaitons. In previous work I demonstrated that TDD performed well for the development of a relatively simple numerical model that simulates the growth of snowflakes, but the results were anecdotal and of limited relevance to far more complex software components typical of climate models. This investigation has now been extended by successfully applying TDD to the implementation of a substantial portion of a new parameterized ice sheet component within a full climate model. After a brief introduction to TDD, I will present techniques that address some of the obstacles encountered with numerical algorithms. I will conclude with some quantitative and qualitative comparisons against climate components developed in a more traditional manner.

Front End Software for Online Database Searching. Part 2: The Marketplace.

ERIC Educational Resources Information Center

Levy, Louise R.; Hawkins, Donald T.

1986-01-01

This article analyzes the front end software marketplace and discusses some of the complex forces influencing it. Discussion covers intermediary market; end users (library customers, scientific and technical professionals, corporate business specialists, consumers); marketing strategies; a British front end development firm; competitive pressures;…

Preparing a scientific manuscript in Linux: Today's possibilities and limitations.

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux.

Requirements Engineering in Building Climate Science Software

ERIC Educational Resources Information Center

Batcheller, Archer L.

2011-01-01

Software has an important role in supporting scientific work. This dissertation studies teams that build scientific software, focusing on the way that they determine what the software should do. These requirements engineering processes are investigated through three case studies of climate science software projects. The Earth System Modeling…

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Lecocq, Thomas; Megies, Tobias; Krischer, Lion; Sales de Andrade, Elliott; Barsch, Robert; Beyreuther, Moritz

2016-04-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides * read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, * a comprehensive signal processing toolbox tuned to the needs of seismologists, * integrated access to all large data centers, web services and databases, and * convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software. ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. This contribution will give a short introduction and overview of ObsPy and highlight a number of use cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; Beyreuther, M.

2015-12-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, a comprehensive signal processing toolbox tuned to the needs of seismologists, integrated access to all large data centers, web services and databases, and convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software.ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it.This contribution will give a short introduction and overview of ObsPy and highlight a number of us cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

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

PubMed

Sanner, Michel F

2005-03-01

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

Two Demonstrations with a New Data-Acquisition System

ERIC Educational Resources Information Center

Kraftmakher, Yaakov

2014-01-01

Nowadays, the use of data-acquisition systems in undergraduate laboratories is routine. Many computer-assisted experiments became possible with the PASCO scientific data-acquisition system based on the 750 Interface and DataStudio software. A new data-acquisition system developed by PASCO includes the 850 Universal Interface and Capstone software.…

Frameworks Coordinate Scientific Data Management

NASA Technical Reports Server (NTRS)

2012-01-01

Jet Propulsion Laboratory computer scientists developed a unique software framework to help NASA manage its massive amounts of science data. Through a partnership with the Apache Software Foundation of Forest Hill, Maryland, the technology is now available as an open-source solution and is in use by cancer researchers and pediatric hospitals.

The open-source movement: an introduction for forestry professionals

Treesearch

Patrick Proctor; Paul C. Van Deusen; Linda S. Heath; Jeffrey H. Gove

2005-01-01

In recent years, the open-source movement has yielded a generous and powerful suite of software and utilities that rivals those developed by many commercial software companies. Open-source programs are available for many scientific needs: operating systems, databases, statistical analysis, Geographic Information System applications, and object-oriented programming....

Nurturing reliable and robust open-source scientific software

NASA Astrophysics Data System (ADS)

Uieda, L.; Wessel, P.

2017-12-01

Scientific results are increasingly the product of software. The reproducibility and validity of published results cannot be ensured without access to the source code of the software used to produce them. Therefore, the code itself is a fundamental part of the methodology and must be published along with the results. With such a reliance on software, it is troubling that most scientists do not receive formal training in software development. Tools such as version control, continuous integration, and automated testing are routinely used in industry to ensure the correctness and robustness of software. However, many scientist do not even know of their existence (although efforts like Software Carpentry are having an impact on this issue; software-carpentry.org). Publishing the source code is only the first step in creating an open-source project. For a project to grow it must provide documentation, participation guidelines, and a welcoming environment for new contributors. Expanding the project community is often more challenging than the technical aspects of software development. Maintainers must invest time to enforce the rules of the project and to onboard new members, which can be difficult to justify in the context of the "publish or perish" mentality. This problem will continue as long as software contributions are not recognized as valid scholarship by hiring and tenure committees. Furthermore, there are still unsolved problems in providing attribution for software contributions. Many journals and metrics of academic productivity do not recognize citations to sources other than traditional publications. Thus, some authors choose to publish an article about the software and use it as a citation marker. One issue with this approach is that updating the reference to include new contributors involves writing and publishing a new article. A better approach would be to cite a permanent archive of individual versions of the source code in services such as Zenodo (zenodo.org). However, citations to these sources are not always recognized when computing citation metrics. In summary, the widespread development of reliable and robust open-source software relies on the creation of formal training programs in software development best practices and the recognition of software as a valid form of scholarship.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations

PubMed Central

2011-01-01

Background Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Findings Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux. PMID:22018246

Plagiarism Detection by Online Solutions.

PubMed

Masic, Izet; Begic, Edin; Dobraca, Amra

2017-01-01

The problem of plagiarism represents one of the burning issues of the modern scientific world. Detection of plagiarism is a problem that the Editorial Board encounters in their daily work. Software solutions represent a good solution for the detection of plagiarism. The problem of plagiarism will become most discussed topic of the modern scientific world, especially due to the development of standard measures, which rank the work of one author. Investment in education, education of young research personnel about the importance of scientific research, with paying particular attention on ethical behavior, becomes an imperative of academic staff. Editors have to invest additional effort in the development of the base of reviewers team as well as in their proper guidance, because after all, despite the software solutions, they are the best weapon to fight plagiarism. Peer review process should be a key of successful operation of each journal.

3-D Imaging In Virtual Environment: A Scientific Clinical and Teaching Tool

NASA Technical Reports Server (NTRS)

Ross, Muriel D.; DeVincenzi, Donald L. (Technical Monitor)

1996-01-01

The advent of powerful graphics workstations and computers has led to the advancement of scientific knowledge through three-dimensional (3-D) reconstruction and imaging of biological cells and tissues. The Biocomputation Center at NASA Ames Research Center pioneered the effort to produce an entirely computerized method for reconstruction of objects from serial sections studied in a transmission electron microscope (TEM). The software developed, ROSS (Reconstruction of Serial Sections), is now being distributed to users across the United States through Space Act Agreements. The software is in widely disparate fields such as geology, botany, biology and medicine. In the Biocomputation Center, ROSS serves as the basis for development of virtual environment technologies for scientific and medical use. This report will describe the Virtual Surgery Workstation Project that is ongoing with clinicians at Stanford University Medical Center, and the role of the Visible Human data in the project.

Do Over or Make Do? Climate Models as a Software Development Challenge (Invited)

NASA Astrophysics Data System (ADS)

Easterbrook, S. M.

2010-12-01

We present the results of a comparative study of the software engineering culture and practices at four different earth system modeling centers: the UK Met Office Hadley Centre, the National Center for Atmospheric Research (NCAR), The Max-Planck-Institut für Meteorologie (MPI-M), and the Institut Pierre Simon Laplace (IPSL). The study investigated the software tools and techniques used at each center to assess their effectiveness. We also investigated how differences in the organizational structures, collaborative relationships, and technical infrastructures constrain the software development and affect software quality. Specific questions for the study included 1) Verification and Validation - What techniques are used to ensure that the code matches the scientists’ understanding of what it should do? How effective are these are at eliminating errors of correctness and errors of understanding? 2) Coordination - How are the contributions from across the modeling community coordinated? For coupled models, how are the differences in the priorities of different, overlapping communities of users addressed? 3) Division of responsibility - How are the responsibilities for coding, verification, and coordination distributed between different roles (scientific, engineering, support) in the organization? 4) Planning and release processes - How do modelers decide on priorities for model development, how do they decide which changes to tackle in a particular release of the model? 5) Debugging - How do scientists debug the models, what types of bugs do they find in their code, and how they find them? The results show that each center has evolved a set of model development practices that are tailored to their needs and organizational constraints. These practices emphasize scientific validity, but tend to neglect other software qualities, and all the centers struggle frequently with software problems. The testing processes are effective at removing software errors prior to release, but the code is hard to understand and hard to change. Software errors and model configuration problems are common during model development, and appear to have a serious impact on scientific productivity. These problems have grown dramatically in recent years with the growth in size and complexity of earth system models. Much of the success in obtaining valid simulations from the models depends on the scientists developing their own code, experimenting with alternatives, running frequent full system tests, and exploring patterns in the results. Blind application of generic software engineering processes is unlikely to work well. Instead, each center needs to lean how to balance the need for better coordination through a more disciplined approach with the freedom to explore, and the value of having scientists work directly with the code. This suggests that each center can learn a lot from comparing their practices with others, but that each might need to develop a different set of best practices.

Report on the Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2)

NASA Astrophysics Data System (ADS)

Katz, Daniel S.; Choi, Sou-Cheng T.; Wilkins-Diehr, Nancy; Chue Hong, Neil; Venters, Colin C.; Howison, James; Seinstra, Frank; Jones, Matthew; Cranston, Karen; Clune, Thomas L.; de Val-Borro, Miguel; Littauer, Richard

2016-02-01

This technical report records and discusses the Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2). The report includes a description of the alternative, experimental submission and review process, two workshop keynote presentations, a series of lightning talks, a discussion on sustainability, and five discussions from the topic areas of exploring sustainability; software development experiences; credit & incentives; reproducibility & reuse & sharing; and code testing & code review. For each topic, the report includes a list of tangible actions that were proposed and that would lead to potential change. The workshop recognized that reliance on scientific software is pervasive in all areas of world-leading research today. The workshop participants then proceeded to explore different perspectives on the concept of sustainability. Key enablers and barriers of sustainable scientific software were identified from their experiences. In addition, recommendations with new requirements such as software credit files and software prize frameworks were outlined for improving practices in sustainable software engineering. There was also broad consensus that formal training in software development or engineering was rare among the practitioners. Significant strides need to be made in building a sense of community via training in software and technical practices, on increasing their size and scope, and on better integrating them directly into graduate education programs. Finally, journals can define and publish policies to improve reproducibility, whereas reviewers can insist that authors provide sufficient information and access to data and software to allow them reproduce the results in the paper. Hence a list of criteria is compiled for journals to provide to reviewers so as to make it easier to review software submitted for publication as a "Software Paper."

Enhanced Master Controller Unit Tester

NASA Technical Reports Server (NTRS)

Benson, Patricia; Johnson, Yvette; Johnson, Brian; Williams, Philip; Burton, Geoffrey; McCoy, Anthony

2007-01-01

The Enhanced Master Controller Unit Tester (EMUT) software is a tool for development and testing of software for a master controller (MC) flight computer. The primary function of the EMUT software is to simulate interfaces between the MC computer and external analog and digital circuitry (including other computers) in a rack of equipment to be used in scientific experiments. The simulations span the range of nominal, off-nominal, and erroneous operational conditions, enabling the testing of MC software before all the equipment becomes available.

Gaia DR1 documentation Chapter 6: Variability

NASA Astrophysics Data System (ADS)

Eyer, L.; Rimoldini, L.; Guy, L.; Holl, B.; Clementini, G.; Cuypers, J.; Mowlavi, N.; Lecoeur-Taïbi, I.; De Ridder, J.; Charnas, J.; Nienartowicz, K.

2017-12-01

This chapter describes the photometric variability processing of the Gaia DR1 data. Coordination Unit 7 is responsible for the variability analysis of over a billion celestial sources. In particular the definition, design, development, validation and provision of a software package for the data processing of photometrically variable objects. Data Processing Centre Geneva (DPCG) responsibilities cover all issues related to the computational part of the CU7 analysis. These span: hardware provisioning, including selection, deployment and optimisation of suitable hardware, choosing and developing software architecture, defining data and scientific workflows as well as operational activities such as configuration management, data import, time series reconstruction, storage and processing handling, visualisation and data export. CU7/DPCG is also responsible for interaction with other DPCs and CUs, software and programming training for the CU7 members, scientific software quality control and management of software and data lifecycle. Details about the specific data treatment steps of the Gaia DR1 data products are found in Eyer et al. (2017) and are not repeated here. The variability content of the Gaia DR1 focusses on a subsample of Cepheids and RR Lyrae stars around the South ecliptic pole, showcasing the performance of the Gaia photometry with respect to variable objects.

OHD/HL/HSMB - Hydrologic Science & Modeling Branch

Science.gov Websites

apply these sciences to application software and data products developed within the HL and as a hydrologic services program. HSMB applies its scientific expertise to training material developed

A Padawan Programmer's Guide to Developing Software Libraries.

PubMed

Yurkovich, James T; Yurkovich, Benjamin J; Dräger, Andreas; Palsson, Bernhard O; King, Zachary A

2017-11-22

With the rapid adoption of computational tools in the life sciences, scientists are taking on the challenge of developing their own software libraries and releasing them for public use. This trend is being accelerated by popular technologies and platforms, such as GitHub, Jupyter, R/Shiny, that make it easier to develop scientific software and by open-source licenses that make it easier to release software. But how do you build a software library that people will use? And what characteristics do the best libraries have that make them enduringly popular? Here, we provide a reference guide, based on our own experiences, for developing software libraries along with real-world examples to help provide context for scientists who are learning about these concepts for the first time. While we can only scratch the surface of these topics, we hope that this article will act as a guide for scientists who want to write great software that is built to last. Copyright © 2017 Elsevier Inc. All rights reserved.

Are Earth System model software engineering practices fit for purpose? A case study.

NASA Astrophysics Data System (ADS)

Easterbrook, S. M.; Johns, T. C.

2009-04-01

We present some analysis and conclusions from a case study of the culture and practices of scientists at the Met Office and Hadley Centre working on the development of software for climate and Earth System models using the MetUM infrastructure. The study examined how scientists think about software correctness, prioritize their requirements in making changes, and develop a shared understanding of the resulting models. We conclude that highly customized techniques driven strongly by scientific research goals have evolved for verification and validation of such models. In a formal software engineering context these represents costly, but invaluable, software integration tests with considerable benefits. The software engineering practices seen also exhibit recognisable features of both agile and open source software development projects - self-organisation of teams consistent with a meritocracy rather than top-down organisation, extensive use of informal communication channels, and software developers who are generally also users and science domain experts. We draw some general conclusions on whether these practices work well, and what new software engineering challenges may lie ahead as Earth System models become ever more complex and petascale computing becomes the norm.

It’s about time: How do sky surveys manage uncertainty about scientific needs many years into the future

NASA Astrophysics Data System (ADS)

Darch, Peter T.; Sands, Ashley E.

2016-06-01

Sky surveys, such as the Sloan Digital Sky Survey (SDSS) and the Large Synoptic Survey Telescope (LSST), generate data on an unprecedented scale. While many scientific projects span a few years from conception to completion, sky surveys are typically on the scale of decades. This paper focuses on critical challenges arising from long timescales, and how sky surveys address these challenges.We present findings from a study of LSST, comprising interviews (n=58) and observation. Conceived in the 1990s, the LSST Corporation was formed in 2003, and construction began in 2014. LSST will commence data collection operations in 2022 for ten years.One challenge arising from this long timescale is uncertainty about future needs of the astronomers who will use these data many years hence. Sources of uncertainty include scientific questions to be posed, astronomical phenomena to be studied, and tools and practices these astronomers will have at their disposal. These uncertainties are magnified by the rapid technological and scientific developments anticipated between now and the start of LSST operations.LSST is implementing a range of strategies to address these challenges. Some strategies involve delaying resolution of uncertainty, placing this resolution in the hands of future data users. Other strategies aim to reduce uncertainty by shaping astronomers’ data analysis practices so that these practices will integrate well with LSST once operations begin.One approach that exemplifies both types of strategy is the decision to make LSST data management software open source, even now as it is being developed. This policy will enable future data users to adapt this software to evolving needs. In addition, LSST intends for astronomers to start using this software well in advance of 2022, thereby embedding LSST software and data analysis approaches in the practices of astronomers.These findings strengthen arguments for making the software supporting sky surveys available as open source. Such arguments usually focus on reuse potential of software, and enhancing replicability of analyses. In this case, however, open source software also promises to mitigate the critical challenge of anticipating the needs of future data users.

Archiving Software Systems: Approaches to Preserve Computational Capabilities

NASA Astrophysics Data System (ADS)

King, T. A.

2014-12-01

A great deal of effort is made to preserve scientific data. Not only because data is knowledge, but it is often costly to acquire and is sometimes collected under unique circumstances. Another part of the science enterprise is the development of software to process and analyze the data. Developed software is also a large investment and worthy of preservation. However, the long term preservation of software presents some challenges. Software often requires a specific technology stack to operate. This can include software, operating systems and hardware dependencies. One past approach to preserve computational capabilities is to maintain ancient hardware long past its typical viability. On an archive horizon of 100 years, this is not feasible. Another approach to preserve computational capabilities is to archive source code. While this can preserve details of the implementation and algorithms, it may not be possible to reproduce the technology stack needed to compile and run the resulting applications. This future forward dilemma has a solution. Technology used to create clouds and process big data can also be used to archive and preserve computational capabilities. We explore how basic hardware, virtual machines, containers and appropriate metadata can be used to preserve computational capabilities and to archive functional software systems. In conjunction with data archives, this provides scientist with both the data and capability to reproduce the processing and analysis used to generate past scientific results.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

Scientific workflows promise to enable efficient scaling-up of researcher code to handle large datasets and workloads, as well as documentation of scientific processing via standardized provenance records, etc. Workflow systems and related frameworks for coordinating the execution of otherwise separate components are limited, however, in their ability to overcome software engineering design problems commonly encountered in pre-existing components, such as scripts developed externally by scientists in their laboratories. In practice, this often means that components must be rewritten or replaced in a time-consuming, expensive process. In the course of an extensive workflow development project involving large-scale oceanographic image processing, we have begun to identify and codify 'anti-patterns'--problematic design characteristics of software--that make components fit poorly into complex automated workflows. We have gone on to develop and document low-effort solutions and best practices that efficiently address the anti-patterns we have identified. The issues, solutions, and best practices can be used to evaluate and improve existing code, as well as guiding the development of new components. For example, we have identified a common anti-pattern we call 'batch-itis' in which a script fails and then cannot perform more work, even if that work is not precluded by the failure. The solution we have identified--removing unnecessary looping over independent units of work--is often easier to code than the anti-pattern, as it eliminates the need for complex control flow logic in the component. Other anti-patterns we have identified are similarly easy to identify and often easy to fix. We have drawn upon experience working with three science teams at Woods Hole Oceanographic Institution, each of which has designed novel imaging instruments and associated image analysis code. By developing use cases and prototypes within these teams, we have undertaken formal evaluations of software components developed by programmers with widely varying levels of expertise, and have been able to discover and characterize a number of anti-patterns. Our evaluation methodology and testbed have also enabled us to assess the efficacy of strategies to address these anti-patterns according to scientifically relevant metrics, such as ability of algorithms to perform faster than the rate of data acquisition and the accuracy of workflow component output relative to ground truth. The set of anti-patterns and solutions we have identified augments of the body of more well-known software engineering anti-patterns by addressing additional concerns that obtain when a software component has to function as part of a workflow assembled out of independently-developed codebases. Our experience shows that identifying and resolving these anti-patterns reduces development time and improves performance without reducing component reusability.

The Hidden Job Requirements for a Software Engineer

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

Marinovici, Maria C.; Kirkham, Harold; Glass, Kevin A.

In a world increasingly operated by computers, where innovation depends on software, the software engineer’s role is changing continuously and gaining new dimensions. In commercial software development as well as scientific research environments, the way software developers are perceived is changing, because they are more important to the business than ever before. Nowadays, their job requires skills extending beyond the regular job description posted by HR, and more is expected. To advance and thrive in their new roles, the software engineers must embrace change, and practice the themes of the new era (integration, collaboration and optimization). The challenges may bemore » somehow intimidating for freshly graduated software engineers. Through this paper the authors hope to set them on a path for success, by helping them relinquish their fear of the unknown.« less

RELAP-7 Software Verification and Validation Plan

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

Smith, Curtis L.; Choi, Yong-Joon; Zou, Ling

This INL plan comprehensively describes the software for RELAP-7 and documents the software, interface, and software design requirements for the application. The plan also describes the testing-based software verification and validation (SV&V) process—a set of specially designed software models used to test RELAP-7. The RELAP-7 (Reactor Excursion and Leak Analysis Program) code is a nuclear reactor system safety analysis code being developed at Idaho National Laboratory (INL). The code is based on the INL’s modern scientific software development framework – MOOSE (Multi-Physics Object-Oriented Simulation Environment). The overall design goal of RELAP-7 is to take advantage of the previous thirty yearsmore » of advancements in computer architecture, software design, numerical integration methods, and physical models. The end result will be a reactor systems analysis capability that retains and improves upon RELAP5’s capability and extends the analysis capability for all reactor system simulation scenarios.« less

Software Writing Skills for Your Research - Lessons Learned from Workshops in the Geosciences

NASA Astrophysics Data System (ADS)

Hammitzsch, Martin

2016-04-01

Findings presented in scientific papers are based on data and software. Once in a while they come along with data - but not commonly with software. However, the software used to gain findings plays a crucial role in the scientific work. Nevertheless, software is rarely seen publishable. Thus researchers may not reproduce the findings without the software which is in conflict with the principle of reproducibility in sciences. For both, the writing of publishable software and the reproducibility issue, the quality of software is of utmost importance. For many programming scientists the treatment of source code, e.g. with code design, version control, documentation, and testing is associated with additional work that is not covered in the primary research task. This includes the adoption of processes following the software development life cycle. However, the adoption of software engineering rules and best practices has to be recognized and accepted as part of the scientific performance. Most scientists have little incentive to improve code and do not publish code because software engineering habits are rarely practised by researchers or students. Software engineering skills are not passed on to followers as for paper writing skill. Thus it is often felt that the software or code produced is not publishable. The quality of software and its source code has a decisive influence on the quality of research results obtained and their traceability. So establishing best practices from software engineering to serve scientific needs is crucial for the success of scientific software. Even though scientists use existing software and code, i.e., from open source software repositories, only few contribute their code back into the repositories. So writing and opening code for Open Science means that subsequent users are able to run the code, e.g. by the provision of sufficient documentation, sample data sets, tests and comments which in turn can be proven by adequate and qualified reviews. This assumes that scientist learn to write and release code and software as they learn to write and publish papers. Having this in mind, software could be valued and assessed as a contribution to science. But this requires the relevant skills that can be passed to colleagues and followers. Therefore, the GFZ German Research Centre for Geosciences performed three workshops in 2015 to address the passing of software writing skills to young scientists, the next generation of researchers in the Earth, planetary and space sciences. Experiences in running these workshops and the lessons learned will be summarized in this presentation. The workshops have received support and funding by Software Carpentry, a volunteer organization whose goal is to make scientists more productive, and their work more reliable, by teaching them basic computing skills, and by FOSTER (Facilitate Open Science Training for European Research), a two-year, EU-Funded (FP7) project, whose goal to produce a European-wide training programme that will help to incorporate Open Access approaches into existing research methodologies and to integrate Open Science principles and practice in the current research workflow by targeting the young researchers and other stakeholders.

NASA Software Cost Estimation Model: An Analogy Based Estimation Model

NASA Technical Reports Server (NTRS)

Hihn, Jairus; Juster, Leora; Menzies, Tim; Mathew, George; Johnson, James

2015-01-01

The cost estimation of software development activities is increasingly critical for large scale integrated projects such as those at DOD and NASA especially as the software systems become larger and more complex. As an example MSL (Mars Scientific Laboratory) developed at the Jet Propulsion Laboratory launched with over 2 million lines of code making it the largest robotic spacecraft ever flown (Based on the size of the software). Software development activities are also notorious for their cost growth, with NASA flight software averaging over 50% cost growth. All across the agency, estimators and analysts are increasingly being tasked to develop reliable cost estimates in support of program planning and execution. While there has been extensive work on improving parametric methods there is very little focus on the use of models based on analogy and clustering algorithms. In this paper we summarize our findings on effort/cost model estimation and model development based on ten years of software effort estimation research using data mining and machine learning methods to develop estimation models based on analogy and clustering. The NASA Software Cost Model performance is evaluated by comparing it to COCOMO II, linear regression, and K-­ nearest neighbor prediction model performance on the same data set.

The Scientific Filesystem

PubMed Central

Sochat, Vanessa

2018-01-01

Abstract Background Here, we present the Scientific Filesystem (SCIF), an organizational format that supports exposure of executables and metadata for discoverability of scientific applications. The format includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within. SCIF makes it easy to expose metadata, multiple environments, installation steps, files, and entry points to render scientific applications consistent, modular, and discoverable. A SCIF can be installed on a traditional host or in a container technology such as Docker or Singularity. We start by reviewing the background and rationale for the SCIF, followed by an overview of the specification and the different levels of internal modules (“apps”) that the organizational format affords. Finally, we demonstrate that SCIF is useful by implementing and discussing several use cases that improve user interaction and understanding of scientific applications. SCIF is released along with a client and integration in the Singularity 2.4 software to quickly install and interact with SCIF. When used inside of a reproducible container, a SCIF is a recipe for reproducibility and introspection of the functions and users that it serves. Results We use SCIF to evaluate container software, provide metrics, serve scientific workflows, and execute a primary function under different contexts. To encourage collaboration and sharing of applications, we developed tools along with an open source, version-controlled, tested, and programmatically accessible web infrastructure. SCIF and associated resources are available at https://sci-f.github.io. The ease of using SCIF, especially in the context of containers, offers promise for scientists’ work to be self-documenting and programatically parseable for maximum reproducibility. SCIF opens up an abstraction from underlying programming languages and packaging logic to work with scientific applications, opening up new opportunities for scientific software development. PMID:29718213

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

PubMed Central

Lapp, Hilmar; Bala, Sendu; Balhoff, James P.; Bouck, Amy; Goto, Naohisa; Holder, Mark; Holland, Richard; Holloway, Alisha; Katayama, Toshiaki; Lewis, Paul O.; Mackey, Aaron J.; Osborne, Brian I.; Piel, William H.; Kosakovsky Pond, Sergei L.; Poon, Art F.Y.; Qiu, Wei-Gang; Stajich, Jason E.; Stoltzfus, Arlin; Thierer, Tobias; Vilella, Albert J.; Vos, Rutger A.; Zmasek, Christian M.; Zwickl, Derrick J.; Vision, Todd J.

2007-01-01

In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.

A study of software standards used in the avionics industry

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.

1994-01-01

Within the past decade, software has become an increasingly common element in computing systems. In particular, the role of software used in the aerospace industry, especially in life- or safety-critical applications, is rapidly expanding. This intensifies the need to use effective techniques for achieving and verifying the reliability of avionics software. Although certain software development processes and techniques are mandated by government regulating agencies, no one methodology has been shown to consistently produce reliable software. The knowledge base for designing reliable software simply has not reached the maturity of its hardware counterpart. In an effort to increase our understanding of software, the Langley Research Center conducted a series of experiments over 15 years with the goal of understanding why and how software fails. As part of this program, the effectiveness of current industry standards for the development of avionics is being investigated. This study involves the generation of a controlled environment to conduct scientific experiments on software processes.

FAST: A multi-processed environment for visualization of computational fluid dynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

1991-01-01

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

Realizing the Living Paper using the ProvONE Model for Reproducible Research

NASA Astrophysics Data System (ADS)

Jones, M. B.; Jones, C. S.; Ludäscher, B.; Missier, P.; Walker, L.; Slaughter, P.; Schildhauer, M.; Cuevas-Vicenttín, V.

2015-12-01

Science has advanced through traditional publications that codify research results as a permenant part of the scientific record. But because publications are static and atomic, researchers can only cite and reference a whole work when building on prior work of colleagues. The open source software model has demonstrated a new approach in which strong version control in an open environment can nurture an open ecosystem of software. Developers now commonly fork and extend software giving proper credit, with less repetition, and with confidence in the relationship to original software. Through initiatives like 'Beyond the PDF', an analogous model has been imagined for open science, in which software, data, analyses, and derived products become first class objects within a publishing ecosystem that has evolved to be finer-grained and is realized through a web of linked open data. We have prototyped a Living Paper concept by developing the ProvONE provenance model for scientific workflows, with prototype deployments in DataONE. ProvONE promotes transparency and openness by describing the authenticity, origin, structure, and processing history of research artifacts and by detailing the steps in computational workflows that produce derived products. To realize the Living Paper, we decompose scientific papers into their constituent products and publish these as compound objects in the DataONE federation of archival repositories. Each individual finding and sub-product of a reseach project (such as a derived data table, a workflow or script, a figure, an image, or a finding) can be independently stored, versioned, and cited. ProvONE provenance traces link these fine-grained products within and across versions of a paper, and across related papers that extend an original analysis. This allows for open scientific publishing in which researchers extend and modify findings, creating a dynamic, evolving web of results that collectively represent the scientific enterprise. The Living Paper provides detailed metadata for properly interpreting and verifying individual research findings, for tracing the origin of ideas, for launching new lines of inquiry, and for implementing transitive credit for research and engineering.

GRIDVIEW: Recent Improvements in Research and Education Software for Exploring Mars Topography

NASA Technical Reports Server (NTRS)

Roark, J. H.; Frey, H. V.

2001-01-01

We have developed an Interactive Data Language (IDL) scientific visualization software tool called GRIDVIEW that can be used in research and education to explore and study the most recent Mars Orbiter Laser Altimeter (MOLA) gridded topography of Mars (http://denali.gsfc.nasa.gov/mola_pub/gridview). Additional information is contained in the original extended abstract.

Caltech/JPL Conference on Image Processing Technology, Data Sources and Software for Commercial and Scientific Applications

NASA Technical Reports Server (NTRS)

Redmann, G. H.

1976-01-01

Recent advances in image processing and new applications are presented to the user community to stimulate the development and transfer of this technology to industrial and commercial applications. The Proceedings contains 37 papers and abstracts, including many illustrations (some in color) and provides a single reference source for the user community regarding the ordering and obtaining of NASA-developed image-processing software and science data.

The Validation by Measurement Theory of Proposed Object-Oriented Software Metrics

NASA Technical Reports Server (NTRS)

Neal, Ralph D.

1996-01-01

Moving software development into the engineering arena requires controllability, and to control a process, it must be measurable. Measuring the process does no good if the product is not also measured, i.e., being the best at producing an inferior product does not define a quality process. Also, not every number extracted from software development is a valid measurement. A valid measurement only results when we are able to verify that the number is representative of the attribute that we wish to measure. Many proposed software metrics are used by practitioners without these metrics ever having been validated, leading to costly but often useless calculations. Several researchers have bemoaned the lack of scientific precision in much of the published software measurement work and have called for validation of software metrics by measurement theory. This dissertation applies measurement theory to validate fifty proposed object-oriented software metrics.

A Component-based Programming Model for Composite, Distributed Applications

NASA Technical Reports Server (NTRS)

Eidson, Thomas M.; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

The nature of scientific programming is evolving to larger, composite applications that are composed of smaller element applications. These composite applications are more frequently being targeted for distributed, heterogeneous networks of computers. They are most likely programmed by a group of developers. Software component technology and computational frameworks are being proposed and developed to meet the programming requirements of these new applications. Historically, programming systems have had a hard time being accepted by the scientific programming community. In this paper, a programming model is outlined that attempts to organize the software component concepts and fundamental programming entities into programming abstractions that will be better understood by the application developers. The programming model is designed to support computational frameworks that manage many of the tedious programming details, but also that allow sufficient programmer control to design an accurate, high-performance application.

AceTree: a major update and case study in the long term maintenance of open-source scientific software.

PubMed

Katzman, Braden; Tang, Doris; Santella, Anthony; Bao, Zhirong

2018-04-04

AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software. Large scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration. By responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.

The Computational Infrastructure for Geodynamics: An Example of Software Curation and Citation in the Geodynamics Community

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2017-12-01

Curation of software promotes discoverability and accessibility and works hand in hand with scholarly citation to ascribe value to, and provide recognition for software development. To meet this challenge, the Computational Infrastructure for Geodynamics (CIG) maintains a community repository built on custom and open tools to promote discovery, access, identification, credit, and provenance of research software for the geodynamics community. CIG (geodynamics.org) originated from recognition of the tremendous effort required to develop sound software and the need to reduce duplication of effort and to sustain community codes. CIG curates software across 6 domains and has developed and follows software best practices that include establishing test cases, documentation, and a citable publication for each software package. CIG software landing web pages provide access to current and past releases; many are also accessible through the CIG community repository on github. CIG has now developed abc - attribution builder for citation to enable software users to give credit to software developers. abc uses zenodo as an archive and as the mechanism to obtain a unique identifier (DOI) for scientific software. To assemble the metadata, we searched the software's documentation and research publications and then requested the primary developers to verify. In this process, we have learned that each development community approaches software attribution differently. The metadata gathered is based on guidelines established by groups such as FORCE11 and OntoSoft. The rollout of abc is gradual as developers are forward-looking, rarely willing to go back and archive prior releases in zenodo. Going forward all actively developed packages will utilize the zenodo and github integration to automate the archival process when a new release is issued. How to handle legacy software, multi-authored libraries, and assigning roles to software remain open issues.

Proceedings of the Workshop on Software Engineering Foundations for End-User Programming (SEEUP 2009)

DTIC Science & Technology

2009-11-01

interest of scientific and technical information exchange. This work is sponsored by the U.S. Department of Defense. The Software Engineering Institute is a...an interesting conti- nuum between how many different requirements a program must satisfy: the more complex and diverse the requirements, the more... Gender differences in approaches to end-user software development have also been reported in debugging feature usage [1] and in end-user web programming

Agile parallel bioinformatics workflow management using Pwrake.

PubMed

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

2011-09-08

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

Agile parallel bioinformatics workflow management using Pwrake

PubMed Central

2011-01-01

Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles may facilitate sharing workflows among the scientific community. Workflows for GATK and Dindel are available at http://github.com/misshie/Workflows. PMID:21899774

Knowledge-Based Parallel Performance Technology for Scientific Application Competitiveness Final Report

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

Malony, Allen D; Shende, Sameer

The primary goal of the University of Oregon's DOE "œcompetitiveness" project was to create performance technology that embodies and supports knowledge of performance data, analysis, and diagnosis in parallel performance problem solving. The target of our development activities was the TAU Performance System and the technology accomplishments reported in this and prior reports have all been incorporated in the TAU open software distribution. In addition, the project has been committed to maintaining strong interactions with the DOE SciDAC Performance Engineering Research Institute (PERI) and Center for Technology for Advanced Scientific Component Software (TASCS). This collaboration has proved valuable for translationmore » of our knowledge-based performance techniques to parallel application development and performance engineering practice. Our outreach has also extended to the DOE Advanced CompuTational Software (ACTS) collection and project. Throughout the project we have participated in the PERI and TASCS meetings, as well as the ACTS annual workshops.« less

Oak Regeneration: A Knowledge Synthesis

Treesearch

H. Michael Rauscher; David L. Loftis; Charles E. McGee; Christopher V. Worth

1997-01-01

This scientific literature is represented by a hypertext software. To view this literature you must download and install the hypertext software.Abstract: The scientific literature concerning oak regeneration problems is lengthy, complex, paradoxical, and often perplexing. Despite a large scientific literature and numerous conference...

Research Prototype: Automated Analysis of Scientific and Engineering Semantics

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.; Follen, Greg (Technical Monitor)

2001-01-01

Physical and mathematical formulae and concepts are fundamental elements of scientific and engineering software. These classical equations and methods are time tested, universally accepted, and relatively unambiguous. The existence of this classical ontology suggests an ideal problem for automated comprehension. This problem is further motivated by the pervasive use of scientific code and high code development costs. To investigate code comprehension in this classical knowledge domain, a research prototype has been developed. The prototype incorporates scientific domain knowledge to recognize code properties (including units, physical, and mathematical quantity). Also, the procedure implements programming language semantics to propagate these properties through the code. This prototype's ability to elucidate code and detect errors will be demonstrated with state of the art scientific codes.

Framework for Small-Scale Experiments in Software Engineering: Guidance and Control Software Project: Software Engineering Case Study

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.

1998-01-01

Software is becoming increasingly significant in today's critical avionics systems. To achieve safe, reliable software, government regulatory agencies such as the Federal Aviation Administration (FAA) and the Department of Defense mandate the use of certain software development methods. However, little scientific evidence exists to show a correlation between software development methods and product quality. Given this lack of evidence, a series of experiments has been conducted to understand why and how software fails. The Guidance and Control Software (GCS) project is the latest in this series. The GCS project is a case study of the Requirements and Technical Concepts for Aviation RTCA/DO-178B guidelines, Software Considerations in Airborne Systems and Equipment Certification. All civil transport airframe and equipment vendors are expected to comply with these guidelines in building systems to be certified by the FAA for use in commercial aircraft. For the case study, two implementations of a guidance and control application were developed to comply with the DO-178B guidelines for Level A (critical) software. The development included the requirements, design, coding, verification, configuration management, and quality assurance processes. This paper discusses the details of the GCS project and presents the results of the case study.

Requirements and specifications of the space telescope for scientific operations

NASA Technical Reports Server (NTRS)

West, D. K.

1976-01-01

Requirements for the scientific operations of the Space Telescope and the Science Institute are used to develop operational interfaces between user scientists and the NASA ground system. General data systems are defined for observatory scheduling, daily science planning, and science data management. Hardware, software, manpower, and space are specified for several science institute locations and support options.

Teaching Radiology Physics Interactively with Scientific Notebook Software.

PubMed

Richardson, Michael L; Amini, Behrang

2018-06-01

The goal of this study is to demonstrate how the teaching of radiology physics can be enhanced with the use of interactive scientific notebook software. We used the scientific notebook software known as Project Jupyter, which is free, open-source, and available for the Macintosh, Windows, and Linux operating systems. We have created a scientific notebook that demonstrates multiple interactive teaching modules we have written for our residents using the Jupyter notebook system. Scientific notebook software allows educators to create teaching modules in a form that combines text, graphics, images, data, interactive calculations, and image analysis within a single document. These notebooks can be used to build interactive teaching modules, which can help explain complex topics in imaging physics to residents. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Implementation of density functional theory method on object-oriented programming (C++) to calculate energy band structure using the projector augmented wave (PAW)

NASA Astrophysics Data System (ADS)

Alfianto, E.; Rusydi, F.; Aisyah, N. D.; Fadilla, R. N.; Dipojono, H. K.; Martoprawiro, M. A.

2017-05-01

This study implemented DFT method into the C++ programming language with object-oriented programming rules (expressive software). The use of expressive software results in getting a simple programming structure, which is similar to mathematical formula. This will facilitate the scientific community to develop the software. We validate our software by calculating the energy band structure of Silica, Carbon, and Germanium with FCC structure using the Projector Augmented Wave (PAW) method then compare the results to Quantum Espresso calculation’s results. This study shows that the accuracy of the software is 85% compared to Quantum Espresso.

Geospatial-enabled Data Exploration and Computation through Data Infrastructure Building Blocks

NASA Astrophysics Data System (ADS)

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

2015-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices and sensors. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. The GABBs project aims at enabling broader access to geospatial data exploration and computation by developing spatial data infrastructure building blocks that leverage capabilities of end-to-end application service and virtualized computing framework in HUBzero. Funded by NSF Data Infrastructure Building Blocks (DIBBS) initiative, GABBs provides a geospatial data architecture that integrates spatial data management, mapping and visualization and will make it available as open source. The outcome of the project will enable users to rapidly create tools and share geospatial data and tools on the web for interactive exploration of data without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the development of geospatial data infrastructure building blocks and the scientific use cases that help drive the software development, as well as seek feedback from the user communities.

Hybrid Modeling Improves Health and Performance Monitoring

NASA Technical Reports Server (NTRS)

2007-01-01

Scientific Monitoring Inc. was awarded a Phase I Small Business Innovation Research (SBIR) project by NASA's Dryden Flight Research Center to create a new, simplified health-monitoring approach for flight vehicles and flight equipment. The project developed a hybrid physical model concept that provided a structured approach to simplifying complex design models for use in health monitoring, allowing the output or performance of the equipment to be compared to what the design models predicted, so that deterioration or impending failure could be detected before there would be an impact on the equipment's operational capability. Based on the original modeling technology, Scientific Monitoring released I-Trend, a commercial health- and performance-monitoring software product named for its intelligent trending, diagnostics, and prognostics capabilities, as part of the company's complete ICEMS (Intelligent Condition-based Equipment Management System) suite of monitoring and advanced alerting software. I-Trend uses the hybrid physical model to better characterize the nature of health or performance alarms that result in "no fault found" false alarms. Additionally, the use of physical principles helps I-Trend identify problems sooner. I-Trend technology is currently in use in several commercial aviation programs, and the U.S. Air Force recently tapped Scientific Monitoring to develop next-generation engine health-management software for monitoring its fleet of jet engines. Scientific Monitoring has continued the original NASA work, this time under a Phase III SBIR contract with a joint NASA-Pratt & Whitney aviation security program on propulsion-controlled aircraft under missile-damaged aircraft conditions.

Satellite-Based Stratospheric and Tropospheric Measurements: Determination of Global Ozone and other Trace Species

NASA Technical Reports Server (NTRS)

Chance, K. V.

2001-01-01

This report summarizes research done under NASA Grant NAG5-3461 from November 1, 1996 through December 31, 2000. The research performed during this reporting period includes development and maintenance of scientific software for the GOME retrieval algorithms, consultation on operational software development for GOME, sensitivity and instrument studies to help finalize the definition of the SCIAMACHY instrument, leading the development of the SCIAMACHY Scientific Requirements Document for Data and Algorithm Development, consultation and development for SCIAMACHY near-real-time (NRT) and off-line (OL) data products, radiative transfer model development for utilization in GOME, SCIAMACHY and other programs, development of infrared line-by-line atmospheric modeling and retrieval capability for SCIAMACHY, and participation in GOME and SCIAMACHY validation studies. The Global Ozone Monitoring Experiment was successfully launched on the ERS-2 satellite on April 20, 1995, and remains working in normal fashion. SCIAMACHY is currently planned for launch in late 2001 on the ESA Envisat satellite. Three GOME-2 instruments are now scheduled to fly on the Metop series of operational meteorological satellites (Eumetsat). K. Chance is a member of the reconstituted GOME Scientific Advisory Group, which will guide the GOME-2 program as well as the continuing ERS-2 GOME program.

The making of the mechanical universe

NASA Technical Reports Server (NTRS)

Blinn, James

1989-01-01

The Mechanical Universe project required the production of over 550 different animated scenes, totaling about 7 and 1/2 hours of screen time. The project required the use of a wide range of techniques and motivated the development of several different software packages. A documentation is presented of many aspects of the project, encompassing artistic design issues, scientific simulations, software engineering, and video engineering.

Software Engineering Support of the Third Round of Scientific Grand Challenge Investigations: Earth System Modeling Software Framework Survey

NASA Technical Reports Server (NTRS)

Talbot, Bryan; Zhou, Shu-Jia; Higgins, Glenn; Zukor, Dorothy (Technical Monitor)

2002-01-01

One of the most significant challenges in large-scale climate modeling, as well as in high-performance computing in other scientific fields, is that of effectively integrating many software models from multiple contributors. A software framework facilitates the integration task, both in the development and runtime stages of the simulation. Effective software frameworks reduce the programming burden for the investigators, freeing them to focus more on the science and less on the parallel communication implementation. while maintaining high performance across numerous supercomputer and workstation architectures. This document surveys numerous software frameworks for potential use in Earth science modeling. Several frameworks are evaluated in depth, including Parallel Object-Oriented Methods and Applications (POOMA), Cactus (from (he relativistic physics community), Overture, Goddard Earth Modeling System (GEMS), the National Center for Atmospheric Research Flux Coupler, and UCLA/UCB Distributed Data Broker (DDB). Frameworks evaluated in less detail include ROOT, Parallel Application Workspace (PAWS), and Advanced Large-Scale Integrated Computational Environment (ALICE). A host of other frameworks and related tools are referenced in this context. The frameworks are evaluated individually and also compared with each other.

Academic and Non-Profit Accessibility to Commercial Remote Sensing Software

NASA Astrophysics Data System (ADS)

O'Connor, A. S.; Farr, B.

2013-12-01

Remote Sensing as a topic of teaching and research at the university and college level continues to increase. As more data is made freely available and software becomes easier to use, more and more academic and non-profits institutions are turning to remote sensing to solve their tough and large spatial scale problems. Exelis Visual Information Solutions (VIS) has been supporting teaching and research endeavors for over 30 years with a special emphasis over the last 5 years with scientifically proven software and accessible training materials. The Exelis VIS academic program extends to US and Canadian 2 year and 4 year colleges and universities with tools for analyzing aerial and satellite multispectral and hyperspectral imagery, airborne LiDAR and Synthetic Aperture Radar. The Exelis VIS academic programs, using the ENVI Platform, enables labs and classrooms to be outfitted with software and makes software accessible to students. The ENVI software provides students hands on experience with remote sensing software, an easy teaching platform for professors and allows researchers scientifically vetted software they can trust. Training materials are provided at no additional cost and can either serve as a basis for course curriculum development or self paced learning. Non-profit organizations like The Nature Conservancy (TNC) and CGIAR have deployed ENVI and IDL enterprise wide licensing allowing researchers all over the world to have cost effective access COTS software for their research. Exelis VIS has also contributed licenses to the NASA DEVELOP program. Exelis VIS is committed to supporting the academic and NGO community with affordable enterprise licensing, access to training materials, and technical expertise to help researchers tackle today's Earth and Planetary science big data challenges.

The SCEC Broadband Platform: A Collaborative Open-Source Software Package for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Maechling, P. J.; Goulet, C. A.; Somerville, P.; Jordan, T. H.

2014-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform is a collaborative software development project involving geoscientists, earthquake engineers, graduate students, and the SCEC Community Modeling Environment. The SCEC Broadband Platform (BBP) is open-source scientific software that can generate broadband (0-100Hz) ground motions for earthquakes, integrating complex scientific modules that implement rupture generation, low and high-frequency seismogram synthesis, non-linear site effects calculation, and visualization into a software system that supports easy on-demand computation of seismograms. The Broadband Platform operates in two primary modes: validation simulations and scenario simulations. In validation mode, the Platform runs earthquake rupture and wave propagation modeling software to calculate seismograms for a well-observed historical earthquake. Then, the BBP calculates a number of goodness of fit measurements that quantify how well the model-based broadband seismograms match the observed seismograms for a certain event. Based on these results, the Platform can be used to tune and validate different numerical modeling techniques. In scenario mode, the Broadband Platform can run simulations for hypothetical (scenario) earthquakes. In this mode, users input an earthquake description, a list of station names and locations, and a 1D velocity model for their region of interest, and the Broadband Platform software then calculates ground motions for the specified stations. Working in close collaboration with scientists and research engineers, the SCEC software development group continues to add new capabilities to the Broadband Platform and to release new versions as open-source scientific software distributions that can be compiled and run on many Linux computer systems. Our latest release includes 5 simulation methods, 7 simulation regions covering California, Japan, and Eastern North America, the ability to compare simulation results against GMPEs, and several new data products, such as map and distance-based goodness of fit plots. As the number and complexity of scenarios simulated using the Broadband Platform increases, we have added batching utilities to substantially improve support for running large-scale simulations on computing clusters.

Scientific Software: How to Find What You Need and Get What You Pay for.

ERIC Educational Resources Information Center

Gabaldon, Diana J.

1984-01-01

Provides examples of software for the sciences, including: packages for pathology/toxicology laboratories (costing over $15,000), DNA sequencing, and data acquisition/analysis; general-purpose software for scientific uses; and "custom" packages, including a program to maintain a listing of "Escherichia coli" strains and a…

Software Development in the Water Sciences: a view from the divide (Invited)

NASA Astrophysics Data System (ADS)

Miles, B.; Band, L. E.

2013-12-01

While training in statistical methods is an important part of many earth scientists' training, these scientists often learn the bulk of their software development skills in an ad hoc, just-in-time manner. Yet to carry out contemporary research scientists are spending more and more time developing software. Here I present perspectives - as an earth sciences graduate student with professional software engineering experience - on the challenges scientists face adopting software engineering practices, with an emphasis on areas of the science software development lifecycle that could benefit most from improved engineering. This work builds on experience gained as part of the NSF-funded Water Science Software Institute (WSSI) conceptualization award (NSF Award # 1216817). Throughout 2013, the WSSI team held a series of software scoping and development sprints with the goals of: (1) adding features to better model green infrastructure within the Regional Hydro-Ecological Simulation System (RHESSys); and (2) infusing test-driven agile software development practices into the processes employed by the RHESSys team. The goal of efforts such as the WSSI is to ensure that investments by current and future scientists in software engineering training will enable transformative science by improving both scientific reproducibility and researcher productivity. Experience with the WSSI indicates: (1) the potential for achieving this goal; and (2) while scientists are willing to adopt some software engineering practices, transformative science will require continued collaboration between domain scientists and cyberinfrastructure experts for the foreseeable future.

Hardware and software for automating the process of studying high-speed gas flows in wind tunnels of short-term action

NASA Astrophysics Data System (ADS)

Yakovlev, V. V.; Shakirov, S. R.; Gilyov, V. M.; Shpak, S. I.

2017-10-01

In this paper, we propose a variant of constructing automation systems for aerodynamic experiments on the basis of modern hardware-software means of domestic development. The structure of the universal control and data collection system for performing experiments in wind tunnels of continuous, periodic or short-term action is proposed. The proposed hardware and software development tools for ICT SB RAS and ITAM SB RAS, as well as subsystems based on them, can be widely applied to any scientific and experimental installations, as well as to the automation of technological processes in production.

Bridging the Particle Physics and Big Data Worlds

NASA Astrophysics Data System (ADS)

Pivarski, James

2017-09-01

For decades, particle physicists have developed custom software because the scale and complexity of our problems were unique. In recent years, however, the ``big data'' industry has begun to tackle similar problems, and has developed some novel solutions. Incorporating scientific Python libraries, Spark, TensorFlow, and machine learning tools into the physics software stack can improve abstraction, reliability, and in some cases performance. Perhaps more importantly, it can free physicists to concentrate on domain-specific problems. Building bridges isn't always easy, however. Physics software and open-source software from industry differ in many incidental ways and a few fundamental ways. I will show work from the DIANA-HEP project to streamline data flow from ROOT to Numpy and Spark, to incorporate ideas of functional programming into histogram aggregation, and to develop real-time, query-style manipulations of particle data.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

A ranking algorithm for spacelab crew and experiment scheduling

NASA Technical Reports Server (NTRS)

Grone, R. D.; Mathis, F. H.

1980-01-01

The problem of obtaining an optimal or near optimal schedule for scientific experiments to be performed on Spacelab missions is addressed. The current capabilities in this regard are examined and a method of ranking experiments in order of difficulty is developed to support the existing software. Experimental data is obtained from applying this method to the sets of experiments corresponding to Spacelab mission 1, 2, and 3. Finally, suggestions are made concerning desirable modifications and features of second generation software being developed for this problem.

Development of Data Processing Software for NBI Spectroscopic Analysis System

NASA Astrophysics Data System (ADS)

Zhang, Xiaodan; Hu, Chundong; Sheng, Peng; Zhao, Yuanzhe; Wu, Deyun; Cui, Qinglong

2015-04-01

A set of data processing software is presented in this paper for processing NBI spectroscopic data. For better and more scientific managment and querying these data, they are managed uniformly by the NBI data server. The data processing software offers the functions of uploading beam spectral original and analytic data to the data server manually and automatically, querying and downloading all the NBI data, as well as dealing with local LZO data. The set software is composed of a server program and a client program. The server software is programmed in C/C++ under a CentOS development environment. The client software is developed under a VC 6.0 platform, which offers convenient operational human interfaces. The network communications between the server and the client are based on TCP. With the help of this set software, the NBI spectroscopic analysis system realizes the unattended automatic operation, and the clear interface also makes it much more convenient to offer beam intensity distribution data and beam power data to operators for operation decision-making. supported by National Natural Science Foundation of China (No. 11075183), the Chinese Academy of Sciences Knowledge Innovation

Computational Aspects of Data Assimilation and the ESMF

NASA Technical Reports Server (NTRS)

daSilva, A.

2003-01-01

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

Automated Scheduling Via Artificial Intelligence

NASA Technical Reports Server (NTRS)

Biefeld, Eric W.; Cooper, Lynne P.

1991-01-01

Artificial-intelligence software that automates scheduling developed in Operations Mission Planner (OMP) research project. Software used in both generation of new schedules and modification of existing schedules in view of changes in tasks and/or available resources. Approach based on iterative refinement. Although project focused upon scheduling of operations of scientific instruments and other equipment aboard spacecraft, also applicable to such terrestrial problems as scheduling production in factory.

Free and Open Source Software for Geospatial in the field of planetary science

NASA Astrophysics Data System (ADS)

Frigeri, A.

2012-12-01

Information technology applied to geospatial analyses has spread quickly in the last ten years. The availability of OpenData and data from collaborative mapping projects increased the interest on tools, procedures and methods to handle spatially-related information. Free Open Source Software projects devoted to geospatial data handling are gaining a good success as the use of interoperable formats and protocols allow the user to choose what pipeline of tools and libraries is needed to solve a particular task, adapting the software scene to his specific problem. In particular, the Free Open Source model of development mimics the scientific method very well, and researchers should be naturally encouraged to take part to the development process of these software projects, as this represent a very agile way to interact among several institutions. When it comes to planetary sciences, geospatial Free Open Source Software is gaining a key role in projects that commonly involve different subjects in an international scenario. Very popular software suites for processing scientific mission data (for example, ISIS) and for navigation/planning (SPICE) are being distributed along with the source code and the interaction between user and developer is often very strict, creating a continuum between these two figures. A very widely spread library for handling geospatial data (GDAL) has started to support planetary data from the Planetary Data System, and recent contributions enabled the support to other popular data formats used in planetary science, as the Vicar one. The use of Geographic Information System in planetary science is now diffused, and Free Open Source GIS, open GIS formats and network protocols allow to extend existing tools and methods developed to solve Earth based problems, also to the case of the study of solar system bodies. A day in the working life of a researcher using Free Open Source Software for geospatial will be presented, as well as benefits and solutions to possible detriments coming from the effort required by using, supporting and contributing.

The validation by measurement theory of proposed object-oriented software metrics

NASA Technical Reports Server (NTRS)

Neal, Ralph D.

1994-01-01

Moving software development into the engineering arena requires controllability, and to control a process, it must be measurable. Measuring the process does no good if the product is not also measured, i.e., being the best at producing an inferior product does not define a quality process. Also, not every number extracted from software development is a valid measurement. A valid measurement only results when we are able to verify that the number is representative of the attribute that we wish to measure. Many proposed software metrics are used by practitioners without these metrics ever having been validated, leading to costly but often useless calculations. Several researchers have bemoaned the lack of scientific precision in much of the published software measurement work and have called for validation of software metrics by measurement theory. This dissertation applies measurement theory to validate fifty proposed object-oriented software metrics (Li and Henry, 1993; Chidamber and Kemerrer, 1994; Lorenz and Kidd, 1994).

Pynamic: the Python Dynamic Benchmark

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

Lee, G L; Ahn, D H; de Supinksi, B R

2007-07-10

Python is widely used in scientific computing to facilitate application development and to support features such as computational steering. Making full use of some of Python's popular features, which improve programmer productivity, leads to applications that access extremely high numbers of dynamically linked libraries (DLLs). As a result, some important Python-based applications severely stress a system's dynamic linking and loading capabilities and also cause significant difficulties for most development environment tools, such as debuggers. Furthermore, using the Python paradigm for large scale MPI-based applications can create significant file IO and further stress tools and operating systems. In this paper, wemore » present Pynamic, the first benchmark program to support configurable emulation of a wide-range of the DLL usage of Python-based applications for large scale systems. Pynamic has already accurately reproduced system software and tool issues encountered by important large Python-based scientific applications on our supercomputers. Pynamic provided insight for our system software and tool vendors, and our application developers, into the impact of several design decisions. As we describe the Pynamic benchmark, we will highlight some of the issues discovered in our large scale system software and tools using Pynamic.« less

Multivariate Statistical Analysis Software Technologies for Astrophysical Research Involving Large Data Bases

NASA Technical Reports Server (NTRS)

Djorgovski, S. G.

1994-01-01

We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complex database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects of the SKICAT system, and of some of the scientific results achieved to date. We also developed a user-friendly package for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications and has produced real, published results.

Development of an Aeromedical Scientific Information System for Aviation Safety

DTIC Science & Technology

2008-01-01

math- ematics, engineering, computer hardware, software , and networking, was assembled to glean the most knowledge from the complicated aeromedical...9, SPlus Enterprise Developer 8, and Insightful Miner version 7. Process flow charts were done with SmartDraw Suite Edition version 7. Static and

Ada Software Design Methods Formulation.

DTIC Science & Technology

1982-10-01

Programmer technical 2018 Principle Scientific Programmer technical 2020 Principle Scientif:c Programmer tnchnical 3001 Junior Programns. entry level...0.570 156 6010-. I---. 0.684 7 1031------------- 0.481 77 3119-. 0.620 94 4034-. ----- 0.696 90 4027-. -- ’---- 0.759 31 2018 -. I-’" 0.823 142 5063-. I...1094-2 0-117 cluster 4 2007 Senior Scientific Programmer technical 2016 Scientific Programmer technical 1080 Senior Software Engineer technical 2018

Ionospheric Simulation System for Satellite Observations and Global Assimilative Model Experiments - ISOGAME

NASA Technical Reports Server (NTRS)

Pi, Xiaoqing; Mannucci, Anthony J.; Verkhoglyadova, Olga; Stephens, Philip; Iijima, Bryron A.

2013-01-01

Modeling and imaging the Earth's ionosphere as well as understanding its structures, inhomogeneities, and disturbances is a key part of NASA's Heliophysics Directorate science roadmap. This invention provides a design tool for scientific missions focused on the ionosphere. It is a scientifically important and technologically challenging task to assess the impact of a new observation system quantitatively on our capability of imaging and modeling the ionosphere. This question is often raised whenever a new satellite system is proposed, a new type of data is emerging, or a new modeling technique is developed. The proposed constellation would be part of a new observation system with more low-Earth orbiters tracking more radio occultation signals broadcast by Global Navigation Satellite System (GNSS) than those offered by the current GPS and COSMIC observation system. A simulation system was developed to fulfill this task. The system is composed of a suite of software that combines the Global Assimilative Ionospheric Model (GAIM) including first-principles and empirical ionospheric models, a multiple- dipole geomagnetic field model, data assimilation modules, observation simulator, visualization software, and orbit design, simulation, and optimization software.

A self-referential HOWTO on release engineering

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

Galassi, Mark C.

Release engineering is a fundamental part of the software development cycle: it is the point at which quality control is exercised and bug fixes are integrated. The way in which software is released also gives the end user her first experience of a software package, while in scientific computing release engineering can guarantee reproducibility. For these reasons and others, the release process is a good indicator of the maturity and organization of a development team. Software teams often do not put in place a release process at the beginning. This is unfortunate because the team does not have early andmore » continuous execution of test suites, and it does not exercise the software in the same conditions as the end users. I describe an approach to release engineering based on the software tools developed and used by the GNU project, together with several specific proposals related to packaging and distribution. I do this in a step-by-step manner, demonstrating how this very paper is written and built using proper release engineering methods. Because many aspects of release engineering are not exercised in the building of the paper, the accompanying software repository also contains examples of software libraries.« less

Integrating a geographic information system, a scientific visualization system and an orographic precipitation model

USGS Publications Warehouse

Hay, L.; Knapp, L.

1996-01-01

Investigating natural, potential, and man-induced impacts on hydrological systems commonly requires complex modelling with overlapping data requirements, and massive amounts of one- to four-dimensional data at multiple scales and formats. Given the complexity of most hydrological studies, the requisite software infrastructure must incorporate many components including simulation modelling, spatial analysis and flexible, intuitive displays. There is a general requirement for a set of capabilities to support scientific analysis which, at this time, can only come from an integration of several software components. Integration of geographic information systems (GISs) and scientific visualization systems (SVSs) is a powerful technique for developing and analysing complex models. This paper describes the integration of an orographic precipitation model, a GIS and a SVS. The combination of these individual components provides a robust infrastructure which allows the scientist to work with the full dimensionality of the data and to examine the data in a more intuitive manner.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy.

PubMed

Barabas, Federico M; Masullo, Luciano A; Stefani, Fernando D

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy

NASA Astrophysics Data System (ADS)

Barabas, Federico M.; Masullo, Luciano A.; Stefani, Fernando D.

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

A Framework for Testing Scientific Software: A Case Study of Testing Amsterdam Discrete Dipole Approximation Software

NASA Astrophysics Data System (ADS)

Shao, Hongbing

Software testing with scientific software systems often suffers from test oracle problem, i.e., lack of test oracles. Amsterdam discrete dipole approximation code (ADDA) is a scientific software system that can be used to simulate light scattering of scatterers of various types. Testing of ADDA suffers from "test oracle problem". In this thesis work, I established a testing framework to test scientific software systems and evaluated this framework using ADDA as a case study. To test ADDA, I first used CMMIE code as the pseudo oracle to test ADDA in simulating light scattering of a homogeneous sphere scatterer. Comparable results were obtained between ADDA and CMMIE code. This validated ADDA for use with homogeneous sphere scatterers. Then I used experimental result obtained for light scattering of a homogeneous sphere to validate use of ADDA with sphere scatterers. ADDA produced light scattering simulation comparable to the experimentally measured result. This further validated the use of ADDA for simulating light scattering of sphere scatterers. Then I used metamorphic testing to generate test cases covering scatterers of various geometries, orientations, homogeneity or non-homogeneity. ADDA was tested under each of these test cases and all tests passed. The use of statistical analysis together with metamorphic testing is discussed as a future direction. In short, using ADDA as a case study, I established a testing framework, including use of pseudo oracles, experimental results and the metamorphic testing techniques to test scientific software systems that suffer from test oracle problems. Each of these techniques is necessary and contributes to the testing of the software under test.

Optimizing CyberShake Seismic Hazard Workflows for Large HPC Resources

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Robotic Software for the Thacher Observatory

NASA Astrophysics Data System (ADS)

Lawrence, George; Luebbers, Julien; Eastman, Jason D.; Johnson, John A.; Swift, Jonathan

2018-06-01

The Thacher Observatory—a research and educational facility located in Ojai, CA—uses a 0.7 meter telescope to conduct photometric research on a variety of targets including eclipsing binaries, exoplanet transits, and supernovae. Currently, observations are automated using commercial software. In order to expand the flexibility for specialized scientific observations and to increase the educational value of the facility on campus, we are adapting and implementing the custom observatory control software and queue scheduling developed for the Miniature Exoplanet Radial Velocity Array (MINERVA) to the Thacher Observatory. We present the design and implementation of this new software as well as its demonstrated functionality on the Thacher Observatory.

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

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

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

Medical device software: defining key terms.

PubMed

Pashkov, Vitalii; Gutorova, Nataliya; Harkusha, Andrii

one of the areas of significant growth in medical devices has been the role of software - as an integral component of a medical device, as a standalone device and more recently as applications on mobile devices. The risk related to a malfunction of the standalone software used within healthcare is in itself not a criterion for its qualification or not as a medical device. It is therefore, necessary to clarify some criteria for the qualification of stand-alone software as medical devices Materials and methods: Ukrainian, European Union, United States of America legislation, Guidelines developed by European Commission and Food and Drug Administration's, recommendations represented by international voluntary group and scientific works. This article is based on dialectical, comparative, analytic, synthetic and comprehensive research methods. the legal regulation of software which is used for medical purpose in Ukraine limited to one definition. In European Union and United States of America were developed and applying special guidelines that help developers, manufactures and end users to difference software on types standing on medical purpose criteria. Software becomes more and more incorporated into medical devices. Developers and manufacturers may not have initially appreciated potential risks to patients and users such situation could have dangerous results for patients or users. It is necessary to develop and adopt the legislation that will intend to define the criteria for the qualification of medical device software and the application of the classification criteria to such software, provide some illustrative examples and step by step recommendations to qualify software as medical device.

Extracting patterns of database and software usage from the bioinformatics literature

PubMed Central

Duck, Geraint; Nenadic, Goran; Brass, Andy; Robertson, David L.; Stevens, Robert

2014-01-01

Motivation: As a natural consequence of being a computer-based discipline, bioinformatics has a strong focus on database and software development, but the volume and variety of resources are growing at unprecedented rates. An audit of database and software usage patterns could help provide an overview of developments in bioinformatics and community common practice, and comparing the links between resources through time could demonstrate both the persistence of existing software and the emergence of new tools. Results: We study the connections between bioinformatics resources and construct networks of database and software usage patterns, based on resource co-occurrence, that correspond to snapshots of common practice in the bioinformatics community. We apply our approach to pairings of phylogenetics software reported in the literature and argue that these could provide a stepping stone into the identification of scientific best practice. Availability and implementation: The extracted resource data, the scripts used for network generation and the resulting networks are available at http://bionerds.sourceforge.net/networks/ Contact: robert.stevens@manchester.ac.uk PMID:25161253

Teaching practice and effect of the curriculum design and simulation courses under the support of professional optical software

NASA Astrophysics Data System (ADS)

Lin, YuanFang; Zheng, XiaoDong; Huang, YuJia

2017-08-01

Curriculum design and simulation courses are bridges to connect specialty theories, engineering practice and experimental skills. In order to help students to have the computer aided optical system design ability adapting to developments of the times, a professional optical software-Advanced System of Analysis Program (ASAP) was used in the research teaching of curriculum design and simulation courses. The ASAP tutorials conducting, exercises both complementing and supplementing the lectures, hands-on practice in class, autonomous learning and independent design after class were bridged organically, to guide students "learning while doing, learning by doing", paying more attention to the process instead of the results. Several years of teaching practice of curriculum design and simulation courses shows that, project-based learning meets society needs of training personnel with knowledge, ability and quality. Students have obtained not only skills of using professional software, but also skills of finding and proposing questions in engineering practice, the scientific method of analyzing and solving questions with specialty knowledge, in addition, autonomous learning ability, teamwork spirit and innovation consciousness, still scientific attitude of facing failure and scientific spirit of admitting deficiency in the process of independent design and exploration.

A Pipeline Software Architecture for NMR Spectrum Data Translation

PubMed Central

Ellis, Heidi J.C.; Weatherby, Gerard; Nowling, Ronald J.; Vyas, Jay; Fenwick, Matthew; Gryk, Michael R.

2012-01-01

The problem of formatting data so that it conforms to the required input for scientific data processing tools pervades scientific computing. The CONNecticut Joint University Research Group (CONNJUR) has developed a data translation tool based on a pipeline architecture that partially solves this problem. The CONNJUR Spectrum Translator supports data format translation for experiments that use Nuclear Magnetic Resonance to determine the structure of large protein molecules. PMID:24634607

The development procedures and tools applied for the attitude control software of the Italian satellite SAX

NASA Astrophysics Data System (ADS)

Hameetman, G. J.; Dekker, G. J.

1993-11-01

The Italian satellite (with a large Dutch contribution) SAX is a scientific satellite which has the mission to study roentgen sources. One main requirement for the Attitude and Orbit Control Subsystem (AOCS) is to achieve and maintain a stable pointing accuracy with a limit cycle of less than 90 arcsec during pointings of maximal 28 hours. The main SAX instrument, the Narrow Field Instrument, is highly sensitive to (indirect) radiation coming from the Sun. This sensitivity leads to another main requirement that under no circumstances the safe attitude domain may be left. The paper describes the application software in relation with the overall SAX AOCS subsystem, the CASE tools that have been used during the development, some advantages and disadvantages of the use of these tools, the measures taken to meet the more or less conflicting requirements of reliability and flexibility, and the lessons learned during development. The quality of the approach to the development has proven the (separately executed) hardware/software integration tests. During these tests, a neglectible number of software errors has been detected in the application software.

Bonsai: an event-based framework for processing and controlling data streams

PubMed Central

Lopes, Gonçalo; Bonacchi, Niccolò; Frazão, João; Neto, Joana P.; Atallah, Bassam V.; Soares, Sofia; Moreira, Luís; Matias, Sara; Itskov, Pavel M.; Correia, Patrícia A.; Medina, Roberto E.; Calcaterra, Lorenza; Dreosti, Elena; Paton, Joseph J.; Kampff, Adam R.

2015-01-01

The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation. PMID:25904861

Software Framework for Peer Data-Management Services

NASA Technical Reports Server (NTRS)

Hughes, John; Hardman, Sean; Crichton, Daniel; Hyon, Jason; Kelly, Sean; Tran, Thuy

2007-01-01

Object Oriented Data Technology (OODT) is a software framework for creating a Web-based system for exchange of scientific data that are stored in diverse formats on computers at different sites under the management of scientific peers. OODT software consists of a set of cooperating, distributed peer components that provide distributed peer-to-peer (P2P) services that enable one peer to search and retrieve data managed by another peer. In effect, computers running OODT software at different locations become parts of an integrated data-management system.

Abstracted Workow Framework with a Structure from Motion Application

NASA Astrophysics Data System (ADS)

Rossi, Adam J.

In scientific and engineering disciplines, from academia to industry, there is an increasing need for the development of custom software to perform experiments, construct systems, and develop products. The natural mindset initially is to shortcut and bypass all overhead and process rigor in order to obtain an immediate result for the problem at hand, with the misconception that the software will simply be thrown away at the end. In a majority of the cases, it turns out the software persists for many years, and likely ends up in production systems for which it was not initially intended. In the current study, a framework that can be used in both industry and academic applications mitigates underlying problems associated with developing scientific and engineering software. This results in software that is much more maintainable, documented, and usable by others, specifically allowing new users to extend capabilities of components already implemented in the framework. There is a multi-disciplinary need in the fields of imaging science, computer science, and software engineering for a unified implementation model, which motivates the development of an abstracted software framework. Structure from motion (SfM) has been identified as one use case where the abstracted workflow framework can improve research efficiencies and eliminate implementation redundancies in scientific fields. The SfM process begins by obtaining 2D images of a scene from different perspectives. Features from the images are extracted and correspondences are established. This provides a sufficient amount of information to initialize the problem for fully automated processing. Transformations are established between views, and 3D points are established via triangulation algorithms. The parameters for the camera models for all views / images are solved through bundle adjustment, establishing a highly consistent point cloud. The initial sparse point cloud and camera matrices are used to generate a dense point cloud through patch based techniques or densification algorithms such as Semi-Global Matching (SGM). The point cloud can be visualized or exploited by both humans and automated techniques. In some cases the point cloud is "draped" with original imagery in order to enhance the 3D model for a human viewer. The SfM workflow can be implemented in the abstracted framework, making it easily leverageable and extensible by multiple users. Like many processes in scientific and engineering domains, the workflow described for SfM is complex and requires many disparate components to form a functional system, often utilizing algorithms implemented by many users in different languages / environments and without knowledge of how the component fits into the larger system. In practice, this generally leads to issues interfacing the components, building the software for desired platforms, understanding its concept of operations, and how it can be manipulated in order to fit the desired function for a particular application. In addition, other scientists and engineers instinctively wish to analyze the performance of the system, establish new algorithms, optimize existing processes, and establish new functionality based on current research. This requires a framework whereby new components can be easily plugged in without affecting the current implemented functionality. The need for a universal programming environment establishes the motivation for the development of the abstracted workflow framework. This software implementation, named Catena, provides base classes from which new components must derive in order to operate within the framework. The derivation mandates requirements be satisfied in order to provide a complete implementation. Additionally, the developer must provide documentation of the component in terms of its overall function and inputs. The interface input and output values corresponding to the component must be defined in terms of their respective data types, and the implementation uses mechanisms within the framework to retrieve and send the values. This process requires the developer to componentize their algorithm rather than implement it monolithically. Although the requirements of the developer are slightly greater, the benefits realized from using Catena far outweigh the overhead, and results in extensible software. This thesis provides a basis for the abstracted workflow framework concept and the Catena software implementation. The benefits are also illustrated using a detailed examination of the SfM process as an example application.

Eleven quick tips for architecting biomedical informatics workflows with cloud computing.

PubMed

Cole, Brian S; Moore, Jason H

2018-03-01

Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world's largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction.

Eleven quick tips for architecting biomedical informatics workflows with cloud computing

PubMed Central

Moore, Jason H.

2018-01-01

Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world’s largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction. PMID:29596416

The Principles for Successful Scientific Data Management Revisited

NASA Astrophysics Data System (ADS)

Walker, R. J.; King, T. A.; Joy, S. P.

2005-12-01

It has been 23 years since the National Research Council's Committee on Data Management and Computation (CODMAC) published its famous list of principles for successful scientific data management that have provided the framework for modern space science data management. CODMAC outlined seven principles: 1. Scientific Involvement in all aspects of space science missions. 2. Scientific Oversight of all scientific data-management activities. 3. Data Availability - Validated data should be made available to the scientific community in a timely manner. They should include appropriate ancillary data, and complete documentation. 4. Facilities - A proper balance between cost and scientific productivity should be maintained. 5. Software - Transportable well documented software should be available to process and analyze the data. 6. Scientific Data Storage - The data should be preserved in retrievable form. 7. Data System Funding - Adequate data funding should be made available at the outset of missions and protected from overruns. In this paper we will review the lessons learned in trying to apply these principles to space derived data. The Planetary Data System created the concept of data curation to carry out the CODMAC principles. Data curators are scientists and technologists who work directly with the mission scientists to create data products. The efficient application of the CODMAC principles requires that data curators and the mission team start early in a mission to plan for data access and archiving. To build the data products the planetary discipline adopted data access and documentation standards and has adhered to them. The data curators and mission team work together to produce data products and make them available. However even with early planning and agreement on standards the needs of the science community frequently far exceed the available resources. This is especially true for smaller principal investigator run missions. We will argue that one way to make data systems for small missions more effective is for the data curators to provide software tools to help develop the mission data system.

THE VIRTUAL INSTRUMENT: SUPPORT FOR GRID-ENABLED MCELL SIMULATIONS

PubMed Central

Casanova, Henri; Berman, Francine; Bartol, Thomas; Gokcay, Erhan; Sejnowski, Terry; Birnbaum, Adam; Dongarra, Jack; Miller, Michelle; Ellisman, Mark; Faerman, Marcio; Obertelli, Graziano; Wolski, Rich; Pomerantz, Stuart; Stiles, Joel

2010-01-01

Ensembles of widely distributed, heterogeneous resources, or Grids, have emerged as popular platforms for large-scale scientific applications. In this paper we present the Virtual Instrument project, which provides an integrated application execution environment that enables end-users to run and interact with running scientific simulations on Grids. This work is performed in the specific context of MCell, a computational biology application. While MCell provides the basis for running simulations, its capabilities are currently limited in terms of scale, ease-of-use, and interactivity. These limitations preclude usage scenarios that are critical for scientific advances. Our goal is to create a scientific “Virtual Instrument” from MCell by allowing its users to transparently access Grid resources while being able to steer running simulations. In this paper, we motivate the Virtual Instrument project and discuss a number of relevant issues and accomplishments in the area of Grid software development and application scheduling. We then describe our software design and report on the current implementation. We verify and evaluate our design via experiments with MCell on a real-world Grid testbed. PMID:20689618

ITK: enabling reproducible research and open science

PubMed Central

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46. PMID:24600387

ITK: enabling reproducible research and open science.

PubMed

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

Software Reuse Within the Earth Science Community

NASA Technical Reports Server (NTRS)

Marshall, James J.; Olding, Steve; Wolfe, Robert E.; Delnore, Victor E.

2006-01-01

Scientific missions in the Earth sciences frequently require cost-effective, highly reliable, and easy-to-use software, which can be a challenge for software developers to provide. The NASA Earth Science Enterprise (ESE) spends a significant amount of resources developing software components and other software development artifacts that may also be of value if reused in other projects requiring similar functionality. In general, software reuse is often defined as utilizing existing software artifacts. Software reuse can improve productivity and quality while decreasing the cost of software development, as documented by case studies in the literature. Since large software systems are often the results of the integration of many smaller and sometimes reusable components, ensuring reusability of such software components becomes a necessity. Indeed, designing software components with reusability as a requirement can increase the software reuse potential within a community such as the NASA ESE community. The NASA Earth Science Data Systems (ESDS) Software Reuse Working Group is chartered to oversee the development of a process that will maximize the reuse potential of existing software components while recommending strategies for maximizing the reusability potential of yet-to-be-designed components. As part of this work, two surveys of the Earth science community were conducted. The first was performed in 2004 and distributed among government employees and contractors. A follow-up survey was performed in 2005 and distributed among a wider community, to include members of industry and academia. The surveys were designed to collect information on subjects such as the current software reuse practices of Earth science software developers, why they choose to reuse software, and what perceived barriers prevent them from reusing software. In this paper, we compare the results of these surveys, summarize the observed trends, and discuss the findings. The results are very similar, with the second, larger survey confirming the basic results of the first, smaller survey. The results suggest that reuse of ESE software can drive down the cost and time of system development, increase flexibility and responsiveness of these systems to new technologies and requirements, and increase effective and accountable community participation.

Clinical software development for the Web: lessons learned from the BOADICEA project

PubMed Central

2012-01-01

Background In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. Results We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. Conclusions We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback. PMID:22490389

Clinical software development for the Web: lessons learned from the BOADICEA project.

PubMed

Cunningham, Alex P; Antoniou, Antonis C; Easton, Douglas F

2012-04-10

In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.

SPLASSH: Open source software for camera-based high-speed, multispectral in-vivo optical image acquisition

PubMed Central

Sun, Ryan; Bouchard, Matthew B.; Hillman, Elizabeth M. C.

2010-01-01

Camera-based in-vivo optical imaging can provide detailed images of living tissue that reveal structure, function, and disease. High-speed, high resolution imaging can reveal dynamic events such as changes in blood flow and responses to stimulation. Despite these benefits, commercially available scientific cameras rarely include software that is suitable for in-vivo imaging applications, making this highly versatile form of optical imaging challenging and time-consuming to implement. To address this issue, we have developed a novel, open-source software package to control high-speed, multispectral optical imaging systems. The software integrates a number of modular functions through a custom graphical user interface (GUI) and provides extensive control over a wide range of inexpensive IEEE 1394 Firewire cameras. Multispectral illumination can be incorporated through the use of off-the-shelf light emitting diodes which the software synchronizes to image acquisition via a programmed microcontroller, allowing arbitrary high-speed illumination sequences. The complete software suite is available for free download. Here we describe the software’s framework and provide details to guide users with development of this and similar software. PMID:21258475

Simulating Technology Processes to Foster Learning.

ERIC Educational Resources Information Center

Krumholtz, Nira

1998-01-01

Based on a spiral model of technology evolution, elementary students used LOGO computer software to become both developers and users of technology. The computerized environment enabled 87% to reach intuitive understanding of physical concepts; 24% expressed more formal scientific understanding. (SK)

TTCI's Scientific Software Suite and NUCARS Overview

DOT National Transportation Integrated Search

2015-06-30

On June 30-July 1 of 2015 the FRA held the Best Practices Workshop on VTI Simulation at the Volpe Center in Cambridge, Massachusetts. The two day workshop was attended by representatives from the government, code developers, researchers, academia, an...

Embracing Open Source for NASA's Earth Science Data Systems

NASA Technical Reports Server (NTRS)

Baynes, Katie; Pilone, Dan; Boller, Ryan; Meyer, David; Murphy, Kevin

2017-01-01

The overarching purpose of NASAs Earth Science program is to develop a scientific understanding of Earth as a system. Scientific knowledge is most robust and actionable when resulting from transparent, traceable, and reproducible methods. Reproducibility includes open access to the data as well as the software used to arrive at results. Additionally, software that is custom-developed for NASA should be open to the greatest degree possible, to enable re-use across Federal agencies, reduce overall costs to the government, remove barriers to innovation, and promote consistency through the use of uniform standards. Finally, Open Source Software (OSS) practices facilitate collaboration between agencies and the private sector. To best meet these ends, NASAs Earth Science Division promotes the full and open sharing of not only all data, metadata, products, information, documentation, models, images, and research results but also the source code used to generate, manipulate and analyze them. This talk focuses on the challenges to open sourcing NASA developed software within ESD and the growing pains associated with establishing policies running the gamut of tracking issues, properly documenting build processes, engaging the open source community, maintaining internal compliance, and accepting contributions from external sources. This talk also covers the adoption of existing open source technologies and standards to enhance our custom solutions and our contributions back to the community. Finally, we will be introducing the most recent OSS contributions from NASA Earth Science program and promoting these projects for wider community review and adoption.

A Guide to Nuclear Weapons Phenomena and Effects Literature

DTIC Science & Technology

1984-10-31

and Disarmament Agency. An article entitled "Limited Nuclear War" in Scientific American (Reference ECE-14) is also of interest because of its rela... Sistems and the Aemosphere’-BCj=9. 43 Personne l; .-EP)- / 47 Civilian .S’ector and the .Environment, (ECE) 50 5 SPECIAL REFERENCE MATERIALS (R) ’<ൾ...approximations. DNA has sponsored the development of software for scientific and military applications of nuclear weapon phenomena and effects information

Developing Argument Skills across Scientific and Social Domains

ERIC Educational Resources Information Center

Iordanou, Kalypso

2010-01-01

Instant-messaging software was used as a method to promote development of argumentation skills in middle schoolers. Transfer of skills across content domains was the major question investigated. Forty sixth graders engaged in electronic dialogues with peers on a controversial topic--for half a science topic (dinosaur extinction) and for half a…

Making it Easy to Construct Accurate Hydrological Models that Exploit High Performance Computers (Invited)

NASA Astrophysics Data System (ADS)

Kees, C. E.; Farthing, M. W.; Terrel, A.; Certik, O.; Seljebotn, D.

2013-12-01

This presentation will focus on two barriers to progress in the hydrological modeling community, and research and development conducted to lessen or eliminate them. The first is a barrier to sharing hydrological models among specialized scientists that is caused by intertwining the implementation of numerical methods with the implementation of abstract numerical modeling information. In the Proteus toolkit for computational methods and simulation, we have decoupled these two important parts of computational model through separate "physics" and "numerics" interfaces. More recently we have begun developing the Strong Form Language for easy and direct representation of the mathematical model formulation in a domain specific language embedded in Python. The second major barrier is sharing ANY scientific software tools that have complex library or module dependencies, as most parallel, multi-physics hydrological models must have. In this setting, users and developer are dependent on an entire distribution, possibly depending on multiple compilers and special instructions depending on the environment of the target machine. To solve these problem we have developed, hashdist, a stateless package management tool and a resulting portable, open source scientific software distribution.

AMPHION: Specification-based programming for scientific subroutine libraries

NASA Technical Reports Server (NTRS)

Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Waldinger, Richard; Stickel, Mark

1994-01-01

AMPHION is a knowledge-based software engineering (KBSE) system that guides a user in developing a diagram representing a formal problem specification. It then automatically implements a solution to this specification as a program consisting of calls to subroutines from a library. The diagram provides an intuitive domain oriented notation for creating a specification that also facilitates reuse and modification. AMPHION'S architecture is domain independent. AMPHION is specialized to an application domain by developing a declarative domain theory. Creating a domain theory is an iterative process that currently requires the joint expertise of domain experts and experts in automated formal methods for software development.

Study on Earthquake Emergency Evacuation Drill Trainer Development

NASA Astrophysics Data System (ADS)

ChangJiang, L.

2016-12-01

With the improvement of China's urbanization, to ensure people survive the earthquake needs scientific routine emergency evacuation drills. Drawing on cellular automaton, shortest path algorithm and collision avoidance, we designed a model of earthquake emergency evacuation drill for school scenes. Based on this model, we made simulation software for earthquake emergency evacuation drill. The software is able to perform the simulation of earthquake emergency evacuation drill by building spatial structural model and selecting the information of people's location grounds on actual conditions of constructions. Based on the data of simulation, we can operate drilling in the same building. RFID technology could be used here for drill data collection which read personal information and send it to the evacuation simulation software via WIFI. Then the simulation software would contrast simulative data with the information of actual evacuation process, such as evacuation time, evacuation path, congestion nodes and so on. In the end, it would provide a contrastive analysis report to report assessment result and optimum proposal. We hope the earthquake emergency evacuation drill software and trainer can provide overall process disposal concept for earthquake emergency evacuation drill in assembly occupancies. The trainer can make the earthquake emergency evacuation more orderly, efficient, reasonable and scientific to fulfill the increase in coping capacity of urban hazard.

Scientific Staff | ast.noao.edu

Science.gov Websites

Emeritus Double stars; stellar rotation; stellar characteristics; publication practices in astronomy Thai formation; infrared astronomy and instrumentation NOAO Associate Director for Kitt Peak National Observatory clumpy media, software development, modeling & SED fitting, big data, HPC in astronomy, visualization

Using Microsoft PowerPoint as an Astronomical Image Analysis Tool

NASA Astrophysics Data System (ADS)

Beck-Winchatz, Bernhard

2006-12-01

Engaging students in the analysis of authentic scientific data is an effective way to teach them about the scientific process and to develop their problem solving, teamwork and communication skills. In astronomy several image processing and analysis software tools have been developed for use in school environments. However, the practical implementation in the classroom is often difficult because the teachers may not have the comfort level with computers necessary to install and use these tools, they may not have adequate computer privileges and/or support, and they may not have the time to learn how to use specialized astronomy software. To address this problem, we have developed a set of activities in which students analyze astronomical images using basic tools provided in PowerPoint. These include measuring sizes, distances, and angles, and blinking images. In contrast to specialized software, PowerPoint is broadly available on school computers. Many teachers are already familiar with PowerPoint, and the skills developed while learning how to analyze astronomical images are highly transferable. We will discuss several practical examples of measurements, including the following: -Variations in the distances to the sun and moon from their angular sizes -Magnetic declination from images of shadows -Diameter of the moon from lunar eclipse images -Sizes of lunar craters -Orbital radii of the Jovian moons and mass of Jupiter -Supernova and comet searches -Expansion rate of the universe from images of distant galaxies

European Hands-on Universe

NASA Astrophysics Data System (ADS)

Doran, Rosa; Ferlet, Roger; Gómez de Castro, Ana I.; Hill, Robert; Horellou, Cathy; Mankiewicz, Lech; Melchior, Anne-Laure; Metaxa, Margarita; Zanazzi, Alessandra

2007-08-01

Hands-on Universe is a project born at UC@Berkeley. A project devoted to enrich the teaching of Astronomy within the classroom environment with a different approach, more connected to the new technologies. Its main goals are not only to promote the use of such technologies but also to reawaken on students the taste for STEM (Science, technologies, engineering and math) related issues and also to increase their scientific culture. Eight countries in Europe decided to adopt the method and, funded by MINERVA, formed the European Hands-on Universe. Several resources were produced and a data reduction software developed http://www.euhou.net/.Other European countries are interested and should join this coordinated effort in the near future. At an international level there are 20 countries using this approach. There are plans to develop scientific cooperation among these countries. Pilot scientific research projects in schools are being tested in EU-HOU schools, Russia and USA. There is also a game being developed to be used as a new tool for teaching scientific content in the classroom environment. An effort to develop an international network of scientific / educational collaboration is the next step.

Computational science: shifting the focus from tools to models

PubMed Central

Hinsen, Konrad

2014-01-01

Computational techniques have revolutionized many aspects of scientific research over the last few decades. Experimentalists use computation for data analysis, processing ever bigger data sets. Theoreticians compute predictions from ever more complex models. However, traditional articles do not permit the publication of big data sets or complex models. As a consequence, these crucial pieces of information no longer enter the scientific record. Moreover, they have become prisoners of scientific software: many models exist only as software implementations, and the data are often stored in proprietary formats defined by the software. In this article, I argue that this emphasis on software tools over models and data is detrimental to science in the long term, and I propose a means by which this can be reversed. PMID:25309728

Software architecture of biomimetic underwater vehicle

NASA Astrophysics Data System (ADS)

Praczyk, Tomasz; Szymak, Piotr

2016-05-01

Autonomous underwater vehicles are vehicles that are entirely or partly independent of human decisions. In order to obtain operational independence, the vehicles have to be equipped with a specialized software. The main task of the software is to move the vehicle along a trajectory with collision avoidance. Moreover, the software has also to manage different devices installed on the vehicle board, e.g. to start and stop cameras, sonars etc. In addition to the software embedded on the vehicle board, the software responsible for managing the vehicle by the operator is also necessary. Its task is to define mission of the vehicle, to start, to stop the mission, to send emergency commands, to monitor vehicle parameters, and to control the vehicle in remotely operated mode. An important objective of the software is also to support development and tests of other software components. To this end, a simulation environment is necessary, i.e. simulation model of the vehicle and all its key devices, the model of the sea environment, and the software to visualize behavior of the vehicle. The paper presents architecture of the software designed for biomimetic autonomous underwater vehicle (BAUV) that is being constructed within the framework of the scientific project financed by Polish National Center of Research and Development.

Software for Planning Scientific Activities on Mars

NASA Technical Reports Server (NTRS)

Ai-Chang, Mitchell; Bresina, John; Jonsson, Ari; Hsu, Jennifer; Kanefsky, Bob; Morris, Paul; Rajan, Kanna; Yglesias, Jeffrey; Charest, Len; Maldague, Pierre

2003-01-01

Mixed-Initiative Activity Plan Generator (MAPGEN) is a ground-based computer program for planning and scheduling the scientific activities of instrumented exploratory robotic vehicles, within the limitations of available resources onboard the vehicle. MAPGEN is a combination of two prior software systems: (1) an activity-planning program, APGEN, developed at NASA s Jet Propulsion Laboratory and (2) the Europa planner/scheduler from NASA Ames Research Center. MAPGEN performs all of the following functions: Automatic generation of plans and schedules for scientific and engineering activities; Testing of hypotheses (or what-if analyses of various scenarios); Editing of plans; Computation and analysis of resources; and Enforcement and maintenance of constraints, including resolution of temporal and resource conflicts among planned activities. MAPGEN can be used in either of two modes: one in which the planner/scheduler is turned off and only the basic APGEN functionality is utilized, or one in which both component programs are used to obtain the full planning, scheduling, and constraint-maintenance functionality.

Data Mining as a Service (DMaaS)

NASA Astrophysics Data System (ADS)

Tejedor, E.; Piparo, D.; Mascetti, L.; Moscicki, J.; Lamanna, M.; Mato, P.

2016-10-01

Data Mining as a Service (DMaaS) is a software and computing infrastructure that allows interactive mining of scientific data in the cloud. It allows users to run advanced data analyses by leveraging the widely adopted Jupyter notebook interface. Furthermore, the system makes it easier to share results and scientific code, access scientific software, produce tutorials and demonstrations as well as preserve the analyses of scientists. This paper describes how a first pilot of the DMaaS service is being deployed at CERN, starting from the notebook interface that has been fully integrated with the ROOT analysis framework, in order to provide all the tools for scientists to run their analyses. Additionally, we characterise the service backend, which combines a set of IT services such as user authentication, virtual computing infrastructure, mass storage, file synchronisation, development portals or batch systems. The added value acquired by the combination of the aforementioned categories of services is discussed, focusing on the opportunities offered by the CERNBox synchronisation service and its massive storage backend, EOS.

Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

PubMed Central

Degenhart, Alan D.; Kelly, John W.; Ashmore, Robin C.; Collinger, Jennifer L.; Tyler-Kabara, Elizabeth C.; Weber, Douglas J.; Wang, Wei

2011-01-01

This paper presents “Craniux,” an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development. PMID:21687575

Craniux: a LabVIEW-based modular software framework for brain-machine interface research.

PubMed

Degenhart, Alan D; Kelly, John W; Ashmore, Robin C; Collinger, Jennifer L; Tyler-Kabara, Elizabeth C; Weber, Douglas J; Wang, Wei

2011-01-01

This paper presents "Craniux," an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development.

The community-driven BiG CZ software system for integration and analysis of bio- and geoscience data in the critical zone

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Mayorga, E.; Horsburgh, J. S.; Lehnert, K. A.; Zaslavsky, I.; Valentine, D. W., Jr.; Richard, S. M.; Cheetham, R.; Meyer, F.; Henry, C.; Berg-Cross, G.; Packman, A. I.; Aronson, E. L.

2014-12-01

Here we present the prototypes of a new scientific software system designed around the new Observations Data Model version 2.0 (ODM2, https://github.com/UCHIC/ODM2) to substantially enhance integration of biological and Geological (BiG) data for Critical Zone (CZ) science. The CZ science community takes as its charge the effort to integrate theory, models and data from the multitude of disciplines collectively studying processes on the Earth's surface. The central scientific challenge of the CZ science community is to develop a "grand unifying theory" of the critical zone through a theory-model-data fusion approach, for which the key missing need is a cyberinfrastructure for seamless 4D visual exploration of the integrated knowledge (data, model outputs and interpolations) from all the bio and geoscience disciplines relevant to critical zone structure and function, similar to today's ability to easily explore historical satellite imagery and photographs of the earth's surface using Google Earth. This project takes the first "BiG" steps toward answering that need. The overall goal of this project is to co-develop with the CZ science and broader community, including natural resource managers and stakeholders, a web-based integration and visualization environment for joint analysis of cross-scale bio and geoscience processes in the critical zone (BiG CZ), spanning experimental and observational designs. We will: (1) Engage the CZ and broader community to co-develop and deploy the BiG CZ software stack; (2) Develop the BiG CZ Portal web application for intuitive, high-performance map-based discovery, visualization, access and publication of data by scientists, resource managers, educators and the general public; (3) Develop the BiG CZ Toolbox to enable cyber-savvy CZ scientists to access BiG CZ Application Programming Interfaces (APIs); and (4) Develop the BiG CZ Central software stack to bridge data systems developed for multiple critical zone domains into a single metadata catalog. The entire BiG CZ Software system is being developed on public repositories as a modular suite of open source software projects. It will be built around a new Observations Data Model Version 2.0 (ODM2) that has been developed by members of the BiG CZ project team, with community input, under separate funding.

A LabVIEW® based generic CT scanner control software platform.

PubMed

Dierick, M; Van Loo, D; Masschaele, B; Boone, M; Van Hoorebeke, L

2010-01-01

UGCT, the Centre for X-ray tomography at Ghent University (Belgium) does research on X-ray tomography and its applications. This includes the development and construction of state-of-the-art CT scanners for scientific research. Because these scanners are built for very different purposes they differ considerably in their physical implementations. However, they all share common principle functionality. In this context a generic software platform was developed using LabVIEW® in order to provide the same interface and functionality on all scanners. This article describes the concept and features of this software, and its potential for tomography in a research setting. The core concept is to rigorously separate the abstract operation of a CT scanner from its actual physical configuration. This separation is achieved by implementing a sender-listener architecture. The advantages are that the resulting software platform is generic, scalable, highly efficient, easy to develop and to extend, and that it can be deployed on future scanners with minimal effort.

Scout: high-performance heterogeneous computing made simple

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

Jablin, James; Mc Cormick, Patrick; Herlihy, Maurice

2011-01-26

Researchers must often write their own simulation and analysis software. During this process they simultaneously confront both computational and scientific problems. Current strategies for aiding the generation of performance-oriented programs do not abstract the software development from the science. Furthermore, the problem is becoming increasingly complex and pressing with the continued development of many-core and heterogeneous (CPU-GPU) architectures. To acbieve high performance, scientists must expertly navigate both software and hardware. Co-design between computer scientists and research scientists can alleviate but not solve this problem. The science community requires better tools for developing, optimizing, and future-proofing codes, allowing scientists to focusmore » on their research while still achieving high computational performance. Scout is a parallel programming language and extensible compiler framework targeting heterogeneous architectures. It provides the abstraction required to buffer scientists from the constantly-shifting details of hardware while still realizing higb-performance by encapsulating software and hardware optimization within a compiler framework.« less

Teaching Science and Mathematics Subjects Using the Excel Spreadsheet Package

ERIC Educational Resources Information Center

Ibrahim, Dogan

2009-01-01

The teaching of scientific subjects usually require laboratories where students can put the theory they have learned into practice. Traditionally, electronic programmable calculators, dedicated software, or expensive software simulation packages, such as MATLAB have been used to simulate scientific experiments. Recently, spreadsheet programs have…

Extreme Programming: A Kuhnian Revolution?

NASA Astrophysics Data System (ADS)

Northover, Mandy; Northover, Alan; Gruner, Stefan; Kourie, Gerrick G.; Boake, Andrew

This paper critically assesses the extent to which the Agile Software community's use of Thomas Kuhn's theory of revolutionary scientific change is justified. It will be argued that Kuhn's concepts of "scientific revolution" and "paradigm shift" cannot adequately explain the change from one type of software methodology to another.

Utility of coupling nonlinear optimization methods with numerical modeling software

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

Murphy, M.J.

1996-08-05

Results of using GLO (Global Local Optimizer), a general purpose nonlinear optimization software package for investigating multi-parameter problems in science and engineering is discussed. The package consists of the modular optimization control system (GLO), a graphical user interface (GLO-GUI), a pre-processor (GLO-PUT), a post-processor (GLO-GET), and nonlinear optimization software modules, GLOBAL & LOCAL. GLO is designed for controlling and easy coupling to any scientific software application. GLO runs the optimization module and scientific software application in an iterative loop. At each iteration, the optimization module defines new values for the set of parameters being optimized. GLO-PUT inserts the new parametermore » values into the input file of the scientific application. GLO runs the application with the new parameter values. GLO-GET determines the value of the objective function by extracting the results of the analysis and comparing to the desired result. GLO continues to run the scientific application over and over until it finds the ``best`` set of parameters by minimizing (or maximizing) the objective function. An example problem showing the optimization of material model is presented (Taylor cylinder impact test).« less

The relationships between software publications and software systems

NASA Astrophysics Data System (ADS)

Hogg, David W.

2017-01-01

When we build software systems or software tools for astronomy, we sometimes do and sometimes don't also write and publish standard scientific papers about those software systems. I will discuss the pros and cons of writing such publications. There are impacts of writing such papers immediately (they can affect the design and structure of the software project itself), in the short term (they can promote adoption and legitimize the software), in the medium term (they can provide a platform for all the literature's mechanisms for citation, criticism, and reuse), and in the long term (they can preserve ideas that are embodied in the software, possibly on timescales much longer than the lifetime of any software context). I will argue that as important as pure software contributions are to astronomy—and I am both a preacher and a practitioner—software contributions are even more valuable when they are associated with traditional scientific publications. There are exceptions and complexities of course, which I will discuss.

Chandra X-ray Center Science Data Systems Regression Testing of CIAO

NASA Astrophysics Data System (ADS)

Lee, N. P.; Karovska, M.; Galle, E. C.; Bonaventura, N. R.

2011-07-01

The Chandra Interactive Analysis of Observations (CIAO) is a software system developed for the analysis of Chandra X-ray Observatory observations. An important component of a successful CIAO release is the repeated testing of the tools across various platforms to ensure consistent and scientifically valid results. We describe the procedures of the scientific regression testing of CIAO and the enhancements made to the testing system to increase the efficiency of run time and result validation.

Simulator predicts transient flow for Malaysian subsea pipeline

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

Inayat-Hussain, A.A.; Ayob, M.S.; Zain, A.B.M.

1996-04-15

In a step towards acquiring in-house capability in multiphase flow technology, Petronas Research and Scientific Services Sdn. Bhd., Kuala Lumpur, has developed two-phase flow simulation software for analyzing slow gas-condensate transient flow. Unlike its general-purpose contemporaries -- TACITE, OLGA, Traflow (OGJ, Jan. 3, 1994, p. 42; OGJ, Jan. 10, 1994, p. 52), and PLAC (AEA Technology, U.K.) -- ABASs is a dedicated software for slow transient flows generated during pigging operations in the Duyong network, offshore Malaysia. This network links the Duyong and Bekok fields to the onshore gas terminal (OGT) on the east coast of peninsular Malaysia. It predictsmore » the steady-state pressure drop vs. flow rates, condensate volume in the network, pigging dynamics including volume of produced slug, and the condensate build-up following pigging. The predictions of ABASs have been verified against field data obtained from the Duyong network. Presented here is an overview of the development, verification, and application of the ABASs software. Field data are presented for verification of the software, and several operational scenarios are simulated using the software. The field data and simulation study documented here will provide software users and developers with a further set of results on which to benchmark their own software and two-phase pipeline operating guidelines.« less

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers.

PubMed

Sochat, Vanessa V; Prybol, Cameron J; Kurtzer, Gregory M

2017-01-01

Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub's primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers.

The software system for the Control and Data Acquisition for the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Wegner, P.; FüBling, M.; Oya, I.; Hagge, L.; Schwanke, U.; Schwarz, J.; Tosti, G.; Conforti, V.; Lyard, E.; Walter, R.; Oliveira Antonino, P.; Morgenstern, A.

2016-10-01

The Cherenkov Telescope Array (CTA), as the next generation ground-based very high-energy gamma-ray observatory, is defining new areas beyond those related to physics. It is also creating new demands on the control and data acquisition system. CTA will consist of two installations, one in each hemisphere, containing tens of telescopes of different sizes. The ACTL (array control and data acquisition) system will consist of the hardware and software that is necessary to control and monitor the CTA array, as well as to time-stamp, read-out, filter and store the scientific data at aggregated rates of a few GB/s. The ACTL system must implement a flexible software architecture to permit the simultaneous automatic operation of multiple sub-arrays of telescopes with a minimum personnel effort on site. In addition ACTL must be able to modify the observation schedule on timescales of a few tens of seconds, to account for changing environmental conditions or to prioritize incoming scientific alerts from time-critical transient phenomena such as gamma-ray bursts. This contribution summarizes the status of the development of the software architecture and the main design choices and plans.

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers

PubMed Central

Prybol, Cameron J.; Kurtzer, Gregory M.

2017-01-01

Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub’s primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers. PMID:29186161

OASYS (OrAnge SYnchrotron Suite): an open-source graphical environment for x-ray virtual experiments

NASA Astrophysics Data System (ADS)

Rebuffi, Luca; Sanchez del Rio, Manuel

2017-08-01

The evolution of the hardware platforms, the modernization of the software tools, the access to the codes of a large number of young people and the popularization of the open source software for scientific applications drove us to design OASYS (ORange SYnchrotron Suite), a completely new graphical environment for modelling X-ray experiments. The implemented software architecture allows to obtain not only an intuitive and very-easy-to-use graphical interface, but also provides high flexibility and rapidity for interactive simulations, making configuration changes to quickly compare multiple beamline configurations. Its purpose is to integrate in a synergetic way the most powerful calculation engines available. OASYS integrates different simulation strategies via the implementation of adequate simulation tools for X-ray Optics (e.g. ray tracing and wave optics packages). It provides a language to make them to communicate by sending and receiving encapsulated data. Python has been chosen as main programming language, because of its universality and popularity in scientific computing. The software Orange, developed at the University of Ljubljana (SLO), is the high level workflow engine that provides the interaction with the user and communication mechanisms.

Three-dimensional electron microscopy simulation with the CASINO Monte Carlo software.

PubMed

Demers, Hendrix; Poirier-Demers, Nicolas; Couture, Alexandre Réal; Joly, Dany; Guilmain, Marc; de Jonge, Niels; Drouin, Dominique

2011-01-01

Monte Carlo softwares are widely used to understand the capabilities of electron microscopes. To study more realistic applications with complex samples, 3D Monte Carlo softwares are needed. In this article, the development of the 3D version of CASINO is presented. The software feature a graphical user interface, an efficient (in relation to simulation time and memory use) 3D simulation model, accurate physic models for electron microscopy applications, and it is available freely to the scientific community at this website: www.gel.usherbrooke.ca/casino/index.html. It can be used to model backscattered, secondary, and transmitted electron signals as well as absorbed energy. The software features like scan points and shot noise allow the simulation and study of realistic experimental conditions. This software has an improved energy range for scanning electron microscopy and scanning transmission electron microscopy applications. Copyright © 2011 Wiley Periodicals, Inc.

Three-Dimensional Electron Microscopy Simulation with the CASINO Monte Carlo Software

PubMed Central

Demers, Hendrix; Poirier-Demers, Nicolas; Couture, Alexandre Réal; Joly, Dany; Guilmain, Marc; de Jonge, Niels; Drouin, Dominique

2011-01-01

Monte Carlo softwares are widely used to understand the capabilities of electron microscopes. To study more realistic applications with complex samples, 3D Monte Carlo softwares are needed. In this paper, the development of the 3D version of CASINO is presented. The software feature a graphical user interface, an efficient (in relation to simulation time and memory use) 3D simulation model, accurate physic models for electron microscopy applications, and it is available freely to the scientific community at this website: www.gel.usherbrooke.ca/casino/index.html. It can be used to model backscattered, secondary, and transmitted electron signals as well as absorbed energy. The software features like scan points and shot noise allow the simulation and study of realistic experimental conditions. This software has an improved energy range for scanning electron microscopy and scanning transmission electron microscopy applications. PMID:21769885

Towards Efficient Scientific Data Management Using Cloud Storage

NASA Technical Reports Server (NTRS)

He, Qiming

2013-01-01

A software prototype allows users to backup and restore data to/from both public and private cloud storage such as Amazon's S3 and NASA's Nebula. Unlike other off-the-shelf tools, this software ensures user data security in the cloud (through encryption), and minimizes users operating costs by using space- and bandwidth-efficient compression and incremental backup. Parallel data processing utilities have also been developed by using massively scalable cloud computing in conjunction with cloud storage. One of the innovations in this software is using modified open source components to work with a private cloud like NASA Nebula. Another innovation is porting the complex backup to- cloud software to embedded Linux, running on the home networking devices, in order to benefit more users.

Software for visualization, analysis, and manipulation of laser scan images

NASA Astrophysics Data System (ADS)

Burnsides, Dennis B.

1997-03-01

The recent introduction of laser surface scanning to scientific applications presents a challenge to computer scientists and engineers. Full utilization of this two- dimensional (2-D) and three-dimensional (3-D) data requires advances in techniques and methods for data processing and visualization. This paper explores the development of software to support the visualization, analysis and manipulation of laser scan images. Specific examples presented are from on-going efforts at the Air Force Computerized Anthropometric Research and Design (CARD) Laboratory.

Software Engineering Tools for Scientific Models

NASA Technical Reports Server (NTRS)

Abrams, Marc; Saboo, Pallabi; Sonsini, Mike

2013-01-01

Software tools were constructed to address issues the NASA Fortran development community faces, and they were tested on real models currently in use at NASA. These proof-of-concept tools address the High-End Computing Program and the Modeling, Analysis, and Prediction Program. Two examples are the NASA Goddard Earth Observing System Model, Version 5 (GEOS-5) atmospheric model in Cell Fortran on the Cell Broadband Engine, and the Goddard Institute for Space Studies (GISS) coupled atmosphere- ocean model called ModelE, written in fixed format Fortran.

Earth Exploration Toolbook Workshops: Helping Teachers and Students Analyze Web-based Scientific Data

NASA Astrophysics Data System (ADS)

McAuliffe, C.; Ledley, T.; Dahlman, L.; Haddad, N.

2007-12-01

One of the challenges faced by Earth science teachers, particularly in K-12 settings, is that of connecting scientific research to classroom experiences. Helping teachers and students analyze Web-based scientific data is one way to bring scientific research to the classroom. The Earth Exploration Toolbook (EET) was developed as an online resource to accomplish precisely that. The EET consists of chapters containing step-by-step instructions for accessing Web-based scientific data and for using a software analysis tool to explore issues or concepts in science, technology, and mathematics. For example, in one EET chapter, users download Earthquake data from the USGS and bring it into a geographic information system (GIS), analyzing factors affecting the distribution of earthquakes. The goal of the EET Workshops project is to provide professional development that enables teachers to incorporate Web-based scientific data and analysis tools in ways that meet their curricular needs. In the EET Workshops project, Earth science teachers participate in a pair of workshops that are conducted in a combined teleconference and Web-conference format. In the first workshop, the EET Data Analysis Workshop, participants are introduced to the National Science Digital Library (NSDL) and the Digital Library for Earth System Education (DLESE). They also walk through an Earth Exploration Toolbook (EET) chapter and discuss ways to use Earth science datasets and tools with their students. In a follow-up second workshop, the EET Implementation Workshop, teachers share how they used these materials in the classroom by describing the projects and activities that they carried out with students. The EET Workshops project offers unique and effective professional development. Participants work at their own Internet-connected computers, and dial into a toll-free group teleconference for step-by-step facilitation and interaction. They also receive support via Elluminate, a Web-conferencing software program. The software allows participants to see the facilitator's computer as the analysis techniques of an EET chapter are demonstrated. If needed, the facilitator can also view individual participant's computers, assisting with technical difficulties. In addition, it enables a large number of end users, often widely distributed, to engage in interactive, real-time instruction. In this presentation, we will describe the elements of an EET Workshop pair, highlighting the capabilities and use of Elluminate. We will share lessons learned through several years of conducting this type of professional development. We will also share findings from survey data gathered from teachers who have participated in our workshops.

GammaLib and ctools. A software framework for the analysis of astronomical gamma-ray data

NASA Astrophysics Data System (ADS)

Knödlseder, J.; Mayer, M.; Deil, C.; Cayrou, J.-B.; Owen, E.; Kelley-Hoskins, N.; Lu, C.-C.; Buehler, R.; Forest, F.; Louge, T.; Siejkowski, H.; Kosack, K.; Gerard, L.; Schulz, A.; Martin, P.; Sanchez, D.; Ohm, S.; Hassan, T.; Brau-Nogué, S.

2016-08-01

The field of gamma-ray astronomy has seen important progress during the last decade, yet to date no common software framework has been developed for the scientific analysis of gamma-ray telescope data. We propose to fill this gap by means of the GammaLib software, a generic library that we have developed to support the analysis of gamma-ray event data. GammaLib was written in C++ and all functionality is available in Python through an extension module. Based on this framework we have developed the ctools software package, a suite of software tools that enables flexible workflows to be built for the analysis of Imaging Air Cherenkov Telescope event data. The ctools are inspired by science analysis software available for existing high-energy astronomy instruments, and they follow the modular ftools model developed by the High Energy Astrophysics Science Archive Research Center. The ctools were written in Python and C++, and can be either used from the command line via shell scripts or directly from Python. In this paper we present the GammaLib and ctools software versions 1.0 that were released at the end of 2015. GammaLib and ctools are ready for the science analysis of Imaging Air Cherenkov Telescope event data, and also support the analysis of Fermi-LAT data and the exploitation of the COMPTEL legacy data archive. We propose using ctools as the science tools software for the Cherenkov Telescope Array Observatory.

The role of the ADS in software discovery and citation

NASA Astrophysics Data System (ADS)

Accomazzi, Alberto

2018-01-01

As the primary index of scholarly content in astronomy and physics, the NASA Astrophysics Data System (ADS) is collaborating with the AAS journals and the Zenodo repository in an effort to promote the preservation of scientific software used in astronomy research and its citation in scholarly publications. In this talk I will discuss how ADS is updating its service infrastructure to allow for the publication, indexing, and citation of software records in scientific articles.

Multivariate statistical analysis software technologies for astrophysical research involving large data bases

NASA Technical Reports Server (NTRS)

Djorgovski, S. George

1994-01-01

We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complete database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful, and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications, and has produced real, published results.

Judicious use of custom development in an open source component architecture

NASA Astrophysics Data System (ADS)

Bristol, S.; Latysh, N.; Long, D.; Tekell, S.; Allen, J.

2014-12-01

Modern software engineering is not as much programming from scratch as innovative assembly of existing components. Seamlessly integrating disparate components into scalable, performant architecture requires sound engineering craftsmanship and can often result in increased cost efficiency and accelerated capabilities if software teams focus their creativity on the edges of the problem space. ScienceBase is part of the U.S. Geological Survey scientific cyberinfrastructure, providing data and information management, distribution services, and analysis capabilities in a way that strives to follow this pattern. ScienceBase leverages open source NoSQL and relational databases, search indexing technology, spatial service engines, numerous libraries, and one proprietary but necessary software component in its architecture. The primary engineering focus is cohesive component interaction, including construction of a seamless Application Programming Interface (API) across all elements. The API allows researchers and software developers alike to leverage the infrastructure in unique, creative ways. Scaling the ScienceBase architecture and core API with increasing data volume (more databases) and complexity (integrated science problems) is a primary challenge addressed by judicious use of custom development in the component architecture. Other data management and informatics activities in the earth sciences have independently resolved to a similar design of reusing and building upon established technology and are working through similar issues for managing and developing information (e.g., U.S. Geoscience Information Network; NASA's Earth Observing System Clearing House; GSToRE at the University of New Mexico). Recent discussions facilitated through the Earth Science Information Partners are exploring potential avenues to exploit the implicit relationships between similar projects for explicit gains in our ability to more rapidly advance global scientific cyberinfrastructure.

A research strategy for the dynamic study of students' concepts and problem solving strategies using science software

NASA Astrophysics Data System (ADS)

Krajcik, Joseph S.; Simmons, Patricia E.; Lunetta, Vincent N.

Microcomputers and appropriate software have the potential to help students learn. They can also serve as appropriate media for investigating how students learn. In this article we describe a research strategy examining learning and behavior when students interacted with microcomputers and software. Results from two preliminary studies illustrate the strategy.A major feature of the strategy included recording students interacting with microcomputer software interfaced with a VCR. The VCR recorded the video output from a microcomputer and students' verbal commentary via microphone input. This technique allowed students' comments about their observations, perceptions, predictions, explanations, and decisions to be recorded simultaneously with their computer input and the display on the microcomputer monitor.The research strategy described can provide important information about cognitive and affective behaviors of students engaged in using instructional software. Research studies utilizing this strategy can enhance our understanding of how students develop and employ important concepts and scientific relationships, how students develop problem-solving skills and solve problems, and how they interact with instructional software. Results of such studies have important implications for teaching and for the design of instructional software.

Long-term Preservation of Data Analysis Capabilities

NASA Astrophysics Data System (ADS)

Gabriel, C.; Arviset, C.; Ibarra, A.; Pollock, A.

2015-09-01

While the long-term preservation of scientific data obtained by large astrophysics missions is ensured through science archives, the issue of data analysis software preservation has hardly been addressed. Efforts by large data centres have contributed so far to maintain some instrument or mission-specific data reduction packages on top of high-level general purpose data analysis software. However, it is always difficult to keep software alive without support and maintenance once the active phase of a mission is over. This is especially difficult in the budgetary model followed by space agencies. We discuss the importance of extending the lifetime of dedicated data analysis packages and review diverse strategies under development at ESA using new paradigms such as Virtual Machines, Cloud Computing, and Software as a Service for making possible full availability of data analysis and calibration software for decades at minimal cost.

Kinematics with the assistance of smartphones: Measuring data via GPS - Visualizing data with Google Earth

NASA Astrophysics Data System (ADS)

Gabriel, Patrik; Backhaus, Udo

2013-04-01

Nearly every smartphone is now GPS capable. The widespread use of GPS navigation has developed alongside less expensive hardware and user-friendly software interfaces, which may help to bring scientific research and teaching closer to real life.

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 Tropical Marine Microbial Natural Products Geobibliography as an Example of Desktop Exploration of Current Research Using Web Visualisation Tools

PubMed Central

Mukherjee, Joydeep; Llewellyn, Lyndon E; Evans-Illidge, Elizabeth A

2008-01-01

Microbial marine biodiscovery is a recent scientific endeavour developing at a time when information and other technologies are also undergoing great technical strides. Global visualisation of datasets is now becoming available to the world through powerful and readily available software such as Worldwind™, ArcGIS Explorer™ and Google Earth™. Overlaying custom information upon these tools is within the hands of every scientist and more and more scientific organisations are making data available that can also be integrated into these global visualisation tools. The integrated global view that these tools enable provides a powerful desktop exploration tool. Here we demonstrate the value of this approach to marine microbial biodiscovery by developing a geobibliography that incorporates citations on tropical and near-tropical marine microbial natural products research with Google Earth™ and additional ancillary global data sets. The tools and software used are all readily available and the reader is able to use and install the material described in this article. PMID:19172194

Joined-up Planetary Information, in the Cloud and on Devices.

NASA Astrophysics Data System (ADS)

Smith, M. J.; Emmott, S.; Purves, D. W.; Joppa, L. N.; Lyutsarev, V.

2014-12-01

In scientific research and development, emphasis is placed on research over development. A significant cost is that the two-way interaction between scientific insights and societal needs does not function effectively to lead to impacts in the wider world. We simply must embrace new software and hardware approaches if we are to provide timely predictive information to address global problems, support businesses and inform governments and citizens. The Microsoft Research Computational Science Lab has been pioneering research into software and methodologies to provide useful and usable new environmental information. Our approach has been very joined-up: from accellerating data acquisition from the field with remote sensor technology, targetted data collection and citizen science, to enabling proces based modelling-using multiple heterogeneous data-sets in the cloud and enabling the resulting planetary information to be accessed from any device. This talk will demonstrate some of the specific research and development we are doing to accerate the pace in which important science has impact on the wider world and will emphasise the important insights gained from advancing the research and develoment together.

Telescience - Concepts And Contributions To The Extreme Ultraviolet Explorer Mission

NASA Astrophysics Data System (ADS)

Marchant, Will; Dobson, Carl; Chakrabarti, Supriya; Malina, Roger F.

1987-10-01

A goal of the telescience concept is to allow scientists to use remotely located instruments as they would in their laboratory. Another goal is to increase reliability and scientific return of these instruments. In this paper we discuss the role of transparent software tools in development, integration, and postlaunch environments to achieve hands on access to the instrument. The use of transparent tools helps to reduce the parallel development of capability and to assure that valuable pre-launch experience is not lost in the operations phase. We also discuss the use of simulation as a rapid prototyping technique. Rapid prototyping provides a cost-effective means of using an iterative approach to instrument design. By allowing inexpensive produc-tion of testbeds, scientists can quickly tune the instrument to produce the desired scientific data. Using portions of the Extreme Ultraviolet Explorer (EUVE) system, we examine some of the results of preliminary tests in the use of simulation and tran-sparent tools. Additionally, we discuss our efforts to upgrade our software "EUVE electronics" simulator to emulate a full instrument, and give the pros and cons of the simulation facilities we have developed.

Satellite-Based Stratospheric and Tropospheric Measurements: Determination of Global Ozone and Other Trace Species

NASA Technical Reports Server (NTRS)

Chance, Kelly

2003-01-01

This grant is an extension to our previous NASA Grant NAG5-3461, providing incremental funding to continue GOME (Global Ozone Monitoring Experiment) and SCIAMACHY (SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY) studies. This report summarizes research done under these grants through December 31, 2002. The research performed during this reporting period includes development and maintenance of scientific software for the GOME retrieval algorithms, consultation on operational software development for GOME, consultation and development for SCIAMACHY near-real-time (NRT) and off-line (OL) data products, and participation in initial SCIAMACHY validation studies. The Global Ozone Monitoring Experiment was successfully launched on the ERS-2 satellite on April 20, 1995, and remains working in normal fashion. SCIAMACHY was launched March 1, 2002 on the ESA Envisat satellite. Three GOME-2 instruments are now scheduled to fly on the Metop series of operational meteorological satellites (Eumetsat). K. Chance is a member of the reconstituted GOME Scientific Advisory Group, which will guide the GOME-2 program as well as the continuing ERS-2 GOME program.

Satellite-Based Stratospheric and Tropospheric Measurements: Determination of Global Ozone and Other Trace Species

NASA Astrophysics Data System (ADS)

Chance, Kelly

2003-02-01

This grant is an extension to our previous NASA Grant NAG5-3461, providing incremental funding to continue GOME (Global Ozone Monitoring Experiment) and SCIAMACHY (SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY) studies. This report summarizes research done under these grants through December 31, 2002. The research performed during this reporting period includes development and maintenance of scientific software for the GOME retrieval algorithms, consultation on operational software development for GOME, consultation and development for SCIAMACHY near-real-time (NRT) and off-line (OL) data products, and participation in initial SCIAMACHY validation studies. The Global Ozone Monitoring Experiment was successfully launched on the ERS-2 satellite on April 20, 1995, and remains working in normal fashion. SCIAMACHY was launched March 1, 2002 on the ESA Envisat satellite. Three GOME-2 instruments are now scheduled to fly on the Metop series of operational meteorological satellites (Eumetsat). K. Chance is a member of the reconstituted GOME Scientific Advisory Group, which will guide the GOME-2 program as well as the continuing ERS-2 GOME program.

The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.

PubMed

Enquobahrie, Andinet; Cheng, Patrick; Gary, Kevin; Ibanez, Luis; Gobbi, David; Lindseth, Frank; Yaniv, Ziv; Aylward, Stephen; Jomier, Julien; Cleary, Kevin

2007-11-01

This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers' mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.

Theoretical bases of project management in conditions of innovative economy based on fuzzy modeling

NASA Astrophysics Data System (ADS)

Beilin, I. L.; Khomenko, V. V.

2018-05-01

In recent years, more and more Russian enterprises (both private and public) are trying to organize their activities on the basis of modern scientific research in order to improve the management of economic processes. Business planning, financial and investment analysis, modern software products based on the latest scientific developments are introduced everywhere. At the same time, there is a growing demand for market research (both at the microeconomic and macroeconomic levels), for financial and general economic information.

Scientific Workflow Management in Proteomics

PubMed Central

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

2012-01-01

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

Research on Occupational Safety, Health Management and Risk Control Technology in Coal Mines.

PubMed

Zhou, Lu-Jie; Cao, Qing-Gui; Yu, Kai; Wang, Lin-Lin; Wang, Hai-Bin

2018-04-26

This paper studies the occupational safety and health management methods as well as risk control technology associated with the coal mining industry, including daily management of occupational safety and health, identification and assessment of risks, early warning and dynamic monitoring of risks, etc.; also, a B/S mode software (Geting Coal Mine, Jining, Shandong, China), i.e., Coal Mine Occupational Safety and Health Management and Risk Control System, is developed to attain the aforementioned objectives, namely promoting the coal mine occupational safety and health management based on early warning and dynamic monitoring of risks. Furthermore, the practical effectiveness and the associated pattern for applying this software package to coal mining is analyzed. The study indicates that the presently developed coal mine occupational safety and health management and risk control technology and the associated software can support the occupational safety and health management efforts in coal mines in a standardized and effective manner. It can also control the accident risks scientifically and effectively; its effective implementation can further improve the coal mine occupational safety and health management mechanism, and further enhance the risk management approaches. Besides, its implementation indicates that the occupational safety and health management and risk control technology has been established based on a benign cycle involving dynamic feedback and scientific development, which can provide a reliable assurance to the safe operation of coal mines.

Research on Occupational Safety, Health Management and Risk Control Technology in Coal Mines

PubMed Central

Zhou, Lu-jie; Cao, Qing-gui; Yu, Kai; Wang, Lin-lin; Wang, Hai-bin

2018-01-01

This paper studies the occupational safety and health management methods as well as risk control technology associated with the coal mining industry, including daily management of occupational safety and health, identification and assessment of risks, early warning and dynamic monitoring of risks, etc.; also, a B/S mode software (Geting Coal Mine, Jining, Shandong, China), i.e., Coal Mine Occupational Safety and Health Management and Risk Control System, is developed to attain the aforementioned objectives, namely promoting the coal mine occupational safety and health management based on early warning and dynamic monitoring of risks. Furthermore, the practical effectiveness and the associated pattern for applying this software package to coal mining is analyzed. The study indicates that the presently developed coal mine occupational safety and health management and risk control technology and the associated software can support the occupational safety and health management efforts in coal mines in a standardized and effective manner. It can also control the accident risks scientifically and effectively; its effective implementation can further improve the coal mine occupational safety and health management mechanism, and further enhance the risk management approaches. Besides, its implementation indicates that the occupational safety and health management and risk control technology has been established based on a benign cycle involving dynamic feedback and scientific development, which can provide a reliable assurance to the safe operation of coal mines. PMID:29701715

Tracking-Data-Conversion Tool

NASA Technical Reports Server (NTRS)

Flora-Adams, Dana; Makihara, Jeanne; Benenyan, Zabel; Berner, Jeff; Kwok, Andrew

2007-01-01

Object Oriented Data Technology (OODT) is a software framework for creating a Web-based system for exchange of scientific data that are stored in diverse formats on computers at different sites under the management of scientific peers. OODT software consists of a set of cooperating, distributed peer components that provide distributed peer-topeer (P2P) services that enable one peer to search and retrieve data managed by another peer. In effect, computers running OODT software at different locations become parts of an integrated data-management system.

[Prenatal risk calculation: comparison between Fast Screen pre I plus software and ViewPoint software. Evaluation of the risk calculation algorithms].

PubMed

Morin, Jean-François; Botton, Eléonore; Jacquemard, François; Richard-Gireme, Anouk

2013-01-01

The Fetal medicine foundation (FMF) has developed a new algorithm called Prenatal Risk Calculation (PRC) to evaluate Down syndrome screening based on free hCGβ, PAPP-A and nuchal translucency. The peculiarity of this algorithm is to use the degree of extremeness (DoE) instead of the multiple of the median (MoM). The biologists measuring maternal seric markers on Kryptor™ machines (Thermo Fisher Scientific) use Fast Screen pre I plus software for the prenatal risk calculation. This software integrates the PRC algorithm. Our study evaluates the data of 2.092 patient files of which 19 show a fœtal abnormality. These files have been first evaluated with the ViewPoint software based on MoM. The link between DoE and MoM has been analyzed and the different calculated risks compared. The study shows that Fast Screen pre I plus software gives the same risk results as ViewPoint software, but yields significantly fewer false positive results.

Bring NASA Scientific Data into GIS

NASA Astrophysics Data System (ADS)

Xu, H.

2016-12-01

NASA's Earth Observation System (EOS) and many other missions produce data of huge volume and near real time which drives the research and understanding of climate change. Geographic Information System (GIS) is a technology used for the management, visualization and analysis of spatial data. Since it's inception in the 1960s, GIS has been applied to many fields at the city, state, national, and world scales. People continue to use it today to analyze and visualize trends, patterns, and relationships from the massive datasets of scientific data. There is great interest in both the scientific and GIS communities in improving technologies that can bring scientific data into a GIS environment, where scientific research and analysis can be shared through the GIS platform to the public. Most NASA scientific data are delivered in the Hierarchical Data Format (HDF), a format is both flexible and powerful. However, this flexibility results in challenges when trying to develop supported GIS software - data stored with HDF formats lack a unified standard and convention among these products. The presentation introduces an information model that enables ArcGIS software to ingest NASA scientific data and create a multidimensional raster - univariate and multivariate hypercubes - for scientific visualization and analysis. We will present the framework how ArcGIS leverages the open source GDAL (Geospatial Data Abstract Library) to support its raster data access, discuss how we overcame the GDAL drivers limitations in handing scientific products that are stored with HDF4 and HDF5 formats and how we improve the way in modeling the multidimensionality with GDAL. In additional, we will talk about the direction of ArcGIS handling NASA products and demonstrate how the multidimensional information model can help scientists work with various data products such as MODIS, MOPPIT, SMAP as well as many data products in a GIS environment.

Navigating through the minefield of read-across: from research to practical tools (WC10)

EPA Science Inventory

Read-across is used for regulatory purposes as a data gap filling technique. Research efforts have focused on the scientific justification and documentation challenges involved in read-across predictions. Software tools have also been developed to facilitate read-across predictio...

Averting Denver Airports on a Chip

NASA Technical Reports Server (NTRS)

Sullivan, Kevin J.

1995-01-01

As a result of recent advances in software engineering capabilities, we are now in a more stable environment. De-facto hardware and software standards are emerging. Work on software architecture and design patterns signals a consensus on the importance of early system-level design decisions, and agreements on the uses of certain paradigmatic software structures. We now routinely build systems that would have been risky or infeasible a few years ago. Unfortunately, technological developments threaten to destabilize software design again. Systems designed around novel computing and peripheral devices will spark ambitious new projects that will stress current software design and engineering capabilities. Micro-electro-mechanical systems (MEMS) and related technologies provide the physical basis for new systems with the potential to produce this kind of destabilizing effect. One important response to anticipated software engineering and design difficulties is carefully directed engineering-scientific research. Two specific problems meriting substantial research attention are: A lack of sufficient means to build software systems by generating, extending, specializing, and integrating large-scale reusable components; and a lack of adequate computational and analytic tools to extend and aid engineers in maintaining intellectual control over complex software designs.

The ImageJ ecosystem: an open platform for biomedical image analysis

PubMed Central

Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W.

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available – from commercial to academic, special-purpose to Swiss army knife, small to large–but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts life science, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. PMID:26153368

The ImageJ ecosystem: An open platform for biomedical image analysis.

PubMed

Schindelin, Johannes; Rueden, Curtis T; Hiner, Mark C; Eliceiri, Kevin W

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. © 2015 Wiley Periodicals, Inc.

Supporting Weather Data

NASA Technical Reports Server (NTRS)

2004-01-01

Since its founding in 1992, Global Science & Technology, Inc. (GST), of Greenbelt, Maryland, has been developing technologies and providing services in support of NASA scientific research. GST specialties include scientific analysis, science data and information systems, data visualization, communications, networking and Web technologies, computer science, and software system engineering. As a longtime contractor to Goddard Space Flight Center s Earth Science Directorate, GST scientific, engineering, and information technology staff have extensive qualifications with the synthesis of satellite, in situ, and Earth science data for weather- and climate-related projects. GST s experience in this arena is end-to-end, from building satellite ground receiving systems and science data systems, to product generation and research and analysis.

Resurrecting Legacy Code Using Ontosoft Knowledge-Sharing and Digital Object Management to Revitalize and Reproduce Software for Groundwater Management Research

NASA Astrophysics Data System (ADS)

Kwon, N.; Gentle, J.; Pierce, S. A.

2015-12-01

Software code developed for research is often used for a relatively short period of time before it is abandoned, lost, or becomes outdated. This unintentional abandonment of code is a valid problem in the 21st century scientific process, hindering widespread reusability and increasing the effort needed to develop research software. Potentially important assets, these legacy codes may be resurrected and documented digitally for long-term reuse, often with modest effort. Furthermore, the revived code may be openly accessible in a public repository for researchers to reuse or improve. For this study, the research team has begun to revive the codebase for Groundwater Decision Support System (GWDSS), originally developed for participatory decision making to aid urban planning and groundwater management, though it may serve multiple use cases beyond those originally envisioned. GWDSS was designed as a java-based wrapper with loosely federated commercial and open source components. If successfully revitalized, GWDSS will be useful for both practical applications as a teaching tool and case study for groundwater management, as well as informing theoretical research. Using the knowledge-sharing approaches documented by the NSF-funded Ontosoft project, digital documentation of GWDSS is underway, from conception to development, deployment, characterization, integration, composition, and dissemination through open source communities and geosciences modeling frameworks. Information assets, documentation, and examples are shared using open platforms for data sharing and assigned digital object identifiers. Two instances of GWDSS version 3.0 are being created: 1) a virtual machine instance for the original case study to serve as a live demonstration of the decision support tool, assuring the original version is usable, and 2) an open version of the codebase, executable installation files, and developer guide available via an open repository, assuring the source for the application is accessible with version control and potential for new branch developments. Finally, metadata about the software has been completed within the OntoSoft portal to provide descriptive curation, make GWDSS searchable, and complete documentation of the scientific software lifecycle.

USGS Scientific Visualization Laboratory

USGS Publications Warehouse

,

1995-01-01

The U.S. Geological Survey's (USGS) Scientific Visualization Laboratory at the National Center in Reston, Va., provides a central facility where USGS employees can use state-of-the-art equipment for projects ranging from presentation graphics preparation to complex visual representations of scientific data. Equipment including color printers, black-and-white and color scanners, film recorders, video equipment, and DOS, Apple Macintosh, and UNIX platforms with software are available for both technical and nontechnical users. The laboratory staff provides assistance and demonstrations in the use of the hardware and software products.

Tectonic Storytelling with Open Source and Digital Object Identifiers - a case study about Plate Tectonics and the Geopark Bergstraße-Odenwald

NASA Astrophysics Data System (ADS)

Löwe, Peter; Barmuta, Jan; Klump, Jens; Neumann, Janna; Plank, Margret

2014-05-01

The communication of advances in research to the common public for both education and decision making is an important aspect of scientific work. An even more crucial task is to gain recognition within the scientific community, which is judged by impact factor and citation counts. Recently, the latter concepts have been extended from textual publications to include data and software publications. This paper presents a case study for science communication and data citation. For this, tectonic models, Free and Open Source Software (FOSS), best practices for data citation and a multimedia online-portal for scientific content are combined. This approach creates mutual benefits for the stakeholders: Target audiences receive information on the latest research results, while the use of Digital Object Identifiers (DOI) increases the recognition and citation of underlying scientific data. This creates favourable conditions for every researcher as DOI names ensure citeability and long term availability of scientific research. In the developed application, the FOSS tool for tectonic modelling GPlates is used to visualise and manipulate plate-tectonic reconstructions and associated data through geological time. These capabilities are augmented by the Science on a Halfsphere project (SoaH) with a robust and intuitive visualisation hardware environment. The tectonic models used for science communication are provided by the AGH University of Science and Technology. They focus on the Silurian to Early Carboniferous evolution of Central Europe (Bohemian Massif) and were interpreted for the area of the Geopark Bergstraße Odenwald based on the GPlates/SoaH hardware- and software stack. As scientific story-telling is volatile by nature, recordings are a natural means of preservation for further use, reference and analysis. For this, the upcoming portal for audiovisual media of the German National Library of Science and Technology TIB is expected to become a critical service infrastructure. It allows complex search queries, including metadata such as DOI and media fragment identifiers (MFI), thereby linking data citation and science communication.

The role of open-source software in innovation and standardization in radiology.

PubMed

Erickson, Bradley J; Langer, Steve; Nagy, Paul

2005-11-01

The use of open-source software (OSS), in which developers release the source code to applications they have developed, is popular in the software industry. This is done to allow others to modify and improve software (which may or may not be shared back to the community) and to allow others to learn from the software. Radiology was an early participant in this model, supporting OSS that implemented the ACR-National Electrical Manufacturers Association (now Digital Imaging and Communications in Medicine) standard for medical image communications. In radiology and in other fields, OSS has promoted innovation and the adoption of standards. Popular OSS is of high quality because access to source code allows many people to identify and resolve errors. Open-source software is analogous to the peer-review scientific process: one must be able to see and reproduce results to understand and promote what is shared. The authors emphasize that support for OSS need not threaten vendors; most vendors embrace and benefit from standards. Open-source development does not replace vendors but more clearly defines their roles, typically focusing on areas in which proprietary differentiators benefit customers and on professional services such as implementation planning and service. Continued support for OSS is essential for the success of our field.

An interfaces approach to TES ground data system processing design with the Science Investigator-led Processing System (SIPS)

NASA Technical Reports Server (NTRS)

Kurian, R.; Grifin, A.

2002-01-01

Developing production-quality software to process the large volumes of scientific data is the responsibility of the TES Ground Data System, which is being developed at the Jet Propulsion Laboratory together with support contractor Raytheon/ITSS. The large data volume and processing requirements of the TES pose significant challenges to the design.

Big Software for SmallSats: Adapting cFS to CubeSat Missions

NASA Technical Reports Server (NTRS)

Cudmore, Alan P.; Crum, Gary Alex; Sheikh, Salman; Marshall, James

2015-01-01

Expanding capabilities and mission objectives for SmallSats and CubeSats is driving the need for reliable, reusable, and robust flight software. While missions are becoming more complicated and the scientific goals more ambitious, the level of acceptable risk has decreased. Design challenges are further compounded by budget and schedule constraints that have not kept pace. NASA's Core Flight Software System (cFS) is an open source solution which enables teams to build flagship satellite level flight software within a CubeSat schedule and budget. NASA originally developed cFS to reduce mission and schedule risk for flagship satellite missions by increasing code reuse and reliability. The Lunar Reconnaissance Orbiter, which launched in 2009, was the first of a growing list of Class B rated missions to use cFS.

[Stressor and stress reduction strategies for computer software engineers].

PubMed

Asakura, Takashi

2002-07-01

First, in this article we discuss 10 significant occupational stressors for computer software engineers, based on the review of the scientific literature on their stress and mental health. The stressors include 1) quantitative work overload, 2) time pressure, 3) qualitative work load, 4) speed and diffusion of technological innovation, and technological divergence, 5) low discretional power, 6) underdeveloped career pattern, 7) low earnings/reward from jobs, 8) difficulties in managing a project team for software development and establishing support system, 9) difficulties in customer relations, and 10) personality characteristics. In addition, we delineate their working and organizational conditions that cause such occupational stressors in order to find strategies to reduce those stressors in their workplaces. Finally, we suggest three stressor and stress reduction strategies for software engineers.

Student’s Entrepreneur Model Development in Creative Industry through Utilization of Web Development Software and Educational Game

NASA Astrophysics Data System (ADS)

Hasan, B.; Hasbullah, H.; Elvyanti, S.; Purnama, W.

2018-02-01

The creative industry is the utilization of creativity, skill and talent of individuals to create wealth and jobs by generating and exploiting creativity power of individual. In the field of design, utilization of information technology can spur creative industry, development of creative industry design will accommodate a lot of creative energy that can pour their ideas and creativity without limitations. Open Source software is a trend in the field of information technology has developed since the 1990s. Examples of applications developed by the Open Source approach is the Apache web services, Linux and Android Operating System, the MySQL database. This community service activities based entrepreneurship aims to: 1). give an idea about the profile of the UPI student’s knowledge of entrepreneurship about the business based creative industries in software by using web software development and educational game 2) create a model for fostering entrepreneurship based on the creative industries in software by leveraging web development and educational games, 3) conduct training and guidance on UPI students who want to develop business in the field of creative industries engaged in the software industry . PKM-based entrepreneurship activity was attended by about 35 students DPTE FPTK UPI had entrepreneurial high interest and competence in information technology. Outcome generated from PKM entrepreneurship is the emergence of entrepreneurs from the students who are interested in the creative industry in the field of software which is able to open up business opportunities for themselves and others. Another outcome of this entrepreneurship PKM activity is the publication of articles or scientific publications in journals of national/international indexed.

CernVM WebAPI - Controlling Virtual Machines from the Web

NASA Astrophysics Data System (ADS)

Charalampidis, I.; Berzano, D.; Blomer, J.; Buncic, P.; Ganis, G.; Meusel, R.; Segal, B.

2015-12-01

Lately, there is a trend in scientific projects to look for computing resources in the volunteering community. In addition, to reduce the development effort required to port the scientific software stack to all the known platforms, the use of Virtual Machines (VMs)u is becoming increasingly popular. Unfortunately their use further complicates the software installation and operation, restricting the volunteer audience to sufficiently expert people. CernVM WebAPI is a software solution addressing this specific case in a way that opens wide new application opportunities. It offers a very simple API for setting-up, controlling and interfacing with a VM instance in the users computer, while in the same time offloading the user from all the burden of downloading, installing and configuring the hypervisor. WebAPI comes with a lightweight javascript library that guides the user through the application installation process. Malicious usage is prohibited by offering a per-domain PKI validation mechanism. In this contribution we will overview this new technology, discuss its security features and examine some test cases where it is already in use.

Current And Future Directions Of Lens Design Software

NASA Astrophysics Data System (ADS)

Gustafson, Darryl E.

1983-10-01

The most effective environment for doing lens design continues to evolve as new computer hardware and software tools become available. Important recent hardware developments include: Low-cost but powerful interactive multi-user 32 bit computers with virtual memory that are totally software-compatible with prior larger and more expensive members of the family. A rapidly growing variety of graphics devices for both hard-copy and screen graphics, including many with color capability. In addition, with optical design software readily accessible in many forms, optical design has become a part-time activity for a large number of engineers instead of being restricted to a small number of full-time specialists. A designer interface that is friendly for the part-time user while remaining efficient for the full-time designer is thus becoming more important as well as more practical. Along with these developments, software tools in other scientific and engineering disciplines are proliferating. Thus, the optical designer is less and less unique in his use of computer-aided techniques and faces the challenge and opportunity of efficiently communicating his designs to other computer-aided-design (CAD), computer-aided-manufacturing (CAM), structural, thermal, and mechanical software tools. This paper will address the impact of these developments on the current and future directions of the CODE VTM optical design software package, its implementation, and the resulting lens design environment.

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C.; Baru, C.

2012-12-01

The NSF-funded OpenTopography facility provides online access to Earth science-oriented high-resolution LIDAR topography data, online processing tools, and derivative products. The underlying cyberinfrastructure employs a multi-tier service oriented architecture that is comprised of an infrastructure tier, a processing services tier, and an application tier. The infrastructure tier consists of storage, compute resources as well as supporting databases. The services tier consists of the set of processing routines each deployed as a Web service. The applications tier provides client interfaces to the system. (e.g. Portal). We propose a "pluggable" infrastructure design that will allow new scientific algorithms and processing routines developed and maintained by the community to be integrated into the OpenTopography system so that the wider earth science community can benefit from its availability. All core components in OpenTopography are available as Web services using a customized open-source Opal toolkit. The Opal toolkit provides mechanisms to manage and track job submissions, with the help of a back-end database. It allows monitoring of job and system status by providing charting tools. All core components in OpenTopography have been developed, maintained and wrapped as Web services using Opal by OpenTopography developers. However, as the scientific community develops new processing and analysis approaches this integration approach is not scalable efficiently. Most of the new scientific applications will have their own active development teams performing regular updates, maintenance and other improvements. It would be optimal to have the application co-located where its developers can continue to actively work on it while still making it accessible within the OpenTopography workflow for processing capabilities. We will utilize a software framework for remote integration of these scientific applications into the OpenTopography system. This will be accomplished by virtually extending the OpenTopography service over the various infrastructures running these scientific applications and processing routines. This involves packaging and distributing a customized instance of the Opal toolkit that will wrap the software application as an OPAL-based web service and integrate it into the OpenTopography framework. We plan to make this as automated as possible. A structured specification of service inputs and outputs along with metadata annotations encoded in XML can be utilized to automate the generation of user interfaces, with appropriate tools tips and user help features, and generation of other internal software. The OpenTopography Opal toolkit will also include the customizations that will enable security authentication, authorization and the ability to write application usage and job statistics back to the OpenTopography databases. This usage information could then be reported to the original service providers and used for auditing and performance improvements. This pluggable framework will enable the application developers to continue to work on enhancing their application while making the latest iteration available in a timely manner to the earth sciences community. This will also help us establish an overall framework that other scientific application providers will also be able to use going forward.

Journal of Open Source Software (JOSS): design and first-year review

NASA Astrophysics Data System (ADS)

Smith, Arfon M.

2018-01-01

JOSS is a free and open-access journal that publishes articles describing research software across all disciplines. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. JOSS published more than 100 articles in its first year, many from the scientific python ecosystem (including a number of articles related to astronomy and astrophysics). JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative.In this presentation, I'll describes the motivation, design, and progress of the Journal of Open Source Software (JOSS) and how it compares to other avenues for publishing research software in astronomy.

Decision Analysis Tools for Volcano Observatories

NASA Astrophysics Data System (ADS)

Hincks, T. H.; Aspinall, W.; Woo, G.

2005-12-01

Staff at volcano observatories are predominantly engaged in scientific activities related to volcano monitoring and instrumentation, data acquisition and analysis. Accordingly, the academic education and professional training of observatory staff tend to focus on these scientific functions. From time to time, however, staff may be called upon to provide decision support to government officials responsible for civil protection. Recognizing that Earth scientists may have limited technical familiarity with formal decision analysis methods, specialist software tools that assist decision support in a crisis should be welcome. A review is given of two software tools that have been under development recently. The first is for probabilistic risk assessment of human and economic loss from volcanic eruptions, and is of practical use in short and medium-term risk-informed planning of exclusion zones, post-disaster response, etc. A multiple branch event-tree architecture for the software, together with a formalism for ascribing probabilities to branches, have been developed within the context of the European Community EXPLORIS project. The second software tool utilizes the principles of the Bayesian Belief Network (BBN) for evidence-based assessment of volcanic state and probabilistic threat evaluation. This is of practical application in short-term volcano hazard forecasting and real-time crisis management, including the difficult challenge of deciding when an eruption is over. An open-source BBN library is the software foundation for this tool, which is capable of combining synoptically different strands of observational data from diverse monitoring sources. A conceptual vision is presented of the practical deployment of these decision analysis tools in a future volcano observatory environment. Summary retrospective analyses are given of previous volcanic crises to illustrate the hazard and risk insights gained from use of these tools.

Evaluation of Visualization Software

NASA Technical Reports Server (NTRS)

Globus, Al; Uselton, Sam

1995-01-01

Visualization software is widely used in scientific and engineering research. But computed visualizations can be very misleading, and the errors are easy to miss. We feel that the software producing the visualizations must be thoroughly evaluated and the evaluation process as well as the results must be made available. Testing and evaluation of visualization software is not a trivial problem. Several methods used in testing other software are helpful, but these methods are (apparently) often not used. When they are used, the description and results are generally not available to the end user. Additional evaluation methods specific to visualization must also be developed. We present several useful approaches to evaluation, ranging from numerical analysis of mathematical portions of algorithms to measurement of human performance while using visualization systems. Along with this brief survey, we present arguments for the importance of evaluations and discussions of appropriate use of some methods.

Evaluating Predictive Models of Software Quality

NASA Astrophysics Data System (ADS)

Ciaschini, V.; Canaparo, M.; Ronchieri, E.; Salomoni, D.

2014-06-01

Applications from High Energy Physics scientific community are constantly growing and implemented by a large number of developers. This implies a strong churn on the code and an associated risk of faults, which is unavoidable as long as the software undergoes active evolution. However, the necessities of production systems run counter to this. Stability and predictability are of paramount importance; in addition, a short turn-around time for the defect discovery-correction-deployment cycle is required. A way to reconcile these opposite foci is to use a software quality model to obtain an approximation of the risk before releasing a program to only deliver software with a risk lower than an agreed threshold. In this article we evaluated two quality predictive models to identify the operational risk and the quality of some software products. We applied these models to the development history of several EMI packages with intent to discover the risk factor of each product and compare it with its real history. We attempted to determine if the models reasonably maps reality for the applications under evaluation, and finally we concluded suggesting directions for further studies.

Parallel computing works

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

Not Available

An account of the Caltech Concurrent Computation Program (C{sup 3}P), a five year project that focused on answering the question: Can parallel computers be used to do large-scale scientific computations '' As the title indicates, the question is answered in the affirmative, by implementing numerous scientific applications on real parallel computers and doing computations that produced new scientific results. In the process of doing so, C{sup 3}P helped design and build several new computers, designed and implemented basic system software, developed algorithms for frequently used mathematical computations on massively parallel machines, devised performance models and measured the performance of manymore » computers, and created a high performance computing facility based exclusively on parallel computers. While the initial focus of C{sup 3}P was the hypercube architecture developed by C. Seitz, many of the methods developed and lessons learned have been applied successfully on other massively parallel architectures.« less

An Active, Collaborative Approach to Learning Skills in Flow Cytometry

ERIC Educational Resources Information Center

Fuller, Kathryn; Linden, Matthew D.; Lee-Pullen, Tracey; Fragall, Clayton; Erber, Wendy N.; Röhrig, Kimberley J.

2016-01-01

Advances in science education research have the potential to improve the way students learn to perform scientific interpretations and understand science concepts. We developed active, collaborative activities to teach skills in manipulating flow cytometry data using FlowJo software. Undergraduate students were given compensated clinical flow…

Prioritizing Scientific Data for Transmission

NASA Technical Reports Server (NTRS)

Castano, Rebecca; Anderson, Robert; Estlin, Tara; DeCoste, Dennis; Gaines, Daniel; Mazzoni, Dominic; Fisher, Forest; Judd, Michele

2004-01-01

A software system has been developed for prioritizing newly acquired geological data onboard a planetary rover. The system has been designed to enable efficient use of limited communication resources by transmitting the data likely to have the most scientific value. This software operates onboard a rover by analyzing collected data, identifying potential scientific targets, and then using that information to prioritize data for transmission to Earth. Currently, the system is focused on the analysis of acquired images, although the general techniques are applicable to a wide range of data modalities. Image prioritization is performed using two main steps. In the first step, the software detects features of interest from each image. In its current application, the system is focused on visual properties of rocks. Thus, rocks are located in each image and rock properties, such as shape, texture, and albedo, are extracted from the identified rocks. In the second step, the features extracted from a group of images are used to prioritize the images using three different methods: (1) identification of key target signature (finding specific rock features the scientist has identified as important), (2) novelty detection (finding rocks we haven t seen before), and (3) representative rock sampling (finding the most average sample of each rock type). These methods use techniques such as K-means unsupervised clustering and a discrimination-based kernel classifier to rank images based on their interest level.

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

Wahanani, Nursinta Adi, E-mail: sintaadi@batan.go.id; Natsir, Khairina, E-mail: sintaadi@batan.go.id; Hartini, Entin, E-mail: sintaadi@batan.go.id

Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this softwaremore » 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.« less

Defining Geodetic Reference Frame using Matlab®: PlatEMotion 2.0

NASA Astrophysics Data System (ADS)

Cannavò, Flavio; Palano, Mimmo

2016-03-01

We describe the main features of the developed software tool, namely PlatE-Motion 2.0 (PEM2), which allows inferring the Euler pole parameters by inverting the observed velocities at a set of sites located on a rigid block (inverse problem). PEM2 allows also calculating the expected velocity value for any point located on the Earth providing an Euler pole (direct problem). PEM2 is the updated version of a previous software tool initially developed for easy-to-use file exchange with the GAMIT/GLOBK software package. The software tool is developed in Matlab® framework and, as the previous version, includes a set of MATLAB functions (m-files), GUIs (fig-files), map data files (mat-files) and user's manual as well as some example input files. New changes in PEM2 include (1) some bugs fixed, (2) improvements in the code, (3) improvements in statistical analysis, (4) new input/output file formats. In addition, PEM2 can be now run under the majority of operating systems. The tool is open source and freely available for the scientific community.

Development of the Software for 30 inch Telescope Control System at KHAO

NASA Astrophysics Data System (ADS)

Mun, B.-S.; Kim, S.-J.; Jang, M.; Min, S.-W.; Seol, K.-H.; Moon, K.-S.

2006-12-01

Even though 30inch optical telescope at Kyung Hee Astronomy Observatory has been used to produce a series of scientific achievements since its first light in 1992, numerous difficulties in the operation of the telescope have hindered the precise observations needed for further researches. Since the currently used PC-TCS (Personal Computer based Telescope Control system) software based on ISA-bus type is outdated, it doesn't have a user friendly interface and make it impossible to scale. Also accumulated errors which are generated by discordance from input and output signals into a motion controller required new control system. Thus we have improved the telescope control system by updating software and modifying mechanical parts. We applied a new BLDC (brushless DC) servo motor system to the mechanical parts of the telescope and developed a control software using Visual Basic 6.0. As a result, we could achieve a high accuracy in controlling of the telescope and use the userfriendly GUI (Graphic User Interface).

Automated Software Acceleration in Programmable Logic for an Efficient NFFT Algorithm Implementation: A Case Study.

PubMed

Rodríguez, Manuel; Magdaleno, Eduardo; Pérez, Fernando; García, Cristhian

2017-03-28

Non-equispaced Fast Fourier transform (NFFT) is a very important algorithm in several technological and scientific areas such as synthetic aperture radar, computational photography, medical imaging, telecommunications, seismic analysis and so on. However, its computation complexity is high. In this paper, we describe an efficient NFFT implementation with a hardware coprocessor using an All-Programmable System-on-Chip (APSoC). This is a hybrid device that employs an Advanced RISC Machine (ARM) as Processing System with Programmable Logic for high-performance digital signal processing through parallelism and pipeline techniques. The algorithm has been coded in C language with pragma directives to optimize the architecture of the system. We have used the very novel Software Develop System-on-Chip (SDSoC) evelopment tool that simplifies the interface and partitioning between hardware and software. This provides shorter development cycles and iterative improvements by exploring several architectures of the global system. The computational results shows that hardware acceleration significantly outperformed the software based implementation.

Automated Software Acceleration in Programmable Logic for an Efficient NFFT Algorithm Implementation: A Case Study

PubMed Central

Rodríguez, Manuel; Magdaleno, Eduardo; Pérez, Fernando; García, Cristhian

2017-01-01

Non-equispaced Fast Fourier transform (NFFT) is a very important algorithm in several technological and scientific areas such as synthetic aperture radar, computational photography, medical imaging, telecommunications, seismic analysis and so on. However, its computation complexity is high. In this paper, we describe an efficient NFFT implementation with a hardware coprocessor using an All-Programmable System-on-Chip (APSoC). This is a hybrid device that employs an Advanced RISC Machine (ARM) as Processing System with Programmable Logic for high-performance digital signal processing through parallelism and pipeline techniques. The algorithm has been coded in C language with pragma directives to optimize the architecture of the system. We have used the very novel Software Develop System-on-Chip (SDSoC) evelopment tool that simplifies the interface and partitioning between hardware and software. This provides shorter development cycles and iterative improvements by exploring several architectures of the global system. The computational results shows that hardware acceleration significantly outperformed the software based implementation. PMID:28350358

The Software Correlator of the Chinese VLBI Network

NASA Technical Reports Server (NTRS)

Zheng, Weimin; Quan, Ying; Shu, Fengchun; Chen, Zhong; Chen, Shanshan; Wang, Weihua; Wang, Guangli

2010-01-01

The software correlator of the Chinese VLBI Network (CVN) has played an irreplaceable role in the CVN routine data processing, e.g., in the Chinese lunar exploration project. This correlator will be upgraded to process geodetic and astronomical observation data. In the future, with several new stations joining the network, CVN will carry out crustal movement observations, quick UT1 measurements, astrophysical observations, and deep space exploration activities. For the geodetic or astronomical observations, we need a wide-band 10-station correlator. For spacecraft tracking, a realtime and highly reliable correlator is essential. To meet the scientific and navigation requirements of CVN, two parallel software correlators in the multiprocessor environments are under development. A high speed, 10-station prototype correlator using the mixed Pthreads and MPI (Massage Passing Interface) parallel algorithm on a computer cluster platform is being developed. Another real-time software correlator for spacecraft tracking adopts the thread-parallel technology, and it runs on the SMP (Symmetric Multiple Processor) servers. Both correlators have the characteristic of flexible structure and scalability.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

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

Tsai, Yingssu; Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080; McPhillips, Scott E.

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data,more » performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.« less

Developing a user-friendly photometric software for exoplanets to increase participation in Citizen Science

NASA Astrophysics Data System (ADS)

Kokori, A.; Tsiaras, A.

2017-09-01

Previous research on Citizen Science projects agree that Citizen Science (CS) would serve as a way of both increasing levels of public understanding of science and public participation in scientific research. Historically, the concept of CS is not new, it dates back to the 20th century when citizens where making skilled observations, particularly in archaeology, ecology, and astronomy. Recently, the idea of CS has been improved due to technological progress and the arrival of Internet. The phrase "astronomy from the chair" that is being used in the literature highlights the extent of the convenience for analysing observational data. Citizen science benefits a variety of communities, such as scientific researchers, volunteers and STEM educators. Participating in CS projects is not only engaging the volunteers with the research goals of a science team, but is also helping them learning more about specialised scientific topics. In the case of astronomy, typical examples of CS projects are gathering observational data or/and analysing them. The Holomon Photometric Software (HOPS) is a user-friendly photometric software for exoplanets, with graphical representations, statistics, models, options are brought together into a single package. It was originally developed to analyse observations of transiting exoplanets obtained from the Holomon Astronomical Station of the Aristotle University of Thessaloniki. Here, we make the case that this software can be used as part of a CS project in analysing transiting exoplanets and producing light-curves. HOPS could contribute to the scientific data analysis but it could be used also as an educational tool for learning and visualizing photometry analyses of transiting exoplanets. Such a tool could be proven very efficient in the context of public participation in the research. In recent successful representative examples such as Galaxy Zoo professional astronomers cooperating with CS discovered a group of rare galaxies by using online software. Also the project "planet hunters" asked people to discover planets in other solar systems using data from large telescopes. HOPS, being in the same direction, could be an effective way of participating in research whether as an amateur astronomer or as a person of the general public that wants to engage with exoplanetary research and data analysis. The software is free of charge under the scope of astronomical research and education. We plan to create an online platform, inspired by HOPS, in the near future. In this platform, everyone will have access by creating an account as a user. Amateur astronomers, who have obtained their own exoplanet observations, will be able to upload and analyse their data. For people who are not familiar with photometric analysis - amateurs or general public users - data, as well as educational video and audio material will be provided.

U.S. Geological Survey Groundwater Modeling Software: Making Sense of a Complex Natural Resource

USGS Publications Warehouse

Provost, Alden M.; Reilly, Thomas E.; Harbaugh, Arlen W.; Pollock, David W.

2009-01-01

Computer models of groundwater systems simulate the flow of groundwater, including water levels, and the transport of chemical constituents and thermal energy. Groundwater models afford hydrologists a framework on which to organize their knowledge and understanding of groundwater systems, and they provide insights water-resources managers need to plan effectively for future water demands. Building on decades of experience, the U.S. Geological Survey (USGS) continues to lead in the development and application of computer software that allows groundwater models to address scientific and management questions of increasing complexity.

Courseware Review.

ERIC Educational Resources Information Center

Risley, John, Ed.

1988-01-01

Compares the features of the sonic rangers available from HRM Software, MICROMEASUREMENTS, NAGAWTIS Software Research, and PASCO Scientific for demonstrations and experiments in mechanics. Presents the advantages of the sonic rangers and the typical graphics displayed by each software package. (YP)

RSEIS and RFOC: Seismic Analysis in R

NASA Astrophysics Data System (ADS)

Lees, J. M.

2015-12-01

Open software is essential for reproducible scientific exchange. R-packages provide a platform for development of seismological investigation software that can be properly documented and traced for data processing. A suite of R packages designed for a wide range of seismic analysis is currently available in the free software platform called R. R is a software platform based on the S-language developed at Bell Labs decades ago. Routines in R can be run as standalone function calls, or developed in object-oriented mode. R comes with a base set of routines, and thousands of user developed packages. The packages developed at UNC include subroutines and interactive codes for processing seismic data, analyzing geographic information (GIS) and inverting data involved in a variety of geophysical applications. On CRAN (Comprehensive R Archive Network, http://www.r-project.org/) currently available packages related to seismic analysis are RSEIS, Rquake, GEOmap, RFOC, zoeppritz, RTOMO, and geophys, Rwave, PEIP, hht, rFDSN. These include signal processing, data management, mapping, earthquake location, deconvolution, focal mechanisms, wavelet transforms, Hilbert-Huang Transforms, tomographic inversion, and Mogi deformation among other useful functionality. All software in R packages is required to have detailed documentation, making the exchange and modification of existing software easy. In this presentation, I will focus on packages RSEIS and RFOC, showing examples from a variety of seismic analyses. The R approach has similarities to the popular (and expensive) MATLAB platform, although R is open source and free to down load.

Ten recommendations for software engineering in research.

PubMed

Hastings, Janna; Haug, Kenneth; Steinbeck, Christoph

2014-01-01

Research in the context of data-driven science requires a backbone of well-written software, but scientific researchers are typically not trained at length in software engineering, the principles for creating better software products. To address this gap, in particular for young researchers new to programming, we give ten recommendations to ensure the usability, sustainability and practicality of research software.

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

NASA Astrophysics Data System (ADS)

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

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

Lessons Learned From Developing A Streaming Data Framework for Scientific Analysis

NASA Technical Reports Server (NTRS)

Wheeler. Kevin R.; Allan, Mark; Curry, Charles

2003-01-01

We describe the development and usage of a streaming data analysis software framework. The framework is used for three different applications: Earth science hyper-spectral imaging analysis, Electromyograph pattern detection, and Electroencephalogram state determination. In each application the framework was used to answer a series of science questions which evolved with each subsequent answer. This evolution is summarized in the form of lessons learned.

Robotic Mission to Mars: Hands-on, minds-on, web-based learning

NASA Astrophysics Data System (ADS)

Mathers, Naomi; Goktogen, Ali; Rankin, John; Anderson, Marion

2012-11-01

Problem-based learning has been demonstrated as an effective methodology for developing analytical skills and critical thinking. The use of scenario-based learning incorporates problem-based learning whilst encouraging students to collaborate with their colleagues and dynamically adapt to their environment. This increased interaction stimulates a deeper understanding and the generation of new knowledge. The Victorian Space Science Education Centre (VSSEC) uses scenario-based learning in its Mission to Mars, Mission to the Orbiting Space Laboratory and Primary Expedition to the M.A.R.S. Base programs. These programs utilize methodologies such as hands-on applications, immersive-learning, integrated technologies, critical thinking and mentoring to engage students in Science, Technology, Engineering and Mathematics (STEM) and highlight potential career paths in science and engineering. The immersive nature of the programs demands specialist environments such as a simulated Mars environment, Mission Control and Space Laboratory, thus restricting these programs to a physical location and limiting student access to the programs. To move beyond these limitations, VSSEC worked with its university partners to develop a web-based mission that delivered the benefits of scenario-based learning within a school environment. The Robotic Mission to Mars allows students to remotely control a real rover, developed by the Australian Centre for Field Robotics (ACFR), on the VSSEC Mars surface. After completing a pre-mission training program and site selection activity, students take on the roles of scientists and engineers in Mission Control to complete a mission and collect data for further analysis. Mission Control is established using software developed by the ACRI Games Technology Lab at La Trobe University using the principles of serious gaming. The software allows students to control the rover, monitor its systems and collect scientific data for analysis. This program encourages students to work scientifically and explores the interaction between scientists and engineers. This paper presents the development of the program, including the involvement of university students in the development of the rover, the software, and the collation of the scientific data. It also presents the results of the trial phase of this program including the impact on student engagement and learning outcomes.

Transportable educational programs for scientific and technical professionals: More effective utilization of automated scientific and technical data base systems

NASA Technical Reports Server (NTRS)

Dominick, Wayne D.

1987-01-01

This grant final report executive summary documents a major, long-term program addressing innovative educational issues associated with the development, administration, evaluation, and widespread distribution of transportable educational programs for scientists and engineers to increase their knowledge of, and facilitate their utilization of automated scientific and technical information storage and retrieval systems. This educational program is of very broad scope, being targeted at Colleges of Engineering and Colleges of Physical sciences at a large number of colleges and universities throughout the United States. The educational program is designed to incorporate extensive hands-on, interactive usage of the NASA RECON system and is supported by a number of microcomputer-based software systems to facilitate the delivery and usage of the educational course materials developed as part of the program.

Use of a secure Internet Web site for collaborative medical research.

PubMed

Marshall, W W; Haley, R W

2000-10-11

Researchers who collaborate on clinical research studies from diffuse locations need a convenient, inexpensive, secure way to record and manage data. The Internet, with its World Wide Web, provides a vast network that enables researchers with diverse types of computers and operating systems anywhere in the world to log data through a common interface. Development of a Web site for scientific data collection can be organized into 10 steps, including planning the scientific database, choosing a database management software system, setting up database tables for each collaborator's variables, developing the Web site's screen layout, choosing a middleware software system to tie the database software to the Web site interface, embedding data editing and calculation routines, setting up the database on the central server computer, obtaining a unique Internet address and name for the Web site, applying security measures to the site, and training staff who enter data. Ensuring the security of an Internet database requires limiting the number of people who have access to the server, setting up the server on a stand-alone computer, requiring user-name and password authentication for server and Web site access, installing a firewall computer to prevent break-ins and block bogus information from reaching the server, verifying the identity of the server and client computers with certification from a certificate authority, encrypting information sent between server and client computers to avoid eavesdropping, establishing audit trails to record all accesses into the Web site, and educating Web site users about security techniques. When these measures are carefully undertaken, in our experience, information for scientific studies can be collected and maintained on Internet databases more efficiently and securely than through conventional systems of paper records protected by filing cabinets and locked doors. JAMA. 2000;284:1843-1849.

Applying AN Object-Oriented Database Model to a Scientific Database Problem: Managing Experimental Data at Cebaf.

NASA Astrophysics Data System (ADS)

Ehlmann, Bryon K.

Current scientific experiments are often characterized by massive amounts of very complex data and the need for complex data analysis software. Object-oriented database (OODB) systems have the potential of improving the description of the structure and semantics of this data and of integrating the analysis software with the data. This dissertation results from research to enhance OODB functionality and methodology to support scientific databases (SDBs) and, more specifically, to support a nuclear physics experiments database for the Continuous Electron Beam Accelerator Facility (CEBAF). This research to date has identified a number of problems related to the practical application of OODB technology to the conceptual design of the CEBAF experiments database and other SDBs: the lack of a generally accepted OODB design methodology, the lack of a standard OODB model, the lack of a clear conceptual level in existing OODB models, and the limited support in existing OODB systems for many common object relationships inherent in SDBs. To address these problems, the dissertation describes an Object-Relationship Diagram (ORD) and an Object-oriented Database Definition Language (ODDL) that provide tools that allow SDB design and development to proceed systematically and independently of existing OODB systems. These tools define multi-level, conceptual data models for SDB design, which incorporate a simple notation for describing common types of relationships that occur in SDBs. ODDL allows these relationships and other desirable SDB capabilities to be supported by an extended OODB system. A conceptual model of the CEBAF experiments database is presented in terms of ORDs and the ODDL to demonstrate their functionality and use and provide a foundation for future development of experimental nuclear physics software using an OODB approach.

Student project of optical system analysis API-library development

NASA Astrophysics Data System (ADS)

Ivanova, Tatiana; Zhukova, Tatiana; Dantcaranov, Ruslan; Romanova, Maria; Zhadin, Alexander; Ivanov, Vyacheslav; Kalinkina, Olga

2017-08-01

In the paper API-library software developed by students of Applied and Computer Optics Department (ITMO University) for optical system design is presented. The library performs paraxial and real ray tracing, calculates 3d order (Seidel) aberration and real ray aberration of axis and non-axis beams (wave, lateral, longitudinal, coma, distortion etc.) and finally, approximate wave aberration by Zernike polynomials. Real aperture can be calculated by considering of real rays tracing failure on each surface. So far we assume optical system is centered, with spherical or 2d order aspherical surfaces. Optical glasses can be set directly by refraction index or by dispersion coefficients. The library can be used for education or research purposes in optical system design area. It provides ready to use software functions for optical system simulation and analysis that developer can simply plug into their software development for different purposes, for example for some specific synthesis tasks or investigation of new optimization modes. In the paper we present an example of using the library for development of cemented doublet synthesis software based on Slusarev's methodology. The library is used in optical system optimization recipes course for deep studying of optimization model and its application for optical system design. Development of such software is an excellent experience for students and help to understanding optical image modeling and quality analysis. This development is organized as student group joint project. We try to organize it as a group in real research and development project, so each student has his own role in the project and then use whole library functionality in his own master or bachelor thesis. Working in such group gives students useful experience and opportunity to work as research and development engineer of scientific software in the future.

An Overview of the Computational Physics and Methods Group at Los Alamos National Laboratory

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

Baker, Randal Scott

CCS Division was formed to strengthen the visibility and impact of computer science and computational physics research on strategic directions for the Laboratory. Both computer science and computational science are now central to scientific discovery and innovation. They have become indispensable tools for all other scientific missions at the Laboratory. CCS Division forms a bridge between external partners and Laboratory programs, bringing new ideas and technologies to bear on today’s important problems and attracting high-quality technical staff members to the Laboratory. The Computational Physics and Methods Group CCS-2 conducts methods research and develops scientific software aimed at the latest andmore » emerging HPC systems.« less

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

Maintaining Quality and Confidence in Open-Source, Evolving Software: Lessons Learned with PFLOTRAN

NASA Astrophysics Data System (ADS)

Frederick, J. M.; Hammond, G. E.

2017-12-01

Software evolution in an open-source framework poses a major challenge to a geoscientific simulator, but when properly managed, the pay-off can be enormous for both the developers and the community at large. Developers must juggle implementing new scientific process models, adopting increasingly efficient numerical methods and programming paradigms, changing funding sources (or total lack of funding), while also ensuring that legacy code remains functional and reported bugs are fixed in a timely manner. With robust software engineering and a plan for long-term maintenance, a simulator can evolve over time incorporating and leveraging many advances in the computational and domain sciences. In this positive light, what practices in software engineering and code maintenance can be employed within open-source development to maximize the positive aspects of software evolution and community contributions while minimizing its negative side effects? This presentation will discusses steps taken in the development of PFLOTRAN (www.pflotran.org), an open source, massively parallel subsurface simulator for multiphase, multicomponent, and multiscale reactive flow and transport processes in porous media. As PFLOTRAN's user base and development team continues to grow, it has become increasingly important to implement strategies which ensure sustainable software development while maintaining software quality and community confidence. In this presentation, we will share our experiences and "lessons learned" within the context of our open-source development framework and community engagement efforts. Topics discussed will include how we've leveraged both standard software engineering principles, such as coding standards, version control, and automated testing, as well unique advantages of object-oriented design in process model coupling, to ensure software quality and confidence. We will also be prepared to discuss the major challenges faced by most open-source software teams, such as on-boarding new developers or one-time contributions, dealing with competitors or lookie-loos, and other downsides of complete transparency, as well as our approach to community engagement, including a user group email list, hosting short courses and workshops for new users, and maintaining a website. SAND2017-8174A

The Sardinia Radio Telescope . From a technological project to a radio observatory

NASA Astrophysics Data System (ADS)

Prandoni, I.; Murgia, M.; Tarchi, A.; Burgay, M.; Castangia, P.; Egron, E.; Govoni, F.; Pellizzoni, A.; Ricci, R.; Righini, S.; Bartolini, M.; Casu, S.; Corongiu, A.; Iacolina, M. N.; Melis, A.; Nasir, F. T.; Orlati, A.; Perrodin, D.; Poppi, S.; Trois, A.; Vacca, V.; Zanichelli, A.; Bachetti, M.; Buttu, M.; Comoretto, G.; Concu, R.; Fara, A.; Gaudiomonte, F.; Loi, F.; Migoni, C.; Orfei, A.; Pilia, M.; Bolli, P.; Carretti, E.; D'Amico, N.; Guidetti, D.; Loru, S.; Massi, F.; Pisanu, T.; Porceddu, I.; Ridolfi, A.; Serra, G.; Stanghellini, C.; Tiburzi, C.; Tingay, S.; Valente, G.

2017-12-01

Context. The Sardinia Radio Telescope (SRT) is the new 64 m dish operated by the Italian National Institute for Astrophysics (INAF). Its active surface, comprised of 1008 separate aluminium panels supported by electromechanical actuators, will allow us to observe at frequencies of up to 116 GHz. At the moment, three receivers, one per focal position, have been installed and tested: a 7-beam K-band receiver, a mono-feed C-band receiver, and a coaxial dual-feed L/P band receiver. The SRT was officially opened in September 2013, upon completion of its technical commissioning phase. In this paper, we provide an overview of the main science drivers for the SRT, describe the main outcomes from the scientific commissioning of the telescope, and discuss a set of observations demonstrating the scientific capabilities of the SRT. Aims: The scientific commissioning phase, carried out in the 2012-2015 period, proceeded in stages following the implementation and/or fine-tuning of advanced subsystems such as the active surface, the derotator, new releases of the acquisition software, etc. One of the main objectives of scientific commissioning was the identification of deficiencies in the instrumentation and/or in the telescope subsystems for further optimization. As a result, the overall telescope performance has been significantly improved. Methods: As part of the scientific commissioning activities, different observing modes were tested and validated, and the first astronomical observations were carried out to demonstrate the science capabilities of the SRT. In addition, we developed astronomer-oriented software tools to support future observers on site. In the following, we refer to the overall scientific commissioning and software development activities as astronomical validation. Results: The astronomical validation activities were prioritized based on technical readiness and scientific impact. The highest priority was to make the SRT available for joint observations as part of European networks. As a result, the SRT started to participate (in shared-risk mode) in European VLBI Network (EVN) and Large European Array for Pulsars (LEAP) observing sessions in early 2014. The validation of single-dish operations for the suite of SRT first light receivers and backends continued in the following year, and was concluded with the first call for shared-risk early-science observations issued at the end of 2015. As discussed in the paper, the SRT capabilities were tested (and optimized when possible) for several different observing modes: imaging, spectroscopy, pulsar timing, and transients.

Future-saving audiovisual content for Data Science: Preservation of geoinformatics video heritage with the TIB|AV-Portal

NASA Astrophysics Data System (ADS)

Löwe, Peter; Plank, Margret; Ziedorn, Frauke

2015-04-01

In data driven research, the access to citation and preservation of the full triad consisting of journal article, research data and -software has started to become good scientific practice. To foster the adoption of this practice the significance of software tools has to be acknowledged, which enable scientists to harness auxiliary audiovisual content in their research work. The advent of ubiquitous computer-based audiovisual recording and corresponding Web 2.0 hosting platforms like Youtube, Slideshare and GitHub has created new ecosystems for contextual information related to scientific software and data, which continues to grow both in size and variety of content. The current Web 2.0 platforms lack capabilities for long term archiving and scientific citation, such as persistent identifiers allowing to reference specific intervals of the overall content. The audiovisual content currently shared by scientists ranges from commented howto-demonstrations on software handling, installation and data-processing, to aggregated visual analytics of the evolution of software projects over time. Such content are crucial additions to the scientific message, as they ensure that software-based data-processing workflows can be assessed, understood and reused in the future. In the context of data driven research, such content needs to be accessible by effective search capabilities, enabling the content to be retrieved and ensuring that the content producers receive credit for their efforts within the scientific community. Improved multimedia archiving and retrieval services for scientific audiovisual content which meet these requirements are currently implemented by the scientific library community. This paper exemplifies the existing challenges, requirements, benefits and the potential of the preservation, accessibility and citability of such audiovisual content for the Open Source communities based on the new audiovisual web service TIB|AV Portal of the German National Library of Science and Technology. The web-based portal allows for extended search capabilities based on enhanced metadata derived by automated video analysis. By combining state-of-the-art multimedia retrieval techniques such as speech-, text-, and image recognition with semantic analysis, content-based access to videos at the segment level is provided. Further, by using the open standard Media Fragment Identifier (MFID), a citable Digital Object Identifier is displayed for each video segment. In addition to the continuously growing footprint of contemporary content, the importance of vintage audiovisual information needs to be considered: This paper showcases the successful application of the TIB|AV-Portal in the preservation and provision of a newly discovered version of a GRASS GIS promotional video produced by US Army -Corps of Enginers Laboratory (US-CERL) in 1987. The video is provides insight into the constraints of the very early days of the GRASS GIS project, which is the oldest active Free and Open Source Software (FOSS) GIS project which has been active for over thirty years. GRASS itself has turned into a collaborative scientific platform and a repository of scientific peer-reviewed code and algorithm/knowledge hub for future generation of scientists [1]. This is a reference case for future preservation activities regarding semantic-enhanced Web 2.0 content from geospatial software projects within Academia and beyond. References: [1] Chemin, Y., Petras V., Petrasova, A., Landa, M., Gebbert, S., Zambelli, P., Neteler, M., Löwe, P.: GRASS GIS: a peer-reviewed scientific platform and future research Repository, Geophysical Research Abstracts, Vol. 17, EGU2015-8314-1, 2015 (submitted)

The Telemetric and Holter ECG Warehouse Initiative (THEW): a Data Repository for the Design, Implementation and Validation of ECG-related Technologies

PubMed Central

Couderc, Jean-Philippe

2011-01-01

We present an initiative supported by the National Heart Lung, and Blood Institute and the Food and Drug Administration for the development of a repository containing continuous electrocardiographic information to be shared with the worldwide scientific community. We believe that sharing data reinforces open scientific inquiry. It encourages diversity of analysis and opinion while promoting new research and facilitating the education of new researchers. In this paper, we present the resources available in this initiative for the scientific community. We describe the set of ECG signals currently hosted and we briefly discuss the associated clinical information (medical history. Disease and study-specific endpoints) and software tools we propose. Currently, the repository contains more than 250GB of data from eight clinical studies including healthy individuals and cardiac patients. This data is available for the development, implementation and validation of technologies related to body-surface ECGs. To conclude, the Telemetric and Holter ECG Warehouse (THEW) is an initiative developed to benefit the scientific community and to advance the field of quantitative electrocardiography and cardiac safety. PMID:21097349

OpenSim: open-source software to create and analyze dynamic simulations of movement.

PubMed

Delp, Scott L; Anderson, Frank C; Arnold, Allison S; Loan, Peter; Habib, Ayman; John, Chand T; Guendelman, Eran; Thelen, Darryl G

2007-11-01

Dynamic simulations of movement allow one to study neuromuscular coordination, analyze athletic performance, and estimate internal loading of the musculoskeletal system. Simulations can also be used to identify the sources of pathological movement and establish a scientific basis for treatment planning. We have developed a freely available, open-source software system (OpenSim) that lets users develop models of musculoskeletal structures and create dynamic simulations of a wide variety of movements. We are using this system to simulate the dynamics of individuals with pathological gait and to explore the biomechanical effects of treatments. OpenSim provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a multi-institutional collaboration. Developing software that enables a concerted effort from many investigators poses technical and sociological challenges. Meeting those challenges will accelerate the discovery of principles that govern movement control and improve treatments for individuals with movement pathologies.

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 .

Sculpting in cyberspace: Parallel processing the development of new software

NASA Technical Reports Server (NTRS)

Fisher, Rob

1993-01-01

Stimulating creativity in problem solving, particularly where software development is involved, is applicable to many disciplines. Metaphorical thinking keeps the problem in focus but in a different light, jarring people out of their mental ruts and sparking fresh insights. It forces the mind to stretch to find patterns between dissimilar concepts, in the hope of discovering unusual ideas in odd associations (Technology Review January 1993, p. 37). With a background in Engineering and Visual Design from MIT, I have for the past 30 years pursued a career as a sculptor of interdisciplinary monumental artworks that bridge the fields of science, engineering and art. Since 1979, I have pioneered the application of computer simulation to solve the complex problems associated with these projects. A recent project for the roof of the Carnegie Science Center in Pittsburgh made particular use of the metaphoric creativity technique described above. The problem-solving process led to the creation of hybrid software combining scientific, architectural and engineering visualization techniques. David Steich, a Doctoral Candidate in Electrical Engineering at Penn State, was commissioned to develop special software that enabled me to create innovative free-form sculpture. This paper explores the process of inventing the software through a detailed analysis of the interaction between an artist and a computer programmer.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

This final report on computational methods and software systems for dynamics and control of large space structures covers progress to date, projected developments in the final months of the grant, and conclusions. Pertinent reports and papers that have not appeared in scientific journals (or have not yet appeared in final form) are enclosed. The grant has supported research in two key areas of crucial importance to the computer-based simulation of large space structure. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area, as reported here, involves massively parallel computers.

The Study on Neuro-IE Management Software in Manufacturing Enterprises. -The Application of Video Analysis Technology

NASA Astrophysics Data System (ADS)

Bian, Jun; Fu, Huijian; Shang, Qian; Zhou, Xiangyang; Ma, Qingguo

This paper analyzes the outstanding problems in current industrial production by reviewing the three stages of the Industrial Engineering Development. Based on investigations and interviews in enterprises, we propose the new idea of applying "computer video analysis technology" to new industrial engineering management software, and add "loose-coefficient" of the working station to this software in order to arrange scientific and humanistic production. Meanwhile, we suggest utilizing Biofeedback Technology to promote further research on "the rules of workers' physiological, psychological and emotional changes in production". This new kind of combination will push forward industrial engineering theories and benefit enterprises in progressing towards flexible social production, thus it will be of great theory innovation value, social significance and application value.

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.

Janus: Graphical Software for Analyzing In-Situ Measurements of Solar-Wind Ions

NASA Astrophysics Data System (ADS)

Maruca, B.; Stevens, M. L.; Kasper, J. C.; Korreck, K. E.

2016-12-01

In-situ observations of solar-wind ions provide tremendous insights into the physics of space plasmas. Instrument on spacecraft measure distributions of ion energies, which can be processed into scientifically useful data (e.g., values for ion densities and temperatures). This analysis requires a strong, technical understanding of the instrument, so it has traditionally been carried out by the instrument teams using automated software that they had developed for that purpose. The automated routines are optimized for typical solar-wind conditions, so they can fail to capture the complex (and scientifically interesting) microphysics of transient solar-wind - such as coronal mass ejections (CME's) and co-rotating interaction regions (CIR's) - which are often better analyzed manually.This presentation reports on the ongoing development of Janus, a new software package for processing in-situ measurement of solar-wind ions. Janus will provide user with an easy-to-use graphical user interface (GUI) for carrying out highly customized analyses. Transparent to the user, Janus will automatically handle the most technical tasks (e.g., the retrieval and calibration of measurements). For the first time, users with only limited knowledge about the instruments (e.g., non-instrumentalists and students) will be able to easily process measurements of solar-wind ions. Version 1 of Janus focuses specifically on such measurements from the Wind spacecraft's Faraday Cups and is slated for public release in time for this presentation.

Bringing your tools to CyVerse Discovery Environment using Docker

PubMed Central

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse’s Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse’s production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use. PMID:27803802

Bringing your tools to CyVerse Discovery Environment using Docker.

PubMed

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use.

ObsPy: A Python toolbox for seismology - Sustainability, New Features, and Applications

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; MacCarthy, J.

2016-12-01

ObsPy (https://www.obspy.org) is a community-driven, open-source project dedicated to offer a bridge for seismology into the scientific Python ecosystem. Amongst other things, it provides Read and write support for essentially every commonly used data format in seismology with a unified interface. This includes waveform data as well as station and event meta information. A signal processing toolbox tuned to the specific needs of seismologists. Integrated access to the largest data centers, web services, and databases. Wrappers around third party codes like libmseed and evalresp. Using ObsPy enables users to take advantage of the vast scientific ecosystem that has developed around Python. In contrast to many other programming languages and tools, Python is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often must be translated to stable and production ready environments, especially in the age of big data. ObsPy has seen constant development for more than six years and enjoys a large rate of adoption in the seismological community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. We will present a short overview of the capabilities of ObsPy and point out several representative use cases and more specialized software built around ObsPy. Additionally we will discuss new and upcoming features, as well as the sustainability of open-source scientific software.

Status report of the SRT radiotelescope control software: the DISCOS project

NASA Astrophysics Data System (ADS)

Orlati, A.; Bartolini, M.; Buttu, M.; Fara, A.; Migoni, C.; Poppi, S.; Righini, S.

2016-08-01

The Sardinia Radio Telescope (SRT) is a 64-m fully-steerable radio telescope. It is provided with an active surface to correct for gravitational deformations, allowing observations from 300 MHz to 100 GHz. At present, three receivers are available: a coaxial LP-band receiver (305-410 MHz and 1.5-1.8 GHz), a C-band receiver (5.7-7.7 GHz) and a 7-feed K-band receiver (18-26.5 GHz). Several back-ends are also available in order to perform the different data acquisition and analysis procedures requested by scientific projects. The design and development of the SRT control software started in 2004, and now belongs to a wider project called DISCOS (Development of the Italian Single-dish COntrol System), which provides a common infrastructure to the three Italian radio telescopes (Medicina, Noto and SRT dishes). DISCOS is based on the Alma Common Software (ACS) framework, and currently consists of more than 500k lines of code. It is organized in a common core and three specific product lines, one for each telescope. Recent developments, carried out after the conclusion of the technical commissioning of the instrument (October 2013), consisted in the addition of several new features in many parts of the observing pipeline, spanning from the motion control to the digital back-ends for data acquisition and data formatting; we brie y describe such improvements. More importantly, in the last two years we have supported the astronomical validation of the SRT radio telescope, leading to the opening of the first public call for proposals in late 2015. During this period, while assisting both the engineering and the scientific staff, we massively employed the control software and were able to test all of its features: in this process we received our first feedback from the users and we could verify how the system performed in a real-life scenario, drawing the first conclusions about the overall system stability and performance. We examine how the system behaves in terms of network load and system load, how it reacts to failures and errors, and what components and services seem to be the most critical parts of our architecture, showing how the ACS framework impacts on these aspects. Moreover, the exposure to public utilization has highlighted the major flaws in our development and software management process, which had to be tuned and improved in order to achieve faster release cycles in response to user feedback, and safer deploy operations. In this regard we show how the introduction of testing practices, along with continuous integration, helped us to meet higher quality standards. Having identified the most critical aspects of our software, we conclude showing our intentions for the future development of DISCOS, both in terms of software features and software infrastructures.

EOS MLS Science Data Processing System: A Description of Architecture and Capabilities

NASA Technical Reports Server (NTRS)

Cuddy, David T.; Echeverri, Mark D.; Wagner, Paul A.; Hanzel, Audrey T.; Fuller, Ryan A.

2006-01-01

This paper describes the architecture and capabilities of the Science Data Processing System (SDPS) for the EOS MLS. The SDPS consists of two major components--the Science Computing Facility and the Science Investigator-led Processing System. The Science Computing Facility provides the facilities for the EOS MLS Science Team to perform the functions of scientific algorithm development, processing software development, quality control of data products, and scientific analyses. The Science Investigator-led Processing System processes and reprocesses the science data for the entire mission and delivers the data products to the Science Computing Facility and to the Goddard Space Flight Center Earth Science Distributed Active Archive Center, which archives and distributes the standard science products.

DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes.

PubMed

Neugebauer, Tomasz; Bordeleau, Eric; Burrus, Vincent; Brzezinski, Ryszard

2015-01-01

Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

CONRAD—A software framework for cone-beam imaging in radiology

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

Maier, Andreas; Choi, Jang-Hwan; Riess, Christian

2013-11-15

Purpose: In the community of x-ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x-ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods: CONRAD is a Java-based state-of-the-art software platform withmore » extensive documentation. It is based on platform-independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy-to-use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results: A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download at http://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C-arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state-of-the-art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions: As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison between the methods of different groups.« less

CoRoTlog

NASA Astrophysics Data System (ADS)

Plasson, Ph.

2006-11-01

LESIA, in close cooperation with CNES, DLR and IWF, is responsible for the tests and validation of the CoRoT instrument digital process unit which is made up of the BEX and DPU assembly. The main part of the work has consisted in validating the DPU software and in testing the BEX/DPU coupling. This work took more than two years due to the central role of the software tested and its technical complexity. The first task, in the validation process, was to carry out the acceptance tests of the DPU software. These tests consisted in checking each of the 325 requirements identified in the URD (User Requirements Document) and were played in a configuration using the DPU coupled to a BEX simulator. During the acceptance tests, all the transversal functionalities of the DPU software, like the TC/TM management, the state machine management, the BEX driving, the system monitoring or the maintenance functionalities were checked in depth. The functionalities associated with the seismology and exoplanetology processing, like the loading of window and mask descriptors or the configuration of the service execution parameters, were also exhaustively tested. After having validated the DPU software against the user requirements using a BEX simulator, the following step consisted in coupling the DPU and the BEX in order to check that the formed unit worked correctly and met the performance requirements. These tests were conducted in two phases: the first one was devoted to the functional aspects and the tests of interface, the second one to the performance aspects. The performance tests were based on the use of the DPU software scientific services and on the use of full images representative of a realistic sky as inputs. These tests were also based on the use of a reference set of windows and parameters, which was provided by the scientific team and was representative, in terms of load and complexity, of the one that could be used during the observation mode of the CoRoT instrument. Theywere played in a configuration using either a BCC simulator or a real BCC coupled to a video simulator, to feed the BEX/DPU unit. The validation of the scientific algorithms was conducted in parallel to the phase of the BEX/DPU coupling tests. The objective of this phase was to check that the algorithms implemented in the scientific services of the DPU software were in good conformity with those specified in the URD and that the obtained numerical precision corresponded to that expected. Forty cases of tests were defined covering the fine and rough angular error measurement processing, the rejection of the brilliant pixels, the subtraction of the offset and the sky background, the photometry algorithms, the SAA handling and reference image management. For each test case, the LESIA scientific team produced, by simulation, using the model instrument, the dynamic data files and the parameter sets allowing to feed the DPU on the one hand, and, on the other hand, a model of the onboard software. These data files correspond to FITS images (black windows, star windows, offset windows) containing more or less disturbances and making it possible to test the DPU software in dynamic mode over durations of up to 48 hours. To perform the test and validation activities of the CoRoT instrument digital process unit, a set of software testing tools was developed by LESIA (Software Ground Support Equipment, hereafter "SGSE"). Thanks to their versatility and modularity, these software testing tools were actually used during all the activities of integration, tests and validation of the instrument and its subsystems CoRoTCase and CoRoTCam. The CoRoT SGSE were specified, designed and developed by LESIA. The objective was to have a software system allowing the users (validation team of the onboard software, instrument integration team, etc.) to remotely control and monitor the whole instrument or only one of the subsystems of the instrument like the DPU coupled to a simulator BEX or the BEX/DPU unit coupled to a BCC simulator. The idea was to be able to interact in real time with the system under test by driving the various EGSE, but also to play test procedures implemented as scripts organized into libraries, to record the telemetries and housekeeping data in a database, and to be able to carry out post-mortem analyses.

The PRISM project

NASA Astrophysics Data System (ADS)

Guilyardi, E.

2003-04-01

The European Union's PRISM infrastructure project (PRogram for Integrated earth System Modelling) aims at designing a flexible environment to easily assemble and run Earth System Models (http://prism.enes.org). Europe's widely distributed modelling expertise is both a strength and a challenge. Recognizing this, the PRISM project aims at developing an efficient shared modelling software infrastructure for climate scientists, providing them with an opportunity for greater focus on scientific issues, including the necessary scientific diversity (models and approaches). The proposed PRISM system includes 1) the use - or definition - and promotion of scientific and technical standards to increase component modularity, 2) an end-to-end software environment (coupler, user interface, diagnostics) to launch, monitor and analyze complex Earth System Models built around the existing and future community models, 3) testing and quality standards to ensure HPC performance on a variety of platforms and 4) community wide inputs and requirements capture in all stages of system specifications and design through user/developers meetings, workshops and thematic schools. This science driven project, led by 22 institutes* and started December 1st 2001, benefits from a unique gathering of scientific and technical expertise. More than 30 models (both global and regional) have expressed interest to be part of the PRISM system and 6 types of components have been identified: atmosphere, atmosphere chemistry, land surface, ocean, sea ice and ocean biochemistry. Progress and overall architecture design will be presented. * MPI-Met (Coordinator), KNMI (co-coordinator), MPI-M&D, Met Office, University of Reading, IPSL, Meteo-France, CERFACS, DMI, SMHI, NERSC, ETH Zurich, INGV, MPI-BGC, PIK, ECMWF, UCL-ASTR, NEC, FECIT, SGI, SUN, CCRLE

The SEL Adapts to Meet Changing Times

NASA Technical Reports Server (NTRS)

Pajerski, Rose S.; Basili, Victor R.

1997-01-01

Since 1976, the Software Engineering Laboratory (SEL) has been dedicated to understanding and improving the way in which one NASA organization, the Flight Dynamics Division (FDD) at Goddard Space Flight Center, develops, maintains, and manages complex flight dynamics systems. It has done this by developing and refining a continual process improvement approach that allows an organization such as the FDD to fine-tune its process for its particular domain. Experimental software engineering and measurement play a significant role in this approach. The SEL is a partnership of NASA Goddard, its major software contractor, Computer Sciences Corporation (CSC), and the University of Maryland's (LTM) Department of Computer Science. The FDD primarily builds software systems that provide ground-based flight dynamics support for scientific satellites. They fall into two sets: ground systems and simulators. Ground systems are midsize systems that average around 250 thousand source lines of code (KSLOC). Ground system development projects typically last 1 - 2 years. Recent systems have been rehosted to workstations from IBM mainframes, and also contain significant new subsystems written in C and C++. The simulators are smaller systems averaging around 60 KSLOC that provide the test data for the ground systems. Simulator development lasts up to 1 year. Most of the simulators have been built in Ada on workstations. The SEL is responsible for the management and continual improvement of the software engineering processes used on these FDD projects.

AIBench: a rapid application development framework for translational research in biomedicine.

PubMed

Glez-Peña, D; Reboiro-Jato, M; Maia, P; Rocha, M; Díaz, F; Fdez-Riverola, F

2010-05-01

Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allow for efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input-processing-output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

Engineering of the LISA Pathfinder mission—making the experiment a practical reality

NASA Astrophysics Data System (ADS)

Warren, Carl; Dunbar, Neil; Backler, Mike

2009-05-01

LISA Pathfinder represents a unique challenge in the development of scientific spacecraft—not only is the LISA Test Package (LTP) payload a complex integrated development, placing stringent requirements on its developers and the spacecraft, but the payload also acts as the core sensor and actuator for the spacecraft, making the tasks of control design, software development and system verification unusually difficult. The micro-propulsion system which provides the remaining actuation also presents substantial development and verification challenges. As the mission approaches the system critical design review, flight hardware is completing verification and the process of verification using software and hardware simulators and test benches is underway. Preparation for operations has started, but critical milestones for LTP and field effect electric propulsion (FEEP) lie ahead. This paper summarizes the status of the present development and outlines the key challenges that must be overcome on the way to launch.

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

PubMed Central

2009-01-01

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

SpecTracer: A Python-Based Interactive Solution for Echelle Spectra Reduction

NASA Astrophysics Data System (ADS)

Romero Matamala, Oscar Fernando; Petit, Véronique; Caballero-Nieves, Saida Maria

2018-01-01

SpecTracer is a newly developed interactive solution to reduce cross dispersed echelle spectra. The use of widgets saves the user the steep learning curves of currently available reduction software. SpecTracer uses well established image processing techniques based on IRAF to succesfully extract the stellar spectra. Comparisons with other reduction software, like IRAF, show comparable results, with the added advantages of ease of use, platform independence and portability. This tool can obtain meaningful scientific data and serve also as a training tool, especially for undergraduates doing research, in the procedure for spectroscopic analysis.

Reviews

NASA Astrophysics Data System (ADS)

2007-09-01

WE RECOMMEND Energy Foresight Valuable and original GCSE curriculum support on DVD Developing Scientific Literacy: Using News Media in the Classroom This book helpfully evaluates science stories in today's media Radioactivity Explained and Electricity Explained Interactive software ideal for classroom use TEP Generator Wind-up generator specially designed for schools SEP Energymeter A joule meter with more uses than its appearance suggests Into the Cool: Energy Flow, Thermodynamics and Life This book explores the physics behind biology CmapTools Handy software for mapping knowledge and resources LogIT Black Box This hub contains multiple sensors for endless experimental fun WEB WATCH Water Web 2.0

Separating Added Value from Hype: Some Experiences and Prognostications

NASA Astrophysics Data System (ADS)

Reed, Dan

2004-03-01

These are exciting times for the interplay of science and computing technology. As new data archives, instruments and computing facilities are connected nationally and internationally, a new model of distributed scientific collaboration is emerging. However, any new technology brings both opportunities and challenges -- Grids are no exception. In this talk, we will discuss some of the experiences deploying Grid software in production environments, illustrated with experiences from the NSF PACI Alliance, the NSF Extensible Terascale Facility (ETF) and other Grid projects. From these experiences, we derive some guidelines for deployment and some suggestions for community engagement, software development and infrastructure

Development of a software for control of the Lidar complex at the IAO SB RAS small Lidar station

NASA Astrophysics Data System (ADS)

Marichev, V. N.; Bochkovskii, D. A.

2015-11-01

The problems are discussed in the wide circles of the scientific community in the end of the last and in the beginning of present century, related with climate change on both global and local scale. The complicated question of changing climatic and ecological systems under the effect of natural and anthropogenic factors requires the development and creation of atmospheric aerosol thermodynamic and spatial-temporal models, development of network of both ground-based and space-based services for monitoring of the atmosphere on a global scale [1, 2]. Measures on collection of great amount of data lead to the need of development of not only technical side of the solution to the problem, but also methodological, algorithmic and software. The last decade is marked by the widespread introduction of computer technology into science and increase of its consumer features, such as speed, volume of RAM and cash memory, as well as the ability of high-quality displaying the data. Therefore, the final item in the development of automation of the experiment and application of mathematical methods is the development of the software tools. Software should carry the main load in the processing and simulation of an experiment, and to be a link between theoreticians, developers of the processing methods and models of physical processes and experimentalists

Open source libraries and frameworks for biological data visualisation: a guide for developers.

PubMed

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-04-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interoperability of Neuroscience Modeling Software

PubMed Central

Cannon, Robert C.; Gewaltig, Marc-Oliver; Gleeson, Padraig; Bhalla, Upinder S.; Cornelis, Hugo; Hines, Michael L.; Howell, Fredrick W.; Muller, Eilif; Stiles, Joel R.; Wils, Stefan; De Schutter, Erik

2009-01-01

Neuroscience increasingly uses computational models to assist in the exploration and interpretation of complex phenomena. As a result, considerable effort is invested in the development of software tools and technologies for numerical simulations and for the creation and publication of models. The diversity of related tools leads to the duplication of effort and hinders model reuse. Development practices and technologies that support interoperability between software systems therefore play an important role in making the modeling process more efficient and in ensuring that published models can be reliably and easily reused. Various forms of interoperability are possible including the development of portable model description standards, the adoption of common simulation languages or the use of standardized middleware. Each of these approaches finds applications within the broad range of current modeling activity. However more effort is required in many areas to enable new scientific questions to be addressed. Here we present the conclusions of the “Neuro-IT Interoperability of Simulators” workshop, held at the 11th computational neuroscience meeting in Edinburgh (July 19-20 2006; http://www.cnsorg.org). We assess the current state of interoperability of neural simulation software and explore the future directions that will enable the field to advance. PMID:17873374

Open source libraries and frameworks for biological data visualisation: A guide for developers

PubMed Central

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. PMID:25475079

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

PubMed

List, Markus

2017-06-10

Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.

The Evolution of Software Publication in Astronomy

NASA Astrophysics Data System (ADS)

Cantiello, Matteo

2018-01-01

Software is a fundamental component of the scientific research process. As astronomical discoveries increasingly rely on complex numerical calculations and the analysis of big data sets, publishing and documenting software is a fundamental step in ensuring transparency and reproducibility of results. I will briefly discuss the recent history of software publication and highlight the challenges and opportunities ahead.

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.

Implementing Kanban for agile process management within the ALMA Software Operations Group

NASA Astrophysics Data System (ADS)

Reveco, Johnny; Mora, Matias; Shen, Tzu-Chiang; Soto, Ruben; Sepulveda, Jorge; Ibsen, Jorge

2014-07-01

After the inauguration of the Atacama Large Millimeter/submillimeter Array (ALMA), the Software Operations Group in Chile has refocused its objectives to: (1) providing software support to tasks related to System Integration, Scientific Commissioning and Verification, as well as Early Science observations; (2) testing the remaining software features, still under development by the Integrated Computing Team across the world; and (3) designing and developing processes to optimize and increase the level of automation of operational tasks. Due to their different stakeholders, each of these tasks presents a wide diversity of importances, lifespans and complexities. Aiming to provide the proper priority and traceability for every task without stressing our engineers, we introduced the Kanban methodology in our processes in order to balance the demand on the team against the throughput of the delivered work. The aim of this paper is to share experiences gained during the implementation of Kanban in our processes, describing the difficulties we have found, solutions and adaptations that led us to our current but still evolving implementation, which has greatly improved our throughput, prioritization and problem traceability.

Development of digital interactive processing system for NOAA satellites AVHRR data

NASA Astrophysics Data System (ADS)

Gupta, R. K.; Murthy, N. N.

The paper discusses the digital image processing system for NOAA/AVHRR data including Land applications - configured around VAX 11/750 host computer supported with FPS 100 Array Processor, Comtal graphic display and HP Plotting devices; wherein the system software for relational Data Base together with query and editing facilities, Man-Machine Interface using form, menu and prompt inputs including validation of user entries for data type and range; preprocessing software for data calibration, Sun-angle correction, Geometric Corrections for Earth curvature effect and Earth rotation offsets and Earth location of AVHRR image have been accomplished. The implemented image enhancement techniques such as grey level stretching, histogram equalization and convolution are discussed. The software implementation details for the computation of vegetative index and normalized vegetative index using NOAA/AVHRR channels 1 and 2 data together with output are presented; scientific background for such computations and obtainability of similar indices from Landsat/MSS data are also included. The paper concludes by specifying the further software developments planned and the progress envisaged in the field of vegetation index studies.

Announcement Notice (AN) 241.4 - Software | OSTI, US Dept of Energy Office

Science.gov Websites

of Scientific and Technical Information Skip to main content Scientific and Technical Information Program The home of the U.S. Department of Energy's Scientific and Technical Information Program ) Scientific and Technical Information (STI) products for announcement and availability. An AN includes review

Uses of the Drupal CMS Collaborative Framework in the Woods Hole Scientific Community (Invited)

NASA Astrophysics Data System (ADS)

Maffei, A. R.; Chandler, C. L.; Work, T. T.; Shorthouse, D.; Furfey, J.; Miller, H.

2010-12-01

Organizations that comprise the Woods Hole scientific community (Woods Hole Oceanographic Institution, Marine Biological Laboratory, USGS Woods Hole Coastal and Marine Science Center, Woods Hole Research Center, NOAA NMFS Northeast Fisheries Science Center, SEA Education Association) have a long history of collaborative activity regarding computing, computer network and information technologies that support common, inter-disciplinary science needs. Over the past several years there has been growing interest in the use of the Drupal Content Management System (CMS) playing a variety of roles in support of research projects resident at several of these organizations. Many of these projects are part of science programs that are national and international in scope. Here we survey the current uses of Drupal within the Woods Hole scientific community and examine reasons it has been adopted. The promise of emerging semantic features in the Drupal framework is examined and projections of how pre-existing Drupal-based websites might benefit are made. Closer examination of Drupal software design exposes it as more than simply a content management system. The flexibility of its architecture; the power of its taxonomy module; the care taken in nurturing the open-source developer community that surrounds it (including organized and often well-attended code sprints); the ability to bind emerging software technologies as Drupal modules; the careful selection process used in adopting core functionality; multi-site hosting and cross-site deployment of updates and a recent trend towards development of use-case inspired Drupal distributions casts Drupal as a general-purpose application deployment framework. Recent work in the semantic arena casts Drupal as an emerging RDF framework as well. Examples of roles played by Drupal-based websites within the Woods Hole scientific community that will be discussed include: science data metadata database, organization main website, biological taxonomy development, bibliographic database, physical media data archive inventory manager, disaster-response website development framework, science project task management, science conference planning, and spreadsheet-to-database converter.

Two-step web-mining approach to study geology/geophysics-related open-source software projects

NASA Astrophysics Data System (ADS)

Behrends, Knut; Conze, Ronald

2013-04-01

Geology/geophysics is a highly interdisciplinary science, overlapping with, for instance, physics, biology and chemistry. In today's software-intensive work environments, geoscientists often encounter new open-source software from scientific fields that are only remotely related to the own field of expertise. We show how web-mining techniques can help to carry out systematic discovery and evaluation of such software. In a first step, we downloaded ~500 abstracts (each consisting of ~1 kb UTF-8 text) from agu-fm12.abstractcentral.com. This web site hosts the abstracts of all publications presented at AGU Fall Meeting 2012, the world's largest annual geology/geophysics conference. All abstracts belonged to the category "Earth and Space Science Informatics", an interdisciplinary label cross-cutting many disciplines such as "deep biosphere", "atmospheric research", and "mineral physics". Each publication was represented by a highly structured record with ~20 short data attributes, the largest authorship-record being the unstructured "abstract" field. We processed texts of the abstracts with the statistics software "R" to calculate a corpus and a term-document matrix. Using R package "tm", we applied text-mining techniques to filter data and develop hypotheses about software-development activities happening in various geology/geophysics fields. Analyzing the term-document matrix with basic techniques (e.g., word frequencies, co-occurences, weighting) as well as more complex methods (clustering, classification) several key pieces of information were extracted. For example, text-mining can be used to identify scientists who are also developers of open-source scientific software, and the names of their programming projects and codes can also be identified. In a second step, based on the intermediate results found by processing the conference-abstracts, any new hypotheses can be tested in another webmining subproject: by merging the dataset with open data from github.com and stackoverflow.com. These popular, developer-centric websites have powerful application-programmer interfaces, and follow an open-data policy. In this regard, these sites offer a web-accessible reservoir of information that can be tapped to study questions such as: which open source software projects are eminent in the various geoscience fields? What are the most popular programming languages? How are they trending? Are there any interesting temporal patterns in committer activities? How large are programming teams and how do they change over time? What free software packages exist in the vast realms of related fields? Does the software from these fields have capabilities that might still be useful to me as a researcher, or can help me perform my work better? Are there any open-source projects that might be commercially interesting? This evaluation strategy reveals programming projects that tend to be new. As many important legacy codes are not hosted on open-source code-repositories, the presented search method might overlook some older projects.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

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

Jurrus, Elizabeth; Engel, Dave; Star, Keith

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suitemore » of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.« less

Open source and healthcare in Europe - time to put leading edge ideas into practice.

PubMed

Murray, Peter J; Wright, Graham; Karopka, Thomas; Betts, Helen; Orel, Andrej

2009-01-01

Free/Libre and Open Source Software (FLOSS) is a process of software development, a method of licensing and a philosophy. Although FLOSS plays a significant role in several market areas, the impact in the health care arena is still limited. FLOSS is promoted as one of the most effective means for overcoming fragmentation in the health care sector and providing a basis for more efficient, timely and cost effective health care provision. The 2008 European Federation for Medical Informatics (EFMI) Special Topic Conference (STC) explored a range of current and future issues related to FLOSS in healthcare (FLOSS-HC). In particular, there was a focus on health records, ubiquitous computing, knowledge sharing, and current and future applications. Discussions resulted in a list of main barriers and challenges for use of FLOSS-HC. Based on the outputs of this event, the 2004 Open Steps events and subsequent workshops at OSEHC2009 and Med-e-Tel 2009, a four-step strategy has been proposed for FLOSS-HC: 1) a FLOSS-HC inventory; 2) a FLOSS-HC collaboration platform, use case database and knowledge base; 3) a worldwide FLOSS-HC network; and 4) FLOSS-HC dissemination activities. The workshop will further refine this strategy and elaborate avenues for FLOSS-HC from scientific, business and end-user perspectives. To gain acceptance by different stakeholders in the health care industry, different activities have to be conducted in collaboration. The workshop will focus on the scientific challenges in developing methodologies and criteria to support FLOSS-HC in becoming a viable alternative to commercial and proprietary software development and deployment.

Virtual Labs (Science Gateways) as platforms for Free and Open Source Science

NASA Astrophysics Data System (ADS)

Lescinsky, David; Car, Nicholas; Fraser, Ryan; Friedrich, Carsten; Kemp, Carina; Squire, Geoffrey

2016-04-01

The Free and Open Source Software (FOSS) movement promotes community engagement in software development, as well as provides access to a range of sophisticated technologies that would be prohibitively expensive if obtained commercially. However, as geoinformatics and eResearch tools and services become more dispersed, it becomes more complicated to identify and interface between the many required components. Virtual Laboratories (VLs, also known as Science Gateways) simplify the management and coordination of these components by providing a platform linking many, if not all, of the steps in particular scientific processes. These enable scientists to focus on their science, rather than the underlying supporting technologies. We describe a modular, open source, VL infrastructure that can be reconfigured to create VLs for a wide range of disciplines. Development of this infrastructure has been led by CSIRO in collaboration with Geoscience Australia and the National Computational Infrastructure (NCI) with support from the National eResearch Collaboration Tools and Resources (NeCTAR) and the Australian National Data Service (ANDS). Initially, the infrastructure was developed to support the Virtual Geophysical Laboratory (VGL), and has subsequently been repurposed to create the Virtual Hazards Impact and Risk Laboratory (VHIRL) and the reconfigured Australian National Virtual Geophysics Laboratory (ANVGL). During each step of development, new capabilities and services have been added and/or enhanced. We plan on continuing to follow this model using a shared, community code base. The VL platform facilitates transparent and reproducible science by providing access to both the data and methodologies used during scientific investigations. This is further enhanced by the ability to set up and run investigations using computational resources accessed through the VL. Data is accessed using registries pointing to catalogues within public data repositories (notably including the NCI National Environmental Research Data Interoperability Platform), or by uploading data directly from user supplied addresses or files. Similarly, scientific software is accessed through registries pointing to software repositories (e.g., GitHub). Runs are configured by using or modifying default templates designed by subject matter experts. After the appropriate computational resources are identified by the user, Virtual Machines (VMs) are spun up and jobs are submitted to service providers (currently the NeCTAR public cloud or Amazon Web Services). Following completion of the jobs the results can be reviewed and downloaded if desired. By providing a unified platform for science, the VL infrastructure enables sophisticated provenance capture and management. The source of input data (including both collection and queries), user information, software information (version and configuration details) and output information are all captured and managed as a VL resource which can be linked to output data sets. This provenance resource provides a mechanism for publication and citation for Free and Open Source Science.

Embracing Open Software Development in Solar Physics

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Christe, S.; Mueller, D.

2012-12-01

We discuss two ongoing software projects in solar physics that have adopted best practices of the open source software community. The first, the Helioviewer Project, is a powerful data visualization tool which includes online and Java interfaces inspired by Google Maps (tm). This effort allows users to find solar features and events of interest, and download the corresponding data. Having found data of interest, the user now has to analyze it. The dominant solar data analysis platform is an open-source library called SolarSoft (SSW). Although SSW itself is open-source, the programming language used is IDL, a proprietary language with licensing costs that are prohibative for many institutions and individuals. SSW is composed of a collection of related scripts written by missions and individuals for solar data processing and analysis, without any consistent data structures or common interfaces. Further, at the time when SSW was initially developed, many of the best software development processes of today (mirrored and distributed version control, unit testing, continuous integration, etc.) were not standard, and have not since been adopted. The challenges inherent in developing SolarSoft led to a second software project known as SunPy. SunPy is an open-source Python-based library which seeks to create a unified solar data analysis environment including a number of core datatypes such as Maps, Lightcurves, and Spectra which have consistent interfaces and behaviors. By taking advantage of the large and sophisticated body of scientific software already available in Python (e.g. SciPy, NumPy, Matplotlib), and by adopting many of the best practices refined in open-source software development, SunPy has been able to develop at a very rapid pace while still ensuring a high level of reliability. The Helioviewer Project and SunPy represent two pioneering technologies in solar physics - simple yet flexible data visualization and a powerful, new data analysis environment. We discuss the development of both these efforts and how they are beginning to influence the solar physics community.

Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat.

PubMed

Zhou, Ji; Applegate, Christopher; Alonso, Albor Dobon; Reynolds, Daniel; Orford, Simon; Mackiewicz, Michal; Griffiths, Simon; Penfield, Steven; Pullen, Nick

2017-01-01

Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic. Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat ( Triticum aestivum ) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image analysis and machine learning libraries, we believe that our software not only can contribute to biological research, but also demonstrates how to utilise existing open numeric and scientific libraries (e.g. Scikit-image, OpenCV, SciPy and Scikit-learn) to build sound plant phenomics analytic solutions, in a efficient and effective way. Leaf-GP is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. Our work presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases.

MCdevelop - a universal framework for Stochastic Simulations

NASA Astrophysics Data System (ADS)

Slawinska, M.; Jadach, S.

2011-03-01

We present MCdevelop, a universal computer framework for developing and exploiting the wide class of Stochastic Simulations (SS) software. This powerful universal SS software development tool has been derived from a series of scientific projects for precision calculations in high energy physics (HEP), which feature a wide range of functionality in the SS software needed for advanced precision Quantum Field Theory calculations for the past LEP experiments and for the ongoing LHC experiments at CERN, Geneva. MCdevelop is a "spin-off" product of HEP to be exploited in other areas, while it will still serve to develop new SS software for HEP experiments. Typically SS involve independent generation of large sets of random "events", often requiring considerable CPU power. Since SS jobs usually do not share memory it makes them easy to parallelize. The efficient development, testing and running in parallel SS software requires a convenient framework to develop software source code, deploy and monitor batch jobs, merge and analyse results from multiple parallel jobs, even before the production runs are terminated. Throughout the years of development of stochastic simulations for HEP, a sophisticated framework featuring all the above mentioned functionality has been implemented. MCdevelop represents its latest version, written mostly in C++ (GNU compiler gcc). It uses Autotools to build binaries (optionally managed within the KDevelop 3.5.3 Integrated Development Environment (IDE)). It uses the open-source ROOT package for histogramming, graphics and the mechanism of persistency for the C++ objects. MCdevelop helps to run multiple parallel jobs on any computer cluster with NQS-type batch system. Program summaryProgram title:MCdevelop Catalogue identifier: AEHW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 48 136 No. of bytes in distributed program, including test data, etc.: 355 698 Distribution format: tar.gz Programming language: ANSI C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system. Operating system: Most UNIX systems, Linux. The application programs were thoroughly tested under Ubuntu 7.04, 8.04 and CERN Scientific Linux 5. Has the code been vectorised or parallelised?: Tools (scripts) for optional parallelisation on a PC farm are included. RAM: 500 bytes Classification: 11.3 External routines: ROOT package version 5.0 or higher ( http://root.cern.ch/drupal/). Nature of problem: Developing any type of stochastic simulation program for high energy physics and other areas. Solution method: Object Oriented programming in C++ with added persistency mechanism, batch scripts for running on PC farms and Autotools.

Crossing the chasm: how to develop weather and climate models for next generation computers?

NASA Astrophysics Data System (ADS)

Lawrence, Bryan N.; Rezny, Michael; Budich, Reinhard; Bauer, Peter; Behrens, Jörg; Carter, Mick; Deconinck, Willem; Ford, Rupert; Maynard, Christopher; Mullerworth, Steven; Osuna, Carlos; Porter, Andrew; Serradell, Kim; Valcke, Sophie; Wedi, Nils; Wilson, Simon

2018-05-01

Weather and climate models are complex pieces of software which include many individual components, each of which is evolving under pressure to exploit advances in computing to enhance some combination of a range of possible improvements (higher spatio-temporal resolution, increased fidelity in terms of resolved processes, more quantification of uncertainty, etc.). However, after many years of a relatively stable computing environment with little choice in processing architecture or programming paradigm (basically X86 processors using MPI for parallelism), the existing menu of processor choices includes significant diversity, and more is on the horizon. This computational diversity, coupled with ever increasing software complexity, leads to the very real possibility that weather and climate modelling will arrive at a chasm which will separate scientific aspiration from our ability to develop and/or rapidly adapt codes to the available hardware. In this paper we review the hardware and software trends which are leading us towards this chasm, before describing current progress in addressing some of the tools which we may be able to use to bridge the chasm. This brief introduction to current tools and plans is followed by a discussion outlining the scientific requirements for quality model codes which have satisfactory performance and portability, while simultaneously supporting productive scientific evolution. We assert that the existing method of incremental model improvements employing small steps which adjust to the changing hardware environment is likely to be inadequate for crossing the chasm between aspiration and hardware at a satisfactory pace, in part because institutions cannot have all the relevant expertise in house. Instead, we outline a methodology based on large community efforts in engineering and standardisation, which will depend on identifying a taxonomy of key activities - perhaps based on existing efforts to develop domain-specific languages, identify common patterns in weather and climate codes, and develop community approaches to commonly needed tools and libraries - and then collaboratively building up those key components. Such a collaborative approach will depend on institutions, projects, and individuals adopting new interdependencies and ways of working.

Automated extraction of chemical structure information from digital raster images

PubMed Central

Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

2009-01-01

Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles. PMID:19196483

Merlin - Massively parallel heterogeneous computing

NASA Technical Reports Server (NTRS)

Wittie, Larry; Maples, Creve

1989-01-01

Hardware and software for Merlin, a new kind of massively parallel computing system, are described. Eight computers are linked as a 300-MIPS prototype to develop system software for a larger Merlin network with 16 to 64 nodes, totaling 600 to 3000 MIPS. These working prototypes help refine a mapped reflective memory technique that offers a new, very general way of linking many types of computer to form supercomputers. Processors share data selectively and rapidly on a word-by-word basis. Fast firmware virtual circuits are reconfigured to match topological needs of individual application programs. Merlin's low-latency memory-sharing interfaces solve many problems in the design of high-performance computing systems. The Merlin prototypes are intended to run parallel programs for scientific applications and to determine hardware and software needs for a future Teraflops Merlin network.

Scientific Software

NASA Technical Reports Server (NTRS)

1995-01-01

The Interactive Data Language (IDL), developed by Research Systems, Inc., is a tool for scientists to investigate their data without having to write a custom program for each study. IDL is based on the Mariners Mars spectral Editor (MMED) developed for studies from NASA's Mars spacecraft flights. The company has also developed Environment for Visualizing Images (ENVI), an image processing system for easily analyzing remotely sensed data written in IDL. The Visible Human CD, another Research Systems product, is the first complete digital reference of photographic images for exploring human anatomy.

Rapid development of Proteomic applications with the AIBench framework.

PubMed

López-Fernández, Hugo; Reboiro-Jato, Miguel; Glez-Peña, Daniel; Méndez Reboredo, José R; Santos, Hugo M; Carreira, Ricardo J; Capelo-Martínez, José L; Fdez-Riverola, Florentino

2011-09-15

In this paper we present two case studies of Proteomics applications development using the AIBench framework, a Java desktop application framework mainly focused in scientific software development. The applications presented in this work are Decision Peptide-Driven, for rapid and accurate protein quantification, and Bacterial Identification, for Tuberculosis biomarker search and diagnosis. Both tools work with mass spectrometry data, specifically with MALDI-TOF spectra, minimizing the time required to process and analyze the experimental data. Copyright 2011 The Author(s). Published by Journal of Integrative Bioinformatics.

Issues in knowledge representation to support maintainability: A case study in scientific data preparation

NASA Technical Reports Server (NTRS)

Chien, Steve; Kandt, R. Kirk; Roden, Joseph; Burleigh, Scott; King, Todd; Joy, Steve

1992-01-01

Scientific data preparation is the process of extracting usable scientific data from raw instrument data. This task involves noise detection (and subsequent noise classification and flagging or removal), extracting data from compressed forms, and construction of derivative or aggregate data (e.g. spectral densities or running averages). A software system called PIPE provides intelligent assistance to users developing scientific data preparation plans using a programming language called Master Plumber. PIPE provides this assistance capability by using a process description to create a dependency model of the scientific data preparation plan. This dependency model can then be used to verify syntactic and semantic constraints on processing steps to perform limited plan validation. PIPE also provides capabilities for using this model to assist in debugging faulty data preparation plans. In this case, the process model is used to focus the developer's attention upon those processing steps and data elements that were used in computing the faulty output values. Finally, the dependency model of a plan can be used to perform plan optimization and runtime estimation. These capabilities allow scientists to spend less time developing data preparation procedures and more time on scientific analysis tasks. Because the scientific data processing modules (called fittings) evolve to match scientists' needs, issues regarding maintainability are of prime importance in PIPE. This paper describes the PIPE system and describes how issues in maintainability affected the knowledge representation used in PIPE to capture knowledge about the behavior of fittings.

Writing references and using citation management software.

PubMed

Sungur, Mukadder Orhan; Seyhan, Tülay Özkan

2013-09-01

The correct citation of references is obligatory to gain scientific credibility, to honor the original ideas of previous authors and to avoid plagiarism. Currently, researchers can easily find, cite and store references using citation management software. In this review, two popular citation management software programs (EndNote and Mendeley) are summarized.

Learning Content and Software Evaluation and Personalisation Problems

ERIC Educational Resources Information Center

Kurilovas, Eugenijus; Serikoviene, Silvija

2010-01-01

The paper aims to analyse several scientific approaches how to evaluate, implement or choose learning content and software suitable for personalised users/learners needs. Learning objects metadata customisation method as well as the Method of multiple criteria evaluation and optimisation of learning software represented by the experts' additive…

The Virtual Brain: a simulator of primate brain network dynamics.

PubMed

Sanz Leon, Paula; Knock, Stuart A; Woodman, M Marmaduke; Domide, Lia; Mersmann, Jochen; McIntosh, Anthony R; Jirsa, Viktor

2013-01-01

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications.

The Virtual Brain: a simulator of primate brain network dynamics

PubMed Central

Sanz Leon, Paula; Knock, Stuart A.; Woodman, M. Marmaduke; Domide, Lia; Mersmann, Jochen; McIntosh, Anthony R.; Jirsa, Viktor

2013-01-01

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications. PMID:23781198

Copyrighted Software | OSTI, US Dept of Energy Office of Scientific and

Science.gov Websites

Technical Information Skip to main content Scientific and Technical Information Program The home of the U.S. Department of Energy's Scientific and Technical Information Program (STIP) Here you Energy U.S. Department of Energy Office of Science Office of Scientific and Technical information Website

The Trial Software version for DEMETER power spectrum files visualization and mapping

NASA Astrophysics Data System (ADS)

Lozbin, Anatoliy; Inchin, Alexander; Shpadi, Maxim

2010-05-01

In the frame of Kazakhstan's Scientific Space System creation for earthquakes precursors research, the hardware and software of DEMETER satellite was investigated. The data processing Software of DEMETER is based on package SWAN under IDL Virtual machine and realizes many features, but we can't find an important tool for the spectrograms analysis - space-time visualization of power spectrum files from electromagnetic devices as ICE and IMSC. For elimination of this problem we have developed Software which is offered to use. The DeSS (DEMETER Spectrogram Software) - it is Software for visualization, analysis and a mapping of power spectrum data from electromagnetic devices ICE and IMSC. The Software primary goal is to give the researcher friendly tool for the analysis of electromagnetic data from DEMETER Satellite for earthquake precursors and other ionosphere events researches. The Input data for DeSS Software is a power spectrum files: - Power spectrum of 1 component of the electric field in the VLF range (APID 1132); - Power spectrum of 1 component of the electric field in the HF range (APID 1134); - Power spectrum of 1 component of the magnetic field in the VLF range (APID 1137). The main features and operations of the software is possible: - various time and frequency filtration; - visualization of time dependence of signal intensity on fixed frequency; - spectral density visualization for fixed frequency range; - spectrogram autosize and smooth spectrogram; - the information in each point of the spectrogram: time, frequency and intensity; - the spectrum information in the separate window, consisting of 4 blocks; - data mapping with 6 range scale. On the map we can browse next information: - satellite orbit; - conjugate point at the satellite altitude; - north conjugate point at the altitude 110 km; - south conjugate point at the altitude 110 km. This is only trial software version to help the researchers and we always ready collaborate with scientists for software improvement. References: 1. D.Lagoutte, J.Y. Brochot, D. de Carvalho, L.Madrias and M. Parrot. DEMETER Microsatellite. Scientific Mission Center. Data product description. DMT-SP-9-CM-6054-LPC. 2. D.Lagoutte, J.Y. Brochot, P.Latremoliere. SWAN - Software for Waveform Analysis. LPCE/NI/003.E - Part 1 (User's guide), Part 2 (Analysis tools), Part 3 (User's project interface).

Development of hybrid 3-D hydrological modeling for the NCAR Community Earth System Model (CESM)

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

Zeng, Xubin; Troch, Peter; Pelletier, Jon

2015-11-15

This is the Final Report of our four-year (3-year plus one-year no cost extension) collaborative project between the University of Arizona (UA) and the National Center for Atmospheric Research (NCAR). The overall objective of our project is to develop and evaluate the first hybrid 3-D hydrological model with a horizontal grid spacing of 1 km for the NCAR Community Earth System Model (CESM). We have made substantial progress in model development and evaluation, computational efficiencies and software engineering, and data development and evaluation, as discussed in Sections 2-4. Section 5 presents our success in data dissemination, while Section 6 discussesmore » the scientific impacts of our work. Section 7 discusses education and mentoring success of our project, while Section 8 lists our relevant DOE services. All peer-reviewed papers that acknowledged this project are listed in Section 9. Highlights of our achievements include: • We have finished 20 papers (most published already) on model development and evaluation, computational efficiencies and software engineering, and data development and evaluation • The global datasets developed under this project have been permanently archived and publicly available • Some of our research results have already been implemented in WRF and CLM • Patrick Broxton and Michael Brunke have received their Ph.D. • PI Zeng has served on DOE proposal review panels and DOE lab scientific focus area (SFA) review panels« less

CubeSat mission design software tool for risk estimating relationships

NASA Astrophysics Data System (ADS)

Gamble, Katharine Brumbaugh; Lightsey, E. Glenn

2014-09-01

In an effort to make the CubeSat risk estimation and management process more scientific, a software tool has been created that enables mission designers to estimate mission risks. CubeSat mission designers are able to input mission characteristics, such as form factor, mass, development cycle, and launch information, in order to determine the mission risk root causes which historically present the highest risk for their mission. Historical data was collected from the CubeSat community and analyzed to provide a statistical background to characterize these Risk Estimating Relationships (RERs). This paper develops and validates the mathematical model based on the same cost estimating relationship methodology used by the Unmanned Spacecraft Cost Model (USCM) and the Small Satellite Cost Model (SSCM). The RER development uses general error regression models to determine the best fit relationship between root cause consequence and likelihood values and the input factors of interest. These root causes are combined into seven overall CubeSat mission risks which are then graphed on the industry-standard 5×5 Likelihood-Consequence (L-C) chart to help mission designers quickly identify areas of concern within their mission. This paper is the first to document not only the creation of a historical database of CubeSat mission risks, but, more importantly, the scientific representation of Risk Estimating Relationships.

Ultraviolet spectrometer and polarimeter (UVSP) software development and hardware tests for the solar maximum mission

NASA Technical Reports Server (NTRS)

Bruner, M. E.; Haisch, B. M.

1986-01-01

The Ultraviolet Spectrometer/Polarimeter Instrument (UVSP) for the Solar Maximum Mission (SMM) was based on the re-use of the engineering model of the high resolution ultraviolet spectrometer developed for the OSO-8 mission. Lockheed assumed four distinct responsibilities in the UVSP program: technical evaluation of the OSO-8 engineering model; technical consulting on the electronic, optical, and mechanical modifications to the OSO-8 engineering model hardware; design and development of the UVSP software system; and scientific participation in the operations and analysis phase of the mission. Lockheed also provided technical consulting and assistance with instrument hardware performance anomalies encountered during the post launch operation of the SMM observatory. An index to the quarterly reports delivered under the contract are contained, and serves as a useful capsule history of the program activity.

Applied and implied semantics in crystallographic publishing

PubMed Central

2012-01-01

Background Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked actively to develop information exchange standards allowing readers of structure reports to access directly, and interact with, the scientific content of the articles. Results Structure reports submitted to some journals of the International Union of Crystallography (IUCr) can be automatically validated and published through an efficient and cost-effective workflow. Readers can view and interact with the structures in three-dimensional visualization applications, and can access the experimental data should they wish to perform their own independent structure solution and refinement. The journals also layer on top of this facility a number of automated annotations and interpretations to add further scientific value. Conclusions The benefits of semantically rich information exchange standards have revolutionised the scholarly publishing process for crystallography, and establish a model relevant to many other physical science disciplines. PMID:22932420

Software for aerospace education: A bibliography, 2nd edition

NASA Technical Reports Server (NTRS)

Vogt, Gregory L.; Roth, Susan Kies; Phelps, Malcom V.

1990-01-01

This is the second aerospace education software bibliography to be published by the NASA Educational Technology Branch in Washington, DC. Unlike many software bibliographies, this bibliography does not evaluate and grade software according to its quality and value to the classroom, nor does it make any endorsements or warrant scientific accuracy. Rather, it describes software, its subject, approach, and technical details. This bibliography is intended as a convenience to educators. The specific software included represents replies to more than 300 queries to software producers for aerospace education programs.

Harnessing scientific literature reports for pharmacovigilance. Prototype software analytical tool development and usability testing.

PubMed

Sorbello, Alfred; Ripple, Anna; Tonning, Joseph; Munoz, Monica; Hasan, Rashedul; Ly, Thomas; Francis, Henry; Bodenreider, Olivier

2017-03-22

We seek to develop a prototype software analytical tool to augment FDA regulatory reviewers' capacity to harness scientific literature reports in PubMed/MEDLINE for pharmacovigilance and adverse drug event (ADE) safety signal detection. We also aim to gather feedback through usability testing to assess design, performance, and user satisfaction with the tool. A prototype, open source, web-based, software analytical tool generated statistical disproportionality data mining signal scores and dynamic visual analytics for ADE safety signal detection and management. We leveraged Medical Subject Heading (MeSH) indexing terms assigned to published citations in PubMed/MEDLINE to generate candidate drug-adverse event pairs for quantitative data mining. Six FDA regulatory reviewers participated in usability testing by employing the tool as part of their ongoing real-life pharmacovigilance activities to provide subjective feedback on its practical impact, added value, and fitness for use. All usability test participants cited the tool's ease of learning, ease of use, and generation of quantitative ADE safety signals, some of which corresponded to known established adverse drug reactions. Potential concerns included the comparability of the tool's automated literature search relative to a manual 'all fields' PubMed search, missing drugs and adverse event terms, interpretation of signal scores, and integration with existing computer-based analytical tools. Usability testing demonstrated that this novel tool can automate the detection of ADE safety signals from published literature reports. Various mitigation strategies are described to foster improvements in design, productivity, and end user satisfaction.

Open high-level data formats and software for gamma-ray astronomy

NASA Astrophysics Data System (ADS)

Deil, Christoph; Boisson, Catherine; Kosack, Karl; Perkins, Jeremy; King, Johannes; Eger, Peter; Mayer, Michael; Wood, Matthew; Zabalza, Victor; Knödlseder, Jürgen; Hassan, Tarek; Mohrmann, Lars; Ziegler, Alexander; Khelifi, Bruno; Dorner, Daniela; Maier, Gernot; Pedaletti, Giovanna; Rosado, Jaime; Contreras, José Luis; Lefaucheur, Julien; Brügge, Kai; Servillat, Mathieu; Terrier, Régis; Walter, Roland; Lombardi, Saverio

2017-01-01

In gamma-ray astronomy, a variety of data formats and proprietary software have been traditionally used, often developed for one specific mission or experiment. Especially for ground-based imaging atmospheric Cherenkov telescopes (IACTs), data and software are mostly private to the collaborations operating the telescopes. However, there is a general movement in science towards the use of open data and software. In addition, the next-generation IACT instrument, the Cherenkov Telescope Array (CTA), will be operated as an open observatory. We have created a Github organisation at https://github.com/open-gamma-ray-astro where we are developing high-level data format specifications. A public mailing list was set up at https://lists.nasa.gov/mailman/listinfo/open-gamma-ray-astro and a first face-to-face meeting on the IACT high-level data model and formats took place in April 2016 in Meudon (France). This open multi-mission effort will help to accelerate the development of open data formats and open-source software for gamma-ray astronomy, leading to synergies in the development of analysis codes and eventually better scientific results (reproducible, multi-mission). This write-up presents this effort for the first time, explaining the motivation and context, the available resources and process we use, as well as the status and planned next steps for the data format specifications. We hope that it will stimulate feedback and future contributions from the gamma-ray astronomy community.

Third Molars on the Internet: A Guide for Assessing Information Quality and Readability.

PubMed

Hanna, Kamal; Brennan, David; Sambrook, Paul; Armfield, Jason

2015-10-06

Directing patients suffering from third molars (TMs) problems to high-quality online information is not only medically important, but also could enable better engagement in shared decision making. This study aimed to develop a scale that measures the scientific information quality (SIQ) for online information concerning wisdom tooth problems and to conduct a quality evaluation for online TMs resources. In addition, the study evaluated whether a specific piece of readability software (Readability Studio Professional 2012) might be reliable in measuring information comprehension, and explored predictors for the SIQ Scale. A cross-sectional sample of websites was retrieved using certain keywords and phrases such as "impacted wisdom tooth problems" using 3 popular search engines. The retrieved websites (n=150) were filtered. The retained 50 websites were evaluated to assess their characteristics, usability, accessibility, trust, readability, SIQ, and their credibility using DISCERN and Health on the Net Code (HoNCode). Websites' mean scale scores varied significantly across website affiliation groups such as governmental, commercial, and treatment provider bodies. The SIQ Scale had a good internal consistency (alpha=.85) and was significantly correlated with DISCERN (r=.82, P<.01) and HoNCode (r=.38, P<.01). Less than 25% of websites had SIQ scores above 75%. The mean readability grade (10.3, SD 1.9) was above the recommended level, and was significantly correlated with the Scientific Information Comprehension Scale (r=.45. P<.01), which provides evidence for convergent validity. Website affiliation and DISCERN were significantly associated with SIQ (P<.01) and explained 76% of the SIQ variance. The developed SIQ Scale was found to demonstrate reliability and initial validity. Website affiliation, DISCERN, and HoNCode were significant predictors for the quality of scientific information. The Readability Studio software estimates were associated with scientific information comprehensiveness measures.

Nektar++: An open-source spectral/ hp element framework

NASA Astrophysics Data System (ADS)

Cantwell, C. D.; Moxey, D.; Comerford, A.; Bolis, A.; Rocco, G.; Mengaldo, G.; De Grazia, D.; Yakovlev, S.; Lombard, J.-E.; Ekelschot, D.; Jordi, B.; Xu, H.; Mohamied, Y.; Eskilsson, C.; Nelson, B.; Vos, P.; Biotto, C.; Kirby, R. M.; Sherwin, S. J.

2015-07-01

Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/ hp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/ hp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains.

Principles and Best Practices Emerging from Data Basin: A Data Platform Supporting Scientific Research and Landscape Conservation Planning

NASA Astrophysics Data System (ADS)

Comendant, T.; Strittholt, J. R.; Ward, B. C.; Bachelet, D. M.; Grossman, D.; Stevenson-Molnar, N.; Henifin, K.; Lundin, M.; Marvin, T. S.; Peterman, W. L.; Corrigan, G. N.; O'Connor, K.

2013-12-01

A multi-disciplinary team of scientists, software engineers, and outreach staff at the Conservation Biology Institute launched an open-access, web-based spatial data platform called Data Basin (www.databasin.org) in 2010. Primarily built to support research and environmental resource planning, Data Basin provides the capability for individuals and organizations to explore, create, interpret, and collaborate around their priority topics and geographies. We used a stakeholder analysis to assess the needs of data consumers/produces and help prioritize primary and secondary audiences. Data Basin's simple and user-friendly interface makes mapping and geo-processing tools more accessible to less technical audiences. Input from users is considered in system planning, testing, and implementation. The team continually develops using an agile software development approach, which allows new features, improvements, and bug fixes to be deployed to the live system on a frequent basis. The data import process is handled through administrative approval and Data Basin requires spatial data (biological, physical, and socio-economic) to be well-documented. Outreach and training is used to convey the scope and appropriate use of the scientific information and available resources.

Examining Mars with SPICE

NASA Technical Reports Server (NTRS)

Acton, Charles H.; Bachman, Nathaniel J.; Bytof, Jeff A.; Semenov, Boris V.; Taber, William; Turner, F. Scott; Wright, Edward D.

1999-01-01

The International Mars Conference highlights the wealth of scientific data now and soon to be acquired from an international armada of Mars-bound robotic spacecraft. Underlying the planning and interpretation of these scientific observations around and upon Mars are ancillary data and associated software needed to deal with trajectories or locations, instrument pointing, timing and Mars cartographic models. The NASA planetary community has adopted the SPICE system of ancillary data standards and allied tools to fill the need for consistent, reliable access to these basic data and a near limitless range of derived parameters. After substantial rapid growth in its formative years, the SPICE system continues to evolve today to meet new needs and improve ease of use. Adaptations to handle landers and rovers were prototyped on the Mars pathfinder mission and will next be used on Mars '01-'05. Incorporation of new methods to readily handle non-inertial reference frames has vastly extended the capability and simplified many computations. A translation of the SPICE Toolkit software suite to the C language has just been announced. To further support cartographic calculations associated with Mars exploration the SPICE developers at JPL have recently been asked by NASA to work with cartographers to develop standards and allied software for storing and accessing control net and shape model data sets; these will be highly integrated with existing SPICE components. NASA specifically supports the widest possible utilization of SPICE capabilities throughout the international space science community. With NASA backing the Russian Space Agency and Russian Academy of Science adopted the SPICE standards for the Mars 96 mission. The SPICE ephemeris component will shortly become the international standard for agencies using the Deep Space Network. U.S. and European scientists hope that ESA will employ SPICE standards on the Mars Express mission. SPICE is an open set of standards, and all related specifications and software are freely distributed around the world. This poster describes the current state of SPICE system development, with special emphasis on current and planned support for Mars exploration missions.

A working environment for digital planetary data processing and mapping using ISIS and GRASS GIS

USGS Publications Warehouse

Frigeri, A.; Hare, T.; Neteler, M.; Coradini, A.; Federico, C.; Orosei, R.

2011-01-01

Since the beginning of planetary exploration, mapping has been fundamental to summarize observations returned by scientific missions. Sensor-based mapping has been used to highlight specific features from the planetary surfaces by means of processing. Interpretative mapping makes use of instrumental observations to produce thematic maps that summarize observations of actual data into a specific theme. Geologic maps, for example, are thematic interpretative maps that focus on the representation of materials and processes and their relative timing. The advancements in technology of the last 30 years have allowed us to develop specialized systems where the mapping process can be made entirely in the digital domain. The spread of networked computers on a global scale allowed the rapid propagation of software and digital data such that every researcher can now access digital mapping facilities on his desktop. The efforts to maintain planetary missions data accessible to the scientific community have led to the creation of standardized digital archives that facilitate the access to different datasets by software capable of processing these data from the raw level to the map projected one. Geographic Information Systems (GIS) have been developed to optimize the storage, the analysis, and the retrieval of spatially referenced Earth based environmental geodata; since the last decade these computer programs have become popular among the planetary science community, and recent mission data start to be distributed in formats compatible with these systems. Among all the systems developed for the analysis of planetary and spatially referenced data, we have created a working environment combining two software suites that have similar characteristics in their modular design, their development history, their policy of distribution and their support system. The first, the Integrated Software for Imagers and Spectrometers (ISIS) developed by the United States Geological Survey, represents the state of the art for processing planetary remote sensing data, from the raw unprocessed state to the map projected product. The second, the Geographic Resources Analysis Support System (GRASS) is a Geographic Information System developed by an international team of developers, and one of the core projects promoted by the Open Source Geospatial Foundation (OSGeo). We have worked on enabling the combined use of these software systems throughout the set-up of a common user interface, the unification of the cartographic reference system nomenclature and the minimization of data conversion. Both software packages are distributed with free open source licenses, as well as the source code, scripts and configuration files hereafter presented. In this paper we describe our work done to merge these working environments into a common one, where the user benefits from functionalities of both systems without the need to switch or transfer data from one software suite to the other one. Thereafter we provide an example of its usage in the handling of planetary data and the crafting of a digital geologic map. ?? 2010 Elsevier Ltd. All rights reserved.

ROSE Version 1.0

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

Quinlan, D.; Yi, Q.; Buduc, R.

2005-02-17

ROSE is an object-oriented software infrastructure for source-to-source translation that provides an interface for programmers to write their own specialized translators for optimizing scientific applications. ROSE is a part of current research on telescoping languages, which provides optimizations of the use of libraries in scientific applications. ROSE defines approaches to extend the optimization techniques, common in well defined languages, to the optimization of scientific applications using well defined libraries. ROSE includes a rich set of tools for generating customized transformations to support optimization of applications codes. We currently support full C and C++ (including template instantiation etc.), with Fortran 90more » support under development as part of a collaboration and contract with Rice to use their version of the open source Open64 F90 front-end. ROSE represents an attempt to define an open compiler infrastructure to handle the full complexity of full scale DOE applications codes using the languages common to scientific computing within DOE. We expect that such an infrastructure will also be useful for the development of numerous tools that may then realistically expect to work on DOE full scale applications.« less

AstroGrid-D: Grid technology for astronomical science

NASA Astrophysics Data System (ADS)

Enke, Harry; Steinmetz, Matthias; Adorf, Hans-Martin; Beck-Ratzka, Alexander; Breitling, Frank; Brüsemeister, Thomas; Carlson, Arthur; Ensslin, Torsten; Högqvist, Mikael; Nickelt, Iliya; Radke, Thomas; Reinefeld, Alexander; Reiser, Angelika; Scholl, Tobias; Spurzem, Rainer; Steinacker, Jürgen; Voges, Wolfgang; Wambsganß, Joachim; White, Steve

2011-02-01

We present status and results of AstroGrid-D, a joint effort of astrophysicists and computer scientists to employ grid technology for scientific applications. AstroGrid-D provides access to a network of distributed machines with a set of commands as well as software interfaces. It allows simple use of computer and storage facilities and to schedule or monitor compute tasks and data management. It is based on the Globus Toolkit middleware (GT4). Chapter 1 describes the context which led to the demand for advanced software solutions in Astrophysics, and we state the goals of the project. We then present characteristic astrophysical applications that have been implemented on AstroGrid-D in chapter 2. We describe simulations of different complexity, compute-intensive calculations running on multiple sites (Section 2.1), and advanced applications for specific scientific purposes (Section 2.2), such as a connection to robotic telescopes (Section 2.2.3). We can show from these examples how grid execution improves e.g. the scientific workflow. Chapter 3 explains the software tools and services that we adapted or newly developed. Section 3.1 is focused on the administrative aspects of the infrastructure, to manage users and monitor activity. Section 3.2 characterises the central components of our architecture: The AstroGrid-D information service to collect and store metadata, a file management system, the data management system, and a job manager for automatic submission of compute tasks. We summarise the successfully established infrastructure in chapter 4, concluding with our future plans to establish AstroGrid-D as a platform of modern e-Astronomy.

Java implementation of Class Association Rule algorithms

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

Tamura, Makio

2007-08-30

Java implementation of three Class Association Rule mining algorithms, NETCAR, CARapriori, and clustering based rule mining. NETCAR algorithm is a novel algorithm developed by Makio Tamura. The algorithm is discussed in a paper: UCRL-JRNL-232466-DRAFT, and would be published in a peer review scientific journal. The software is used to extract combinations of genes relevant with a phenotype from a phylogenetic profile and a phenotype profile. The phylogenetic profiles is represented by a binary matrix and a phenotype profile is represented by a binary vector. The present application of this software will be in genome analysis, however, it could be appliedmore » more generally.« less

Four aspects to make science open "by design" and not as an after-thought.

PubMed

Halchenko, Yaroslav O; Hanke, Michael

2015-01-01

Unrestricted dissemination of methodological developments in neuroimaging became the propelling force in advancing our understanding of brain function. However, despite such a rich legacy, it remains not uncommon to encounter software and datasets that are distributed under unnecessarily restricted terms, or that violate terms of third-party products (software or data). With this brief correspondence we would like to recapitulate four important aspects of scientific research practice, which should be taken into consideration as early as possible in the course of any project. Keeping these in check will help neuroimaging to stay at the forefront of the open science movement.

EPOS Data and Service Provision

NASA Astrophysics Data System (ADS)

Bailo, Daniele; Jeffery, Keith G.; Atakan, Kuvvet; Harrison, Matt

2017-04-01

EPOS is now in IP (implementation phase) after a successful PP (preparatory phase). EPOS consists of essentially two components, one ICS (Integrated Core Services) representing the integrating ICT (Information and Communication Technology) and many TCS (Thematic Core Services) representing the scientific domains. The architecture developed, demonstrated and agreed within the project during the PP is now being developed utilising co-design with the TCS teams and agile, spiral methods within the ICS team. The 'heart' of EPOS is the metadata catalog. This provides for the ICS a digital representation of the TCS assets (services, data, software, equipment, expertise…) thus facilitating access, interoperation and (re-)use. A major part of the work has been interactions with the TCS. The original intention to harvest information from the TCS required (and still requires) discussions to understand fully the TCS organisational structures linked with rights, security and privacy; their (meta)data syntax (structure) and semantics (meaning); their workflows and methods of working and the services offered. To complicate matters further the TCS are each at varying stages of development and the ICS design has to accommodate pre-existing, developing and expected future standards for metadata, data, software and processes. Through information documents, questionnaires and interviews/meetings the EPOS ICS team has collected DDSS (Data, Data Products, Software and Services) information from the TCS. The ICS team developed a simplified metadata model for presentation to the TCS and the ICS team will perform the mapping and conversion from this model to the internal detailed technical metadata model using (CERIF: a EU recommendation to Member States maintained, developed and promoted by euroCRIS www.eurocris.org ). At the time of writing the final modifications of the EPOS metadata model are being made, and the mappings to CERIF designed, prior to the main phase of (meta)data collection into the EPOS metadata catalog. In parallel work proceeds on the user interface softsare, the APIs (Application Programming Interfaces) to the TCS services, the harvesting method and software, the AAAI (Authentication, Authorisation, Accounting Infrastructure) and the system manager. The next steps will involve interfaces to ICS-D (Distributed ICS i.e. facilities and services for computing, data storage, detectors and instruments for data collection etc.) to which requests, software and data will be deployed and from which data will be generated. Associated with this will be the development of the workflow system which will assist the end-user in building a workflow to achieve the scientific objectives.

SAHM:VisTrails (Software for Assisted Habitat Modeling for VisTrails): training course

USGS Publications Warehouse

Holcombe, Tracy

2014-01-01

VisTrails is an open-source management and scientific workflow system designed to integrate the best of both scientific workflow and scientific visualization systems. Developers can extend the functionality of the VisTrails system by creating custom modules for bundled VisTrails packages. The Invasive Species Science Branch of the U.S. Geological Survey (USGS) Fort Collins Science Center (FORT) and the U.S. Department of the Interior’s North Central Climate Science Center have teamed up to develop and implement such a module—the Software for Assisted Habitat Modeling (SAHM). SAHM expedites habitat modeling and helps maintain a record of the various input data, the steps before and after processing, and the modeling options incorporated in the construction of an ecological response model. There are four main advantages to using the SAHM:VisTrails combined package for species distribution modeling: (1) formalization and tractable recording of the entire modeling process; (2) easier collaboration through a common modeling framework; (3) a user-friendly graphical interface to manage file input, model runs, and output; and (4) extensibility to incorporate future and additional modeling routines and tools. In order to meet increased interest in the SAHM:VisTrails package, the FORT offers a training course twice a year. The course includes a combination of lecture, hands-on work, and discussion. Please join us and other ecological modelers to learn the capabilities of the SAHM:VisTrails package.

The Cloud-Based Integrated Data Viewer (IDV)

NASA Astrophysics Data System (ADS)

Fisher, Ward

2015-04-01

Maintaining software compatibility across new computing environments and the associated underlying hardware is a common problem for software engineers and scientific programmers. While there are a suite of tools and methodologies used in traditional software engineering environments to mitigate this issue, they are typically ignored by developers lacking a background in software engineering. The result is a large body of software which is simultaneously critical and difficult to maintain. Visualization software is particularly vulnerable to this problem, given the inherent dependency on particular graphics hardware and software API's. The advent of cloud computing has provided a solution to this problem, which was not previously practical on a large scale; Application Streaming. This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations, with little-to-no re-engineering required. Through application streaming we are able to bring the same visualization to a desktop, a netbook, a smartphone, and the next generation of hardware, whatever it may be. Unidata has been able to harness Application Streaming to provide a tablet-compatible version of our visualization software, the Integrated Data Viewer (IDV). This work will examine the challenges associated with adapting the IDV to an application streaming platform, and include a brief discussion of the underlying technologies involved. We will also discuss the differences between local software and software-as-a-service.

Comparing Emerging XML Based Formats from a Multi-discipline Perspective

NASA Astrophysics Data System (ADS)

Sawyer, D. M.; Reich, L. I.; Nikhinson, S.

2002-12-01

This paper analyzes the similarity and differences among several examples of an emerging generation of Scientific Data Formats that are based on XML technologies. Some of the factors evaluated include the goals of these efforts, the data models, and XML technologies used, and the maturity of currently available software. This paper then investigates the practicality of developing a single set of structural data objects and basic scientific concepts, such as units, that could be used across discipline boundaries and extended by disciplines and missions to create Scientific Data Formats for their communities. This analysis is partly based on an effort sponsored by the ESDIS office at GSFC to compare the Earth Science Markup Language (ESML) and the eXtensible Data Format( XDF), two members of this new generation of XML based Data Description Languages that have been developed by NASA funded efforts in recent years. This paper adds FITSML and potentially CDFML to the list of XML based Scientific Data Formats discussed. This paper draws heavily a Formats Evolution Process Committee (http://ssdoo.gsfc.nasa.gov/nost/fep/) draft white paper primarily developed by Lou Reich, Mike Folk and Don Sawyer to assist the Space Science community in understanding Scientific Data Formats. One of primary conclusions of that paper is that a scientific data format object model should be examined along two basic axes. The first is the complexity of the computer/mathematical data types supported and the second is the level of scientific domain specialization incorporated. This paper also discusses several of the issues that affect the decision on whether to implement a discipline or project specific Scientific Data Format as a formal extension of a general purpose Scientific Data Format or to implement the APIs independently.

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience.

PubMed

Hodge, Victoria; Jessop, Mark; Fletcher, Martyn; Weeks, Michael; Turner, Aaron; Jackson, Tom; Ingram, Colin; Smith, Leslie; Austin, Jim

2016-01-01

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met.

HPC Software Stack Testing Framework

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

Garvey, Cormac

The HPC Software stack testing framework (hpcswtest) is used in the INL Scientific Computing Department to test the basic sanity and integrity of the HPC Software stack (Compilers, MPI, Numerical libraries and Applications) and to quickly discover hard failures, and as a by-product it will indirectly check the HPC infrastructure (network, PBS and licensing servers).

Writing references and using citation management software

PubMed Central

Sungur, Mukadder Orhan; Seyhan, Tülay Özkan

2013-01-01

The correct citation of references is obligatory to gain scientific credibility, to honor the original ideas of previous authors and to avoid plagiarism. Currently, researchers can easily find, cite and store references using citation management software. In this review, two popular citation management software programs (EndNote and Mendeley) are summarized. PMID:26328132

Development of a testlet generator in re-engineering the Indonesian physics national-exams

NASA Astrophysics Data System (ADS)

Mindyarto, Budi Naini; Mardapi, Djemari; Bastari

2017-08-01

The Indonesian Physics national-exams are end-of-course summative assessments that could be utilized to support the assessment for learning in physics educations. This paper discusses the development and evaluation of a testlet generator based on a re-engineering of Indonesian physics national exams. The exam problems were dissected and decomposed into testlets revealing the deeper understanding of the underlying physical concepts by inserting a qualitative question and its scientific reasoning question. A template-based generator was built to facilitate teachers in generating testlet variants that would be more conform to students' scientific attitude development than their original simple multiple-choice formats. The testlet generator was built using open source software technologies and was evaluated focusing on the black-box testing by exploring the generator's execution, inputs and outputs. The results showed the correctly-performed functionalities of the developed testlet generator in validating inputs, generating testlet variants, and accommodating polytomous item characteristics.

An Object-Oriented Network-Centric Software Architecture for Physical Computing

NASA Astrophysics Data System (ADS)

Palmer, Richard

1997-08-01

Recent developments in object-oriented computer languages and infrastructure such as the Internet, Web browsers, and the like provide an opportunity to define a more productive computational environment for scientific programming that is based more closely on the underlying mathematics describing physics than traditional programming languages such as FORTRAN or C++. In this talk I describe an object-oriented software architecture for representing physical problems that includes classes for such common mathematical objects as geometry, boundary conditions, partial differential and integral equations, discretization and numerical solution methods, etc. In practice, a scientific program written using this architecture looks remarkably like the mathematics used to understand the problem, is typically an order of magnitude smaller than traditional FORTRAN or C++ codes, and hence easier to understand, debug, describe, etc. All objects in this architecture are ``network-enabled,'' which means that components of a software solution to a physical problem can be transparently loaded from anywhere on the Internet or other global network. The architecture is expressed as an ``API,'' or application programmers interface specification, with reference embeddings in Java, Python, and C++. A C++ class library for an early version of this API has been implemented for machines ranging from PC's to the IBM SP2, meaning that phidentical codes run on all architectures.

SCIFIO: an extensible framework to support scientific image formats.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

Representation of Serendipitous Scientific Data

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

A computer program defines and implements an innovative kind of data structure than can be used for representing information derived from serendipitous discoveries made via collection of scientific data on long exploratory spacecraft missions. Data structures capable of collecting any kind of data can easily be implemented in advance, but the task of designing a fixed and efficient data structure suitable for processing raw data into useful information and taking advantage of serendipitous scientific discovery is becoming increasingly difficult as missions go deeper into space. The present software eases the task by enabling definition of arbitrarily complex data structures that can adapt at run time as raw data are transformed into other types of information. This software runs on a variety of computers, and can be distributed in either source code or binary code form. It must be run in conjunction with any one of a number of Lisp compilers that are available commercially or as shareware. It has no specific memory requirements and depends upon the other software with which it is used. This program is implemented as a library that is called by, and becomes folded into, the other software with which it is used.

CILogon: An Integrated Identity and Access Management Platform for Science

NASA Astrophysics Data System (ADS)

Basney, J.

2016-12-01

When scientists work together, they use web sites and other software to share their ideas and data. To ensure the integrity of their work, these systems require the scientists to log in and verify that they are part of the team working on a particular science problem. Too often, the identity and access verification process is a stumbling block for the scientists. Scientific research projects are forced to invest time and effort into developing and supporting Identity and Access Management (IAM) services, distracting them from the core goals of their research collaboration. CILogon provides an IAM platform that enables scientists to work together to meet their IAM needs more effectively so they can allocate more time and effort to their core mission of scientific research. The CILogon platform enables federated identity management and collaborative organization management. Federated identity management enables researchers to use their home organization identities to access cyberinfrastructure, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to collaboration platforms (e.g., wikis, mailing lists, and domain applications). CILogon's IAM platform serves the unique needs of research collaborations, namely the need to dynamically form collaboration groups across organizations and countries, sharing access to data, instruments, compute clusters, and other resources to enable scientific discovery. CILogon provides a software-as-a-service platform to ease integration with cyberinfrastructure, while making all software components publicly available under open source licenses to enable re-use. Figure 1 illustrates the components and interfaces of this platform. CILogon has been operational since 2010 and has been used by over 7,000 researchers from more than 170 identity providers to access cyberinfrastructure including Globus, LIGO, Open Science Grid, SeedMe, and XSEDE. The "CILogon 2.0" platform, launched in 2016, adds support for virtual organization (VO) membership management, identity linking, international collaborations, and standard integration protocols, through integration with the Internet2 COmanage collaboration software.

Application of a data base management system to a finite element model

NASA Technical Reports Server (NTRS)

Rogers, J. L., Jr.

1980-01-01

In today's software market, much effort is being expended on the development of data base management systems (DBMS). Most commercially available DBMS were designed for business use. However, the need for such systems within the engineering and scientific communities is becoming apparent. A potential DBMS application that appears attractive is the handling of data for finite element engineering models. The applications of a commercially available, business-oriented DBMS to a structural engineering, finite element model is explored. The model, DBMS, an approach to using the DBMS, advantages and disadvantages are described. Plans for research on a scientific and engineering DBMS are discussed.

The Geoscience Paper of the Future: Best Practices for Documenting and Sharing Research from Data to Software to Provenance

NASA Astrophysics Data System (ADS)

Gil, Y.; Yu, X.; David, C. H.; Demir, I.; Essawy, B.; Fulweiler, R. W.; Goodall, J. L.; Karlstrom, L.; Lee, H.; Mills, H. J.; Pierce, S. A.; Pope, A.; Tzeng, M.; Villamizar, S. R.

2016-12-01

Geoscientists live in a world rich with digital data and methods, and their computational research cannot be fully captured in traditional publications. The Geoscience Paper of the Future (GPF) proposes best practices for GPF authors to make data, software, and methods openly accessible, citable, and well documented. Those best practices come from recommendations by both scholars and organizations concerning open science, reproducible publications, and digital scholarship. The publication of digital objects empowers scientists to manage their research products as valuable scientific assets in an open and transparent way that enables broader access by other scientists, students, decision makers, and the public. Improving documentation and dissemination of research will accelerate the pace of scientific discovery by improving the ability of others to build upon published work. This presentation summarizes these best practices, as well as the practical experiences of several GPF authors in different geosciences disciplines. It will also discuss existing challenges for authors and publishers to produce GPFs in practice, and the opportunities to develop new approaches and infrastructure to implement those best practices. The adoption of GPF recommendations requires awareness and social change in the scientific community, including clear communication of the benefits and best practices that may be new to geoscientists.

Science Gateways, Scientific Workflows and Open Community Software

NASA Astrophysics Data System (ADS)

Pierce, M. E.; Marru, S.

2014-12-01

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

Improvements to the APBS biomolecular solvation software suite.

PubMed

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

Summary of the ACAT Round Table Discussion: Open-source, knowledge sharing and scientific collaboration

NASA Astrophysics Data System (ADS)

Carminati, Federico; Perret-Gallix, Denis; Riemann, Tord

2014-06-01

Round table discussions are in the tradition of ACAT. This year's plenary round table discussion was devoted to questions related to the use of scientific software in High Energy Physics and beyond. The 90 minutes of discussion were lively, and quite a lot of diverse opinions were spelled out. Although the discussion was, in part, controversial, the participants agreed unanimously on several basic issues in software sharing: • The importance of having various licensing models in academic research; • The basic value of proper recognition and attribution of intellectual property, including scientific software; • The user respect for the conditions of use, including licence statements, as formulated by the author. The need of a similar discussion on the issues of data sharing was emphasized and it was recommended to cover this subject at the conference round table discussion of next ACAT. In this contribution, we summarise selected topics that were covered in the introductory talks and in the following discussion.

Scientific Use Cases for the Virtual Atomic and Molecular Data Center

NASA Astrophysics Data System (ADS)

Dubernet, M. L.; Aboudarham, J.; Ba, Y. A.; Boiziot, M.; Bottinelli, S.; Caux, E.; Endres, C.; Glorian, J. M.; Henry, F.; Lamy, L.; Le Sidaner, P.; Møller, T.; Moreau, N.; Rénié, C.; Roueff, E.; Schilke, P.; Vastel, C.; Zwoelf, C. M.

2014-12-01

VAMDC Consortium is a worldwide consortium which federates interoperable Atomic and Molecular databases through an e-science infrastructure. The contained data are of the highest scientific quality and are crucial for many applications: astrophysics, atmospheric physics, fusion, plasma and lighting technologies, health, etc. In this paper we present astrophysical scientific use cases in relation to the use of the VAMDC e-infrastructure. Those will cover very different applications such as: (i) modeling the spectra of interstellar objects using the myXCLASS software tool implemented in the Common Astronomy Software Applications package (CASA) or using the CASSIS software tool, in its stand-alone version or implemented in the Herschel Interactive Processing Environment (HIPE); (ii) the use of Virtual Observatory tools accessing VAMDC databases; (iii) the access of VAMDC from the Paris solar BASS2000 portal; (iv) the combination of tools and database from the APIS service (Auroral Planetary Imaging and Spectroscopy); (v) combination of heterogeneous data for the application to the interstellar medium from the SPECTCOL tool.

The Globus Galaxies Platform. Delivering Science Gateways as a Service

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

Madduri, Ravi; Chard, Kyle; Chard, Ryan

We use public cloud computers to host sophisticated scientific data; software is then used to transform scientific practice by enabling broad access to capabilities previously available only to the few. The primary obstacle to more widespread use of public clouds to host scientific software (‘cloud-based science gateways’) has thus far been the considerable gap between the specialized needs of science applications and the capabilities provided by cloud infrastructures. We describe here a domain-independent, cloud-based science gateway platform, the Globus Galaxies platform, which overcomes this gap by providing a set of hosted services that directly address the needs of science gatewaymore » developers. The design and implementation of this platform leverages our several years of experience with Globus Genomics, a cloud-based science gateway that has served more than 200 genomics researchers across 30 institutions. Building on that foundation, we have also implemented a platform that leverages the popular Galaxy system for application hosting and workflow execution; Globus services for data transfer, user and group management, and authentication; and a cost-aware elastic provisioning model specialized for public cloud resources. We describe here the capabilities and architecture of this platform, present six scientific domains in which we have successfully applied it, report on user experiences, and analyze the economics of our deployments. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.« less

A Tale of Two Observing Systems: Interoperability in the World of Microsoft Windows

NASA Astrophysics Data System (ADS)

Babin, B. L.; Hu, L.

2008-12-01

Louisiana Universities Marine Consortium's (LUMCON) and Dauphin Island Sea Lab's (DISL) Environmental Monitoring System provide a unified coastal ocean observing system. These two systems are mirrored to maintain autonomy while offering an integrated data sharing environment. Both systems collect data via Campbell Scientific Data loggers, store the data in Microsoft SQL servers, and disseminate the data in real- time on the World Wide Web via Microsoft Internet Information Servers and Active Server Pages (ASP). The utilization of Microsoft Windows technologies presented many challenges to these observing systems as open source tools for interoperability grow. The current open source tools often require the installation of additional software. In order to make data available through common standards formats, "home grown" software has been developed. One example of this is the development of software to generate xml files for transmission to the National Data Buoy Center (NDBC). OOSTethys partners develop, test and implement easy-to-use, open-source, OGC-compliant software., and have created a working prototype of networked, semantically interoperable, real-time data systems. Partnering with OOSTethys, we are developing a cookbook to implement OGC web services. The implementation will be written in ASP, will run in a Microsoft operating system environment, and will serve data via Sensor Observation Services (SOS). This cookbook will give observing systems running Microsoft Windows the tools to easily participate in the Open Geospatial Consortium (OGC) Oceans Interoperability Experiment (OCEANS IE).

Developing Software for NASA Missions in the New Millennia

NASA Technical Reports Server (NTRS)

Truszkowski, Walt; Rash, James; Rouff, Christopher; Hinchey, Mike

2004-01-01

NASA is working on new mission concepts for exploration of the solar system. The concepts for these missions include swarms of hundreds of cooperating intelligent spacecraft which will be able to work in teams and gather more data than current single spacecraft missions. These spacecraft will not only have to operate independently for long periods of time on their own and in teams, but will also need to have autonomic properties of self healing, self configuring, self optimizing and self protecting for them to survive in the harsh space environment. Software for these types of missions has never been developed before and represents some of the challenges of software development in the new millennia. The Autonomous Nano Technology Swarm (ANTS) mission is an example of one of the swarm missions NASA is considering. The ANTS mission will use a swarm of one thousand pico-spacecraft that weigh less than five pounds. Using an insect colony analog, ANTS will explore the asteroid belt and catalog the mass, density, morphology, and chemical composition of the asteroids. Due to the size of the spacecraft, each will only carry a single miniaturized science instrument which will require them to cooperate in searching for asteroids that are of scientific interest. This article also discusses the ANTS mission, the properties the spacecraft will need and how that will effect future software development.

A distributed analysis and visualization system for model and observational data

NASA Technical Reports Server (NTRS)

Wilhelmson, Robert B.

1994-01-01

Software was developed with NASA support to aid in the analysis and display of the massive amounts of data generated from satellites, observational field programs, and from model simulations. This software was developed in the context of the PATHFINDER (Probing ATmospHeric Flows in an Interactive and Distributed EnviRonment) Project. The overall aim of this project is to create a flexible, modular, and distributed environment for data handling, modeling simulations, data analysis, and visualization of atmospheric and fluid flows. Software completed with NASA support includes GEMPAK analysis, data handling, and display modules for which collaborators at NASA had primary responsibility, and prototype software modules for three-dimensional interactive and distributed control and display as well as data handling, for which NSCA was responsible. Overall process control was handled through a scientific and visualization application builder from Silicon Graphics known as the Iris Explorer. In addition, the GEMPAK related work (GEMVIS) was also ported to the Advanced Visualization System (AVS) application builder. Many modules were developed to enhance those already available in Iris Explorer including HDF file support, improved visualization and display, simple lattice math, and the handling of metadata through development of a new grid datatype. Complete source and runtime binaries along with on-line documentation is available via the World Wide Web at: http://redrock.ncsa.uiuc.edu/ PATHFINDER/pathre12/top/top.html.

Software Testing and Verification in Climate Model Development

NASA Technical Reports Server (NTRS)

Clune, Thomas L.; Rood, RIchard B.

2011-01-01

Over the past 30 years most climate models have grown from relatively simple representations of a few atmospheric processes to a complex multi-disciplinary system. Computer infrastructure over that period has gone from punch card mainframes to modem parallel clusters. Model implementations have become complex, brittle, and increasingly difficult to extend and maintain. Existing verification processes for model implementations rely almost exclusively upon some combination of detailed analysis of output from full climate simulations and system-level regression tests. In additional to being quite costly in terms of developer time and computing resources, these testing methodologies are limited in terms of the types of defects that can be detected, isolated and diagnosed. Mitigating these weaknesses of coarse-grained testing with finer-grained "unit" tests has been perceived as cumbersome and counter-productive. In the commercial software sector, recent advances in tools and methodology have led to a renaissance for systematic fine-grained testing. We discuss the availability of analogous tools for scientific software and examine benefits that similar testing methodologies could bring to climate modeling software. We describe the unique challenges faced when testing complex numerical algorithms and suggest techniques to minimize and/or eliminate the difficulties.

The Impact of Software Culture on the Management of Community Data

NASA Astrophysics Data System (ADS)

Collins, J. A.; Pulsifer, P. L.; Sheffield, E.; Lewis, S.; Oldenburg, J.

2013-12-01

The Exchange for Local Observations and Knowledge of the Arctic (ELOKA), a program hosted at the National Snow and Ice Data Center (NSIDC), supports the collection, curation, and distribution of Local and Traditional Knowledge (LTK) data, as well as some quantitative data products. Investigations involving LTK data often involve community participation, and therefore require flexible and robust user interfaces to support a reliable process of data collection and management. Often, investigators focused on LTK and community-based monitoring choose to use ELOKA's data services based on our ability to provide rapid proof-of-concepts and economical delivery of a usable product. To satisfy these two overarching criteria, ELOKA is experimenting with modifications to its software development culture both in terms of how the software applications are developed as well as the kind of software applications (or components) being developed. Over the past several years, NSIDC has shifted its software development culture from one of assigning individual scientific programmers to support particular principal investigators or projects, to an Agile Software Methodology implementation using Scrum practices. ELOKA has participated in this process by working with other product owners to schedule and prioritize development work which is then implemented by a team of application developers. Scrum, along with practices such as Test Driven Development (TDD) and paired programming, improves the quality of the software product delivered to the user community. To meet the need for rapid prototyping and to maximize product development and support with limited developer input, our software development efforts are now focused on creating a platform of application modules that can be quickly customized to suit the needs of a variety of LTK projects. This approach is in contrast to the strategy of delivering custom applications for individual projects. To date, we have integrated components of the Nunaliit Atlas framework (a Java/JavaScript client-server web-based application) with an existing Ruby on Rails application. This approach requires transitioning individual applications to expose a service layer, thus allowing interapplication communication via RESTful services. In this presentation we will report on our experiences using Agile Scrum practices, our efforts to move from custom solutions to a platform of customizable modules, and the impact of each on our ability to support researchers and Arctic residents in the domain of community-based observations and knowledge.

Experience Paper: Software Engineering and Community Codes Track in ATPESC

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

Dubey, Anshu; Riley, Katherine M.

Argonne Training Program in Extreme Scale Computing (ATPESC) was started by the Argonne National Laboratory with the objective of expanding the ranks of better prepared users of high performance computing (HPC) machines. One of the unique aspects of the program was inclusion of software engineering and community codes track. The inclusion was motivated by the observation that the projects with a good scientific and software process were better able to meet their scientific goals. In this paper we present our experience of running the software track from the beginning of the program until now. We discuss the motivations, the reception,more » and the evolution of the track over the years. We welcome discussion and input from the community to enhance the track in ATPESC, and also to facilitate inclusion of similar tracks in other HPC oriented training programs.« less

A Scalable, Open Source Platform for Data Processing, Archiving and Dissemination

DTIC Science & Technology

2016-01-01

Object Oriented Data Technology (OODT) big data toolkit developed by NASA and the Work-flow INstance Generation and Selection (WINGS) scientific work...to several challenge big data problems and demonstrated the utility of OODT-WINGS in addressing them. Specific demonstrated analyses address i...source software, Apache, Object Oriented Data Technology, OODT, semantic work-flows, WINGS, big data , work- flow management 16. SECURITY CLASSIFICATION OF

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.

The use of Virtual Analogy Simulation (VAS) in physics learning

NASA Astrophysics Data System (ADS)

Faizin, M. Noor; Samsudin, A.

2018-05-01

The purpose of this research is to explore the use of VAS software in electrical dynamic learning in junior high student, so as to obtain an overview of this software consistency in help students build a scientific conception. This research was administered via research and Development (R & D) with the design of embedded experimental models. The respondents which were involved in this research were 60 students of ninth grade in one of junior high schools in Kudus central java. The improving process of students’ concept is examined based on normalized gain analysis from pretest and posttest scores. The result of this research shows that there was difference between learning using conventional learning (power point software) with VAS software. VAS is more effective to assist students in understanding the electrical dynamic concept shown with N-gain of 0.36, or 36 % were included in the medium category, whereas the conventional learning with N-gain of 0.28, or 28%.

High Efficiency Traveling-Wave Tube Power Amplifier for Ka-Band Software Defined Radio on International Space Station-A Platform for Communications Technology Development

NASA Technical Reports Server (NTRS)

Simons, Rainee N.; Force, Dale A.; Kacpura, Thomas J.

2013-01-01

The design, fabrication and RF performance of the output traveling-wave tube amplifier (TWTA) for a space based Ka-band software defined radio (SDR) is presented. The TWTA, the SDR and the supporting avionics are integrated to forms a testbed, which is currently located on an exterior truss of the International Space Station (ISS). The SDR in the testbed communicates at Ka-band frequencies through a high-gain antenna directed to NASA s Tracking and Data Relay Satellite System (TDRSS), which communicates to the ground station located at White Sands Complex. The application of the testbed is for demonstrating new waveforms and software designed to enhance data delivery from scientific spacecraft and, the waveforms and software can be upgraded and reconfigured from the ground. The construction and the salient features of the Ka-band SDR are discussed. The testbed is currently undergoing on-orbit checkout and commissioning and is expected to operate for 3 to 5 years in space.

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

Virtual immunology: software for teaching basic immunology.

PubMed

Berçot, Filipe Faria; Fidalgo-Neto, Antônio Augusto; Lopes, Renato Matos; Faggioni, Thais; Alves, Luiz Anastácio

2013-01-01

As immunology continues to evolve, many educational methods have found difficulty in conveying the degree of complexity inherent in its basic principles. Today, the teaching-learning process in such areas has been improved with tools such as educational software. This article introduces "Virtual Immunology," a software program available free of charge in Portuguese and English, which can be used by teachers and students in physiology, immunology, and cellular biology classes. We discuss the development of the initial two modules: "Organs and Lymphoid Tissues" and "Inflammation" and the use of interactive activities to provide microscopic and macroscopic understanding in immunology. Students, both graduate and undergraduate, were questioned along with university level professors about the quality of the software and intuitiveness of use, facility of navigation, and aesthetic organization using a Likert scale. An overwhelmingly satisfactory result was obtained with both students and immunology teachers. Programs such as "Virtual Immunology" are offering more interactive, multimedia approaches to complex scientific principles that increase student motivation, interest, and comprehension. © 2013 by The International Union of Biochemistry and Molecular Biology.

A new background subtraction method for Western blot densitometry band quantification through image analysis software.

PubMed

Gallo-Oller, Gabriel; Ordoñez, Raquel; Dotor, Javier

2018-06-01

Since its first description, Western blot has been widely used in molecular labs. It constitutes a multistep method that allows the detection and/or quantification of proteins from simple to complex protein mixtures. Western blot quantification method constitutes a critical step in order to obtain accurate and reproducible results. Due to the technical knowledge required for densitometry analysis together with the resources availability, standard office scanners are often used for the imaging acquisition of developed Western blot films. Furthermore, the use of semi-quantitative software as ImageJ (Java-based image-processing and analysis software) is clearly increasing in different scientific fields. In this work, we describe the use of office scanner coupled with the ImageJ software together with a new image background subtraction method for accurate Western blot quantification. The proposed method represents an affordable, accurate and reproducible approximation that could be used in the presence of limited resources availability. Copyright © 2018 Elsevier B.V. All rights reserved.

IBM techexplorer and MathML: Interactive Multimodal Scientific Documents

NASA Astrophysics Data System (ADS)

Diaz, Angel

2001-06-01

The World Wide Web provides a standard publishing platform for disseminating scientific and technical articles, books, journals, courseware, or even homework on the internet; however, the transition from paper to web-based interactive content has brought new opportunities for creating interactive content. Students, scientists, and engineers are now faced with the task of rendering the 2D presentational structure of mathematics, harnessing the wealth of scientific and technical software, and creating truly accessible scientific portals across international boundaries and markets. The recent emergence of World Wide Web Consortium (W3C) standards such as the Mathematical Markup Language (MathML), Language (XSL), and Aural CSS (ACSS) provide a foundation whereby mathematics can be displayed, enlivened, computed, and audio formatted. With interoperability ensured by standards, software applications can be easily brought together to create extensible and interactive scientific content. In this presentation we will provide an overview of the IBM techexplorer Hypermedia Browser, a web browser plug-in and ActiveX control aimed at bringing interactive mathematics to the masses across platforms and applications. We will demonstrate "live" mathematics where documents that contain MathML expressions can be edited and computed right inside your favorite web browser. This demonstration will be generalized as we show how MathML can be used to enliven even PowerPoint presentations. Finally, we will close the loop by demonstrating a novel approach to spoken mathematics based on MathML, DOM, XSL, ACSS, techexplorer, and IBM ViaVoice. By making use of techexplorer as the glue that binds the rendered content to the web browser, the back-end computation software, the Java applets that augment the exposition, and voice-rendering systems such as ViaVoice, authors can indeed create truly extensible and interactive scientific content. For more information see: [http://www.software.ibm.com/techexplorer] [http://www.alphaworks.ibm.com] [http://www.w3.org

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

Space astronomy for the mid-21st century: Robotically maintained space telescopes

NASA Astrophysics Data System (ADS)

Schartel, N.

2012-04-01

The historical development of ground based astronomical telescopes leads us to expect that space-based astronomical telescopes will need to be operational for many decades. The exchange of scientific instruments in space will be a prerequisite for the long lasting scientific success of such missions. Operationally, the possibility to repair or replace key spacecraft components in space will be mandatory. We argue that these requirements can be fulfilled with robotic missions and see the development of the required engineering as the main challenge. Ground based operations, scientifically and technically, will require a low operational budget of the running costs. These can be achieved through enhanced autonomy of the spacecraft and mission independent concepts for the support of the software. This concept can be applied to areas where the mirror capabilities do not constrain the lifetime of the mission. Online material is available at the CDS via http://cdsarc.u-strasbg.fr/cgi-bin/qcat?J/AN/333/209

Inspiring Collaboration: The Legacy of Theo Colborn's Transdisciplinary Research on Fracking.

PubMed

Wylie, Sara; Schultz, Kim; Thomas, Deborah; Kassotis, Chris; Nagel, Susan

2016-09-13

This article describes Dr Theo Colborn's legacy of inspiring complementary and synergistic environmental health research and advocacy. Colborn, a founder of endocrine disruption research, also stimulated study of hydraulic fracturing (fracking). In 2014, the United States led the world in oil and gas production, with fifteen million Americans living within one mile of an oil or gas well. Colborn pioneered efforts to understand and control the impacts of this sea change in energy production. In 2005, her research organization The Endocrine Disruption Exchange (TEDX) developed a database of chemicals used in natural gas extraction and their health effects. This database stimulated novel scientific and social scientific research and informed advocacy by (1) connecting communities' diverse health impacts to chemicals used in natural gas development, (2) inspiring social science research on open-source software and hardware for citizen science, and (3) posing new scientific questions about the endocrine-disrupting properties of fracking chemicals. © The Author(s) 2016.

An object-oriented programming system for the integration of internet-based bioinformatics resources.

PubMed

Beveridge, Allan

2006-01-01

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.

A Study of Cloud Radiative Forcing and Feedback

NASA Technical Reports Server (NTRS)

Ramanathan, Veerabhadran

2000-01-01

The main objective of the grant proposal was to participate in the CERES (Cloud and Earth's Radiant Energy System) Satellite experiment and perform interdisciplinary investigation of NASA's Earth Observing System (EOS). During the grant period, massive amounts of scientific data from diverse platforms have been accessed, processed and archived for continuing use; several software packages have been developed for integration of different data streams for performing scientific evaluation; extensive validation studies planned have been completed culminating in the development of important algorithms that are being used presently in the operational production of data from the CERES. Contributions to the inter-disciplinary science investigations have been significantly more than originally envisioned. The results of these studies have appeared in several refereed journals and conference proceedings. They are listed at the end of this report.

Guidance, Navigation, and Control Technology Assessment for Future Planetary Science Missions

NASA Technical Reports Server (NTRS)

Beauchamp, Pat; Cutts, James; Quadrelli, Marco B.; Wood, Lincoln J.; Riedel, Joseph E.; McHenry, Mike; Aung, MiMi; Cangahuala, Laureano A.; Volpe, Rich

2013-01-01

Future planetary explorations envisioned by the National Research Council's (NRC's) report titled Vision and Voyages for Planetary Science in the Decade 2013-2022, developed for NASA Science Mission Directorate (SMD) Planetary Science Division (PSD), seek to reach targets of broad scientific interest across the solar system. This goal requires new capabilities such as innovative interplanetary trajectories, precision landing, operation in close proximity to targets, precision pointing, multiple collaborating spacecraft, multiple target tours, and advanced robotic surface exploration. Advancements in Guidance, Navigation, and Control (GN&C) and Mission Design in the areas of software, algorithm development and sensors will be necessary to accomplish these future missions. This paper summarizes the key GN&C and mission design capabilities and technologies needed for future missions pursuing SMD PSD's scientific goals.

Reusable Software Technology

NASA Technical Reports Server (NTRS)

Morgan, Timothy E.

1995-01-01

The objective of the Reusable Software System (RSS) is to provide NASA Langley Research Center and its contractor personnel with a reusable software technology through the Internet. The RSS is easily accessible, provides information that is extractable, and the capability to submit information or data for the purpose of scientific research at NASA Langley Research Center within the Atmospheric Science Division.

Building Student Proficiency with Scientific Literature Using the Zotero Reference Manager Platform

ERIC Educational Resources Information Center

Kim, Thomas

2011-01-01

While mastery of the scientific literature is a strongly desirable trait for undergraduate students, the sheer volume of the current literature has complicated the challenge of teaching scientific literacy. Part of the response to this ever-increasing volume of resources includes formal instruction in the use of reference manager software while…

National policies for technical change: Where are the increasing returns to economic research?

PubMed Central

Pavitt, Keith

1996-01-01

Improvements over the past 30 years in statistical data, analysis, and related theory have strengthened the basis for science and technology policy by confirming the importance of technical change in national economic performance. But two important features of scientific and technological activities in the Organization for Economic Cooperation and Development countries are still not addressed adequately in mainstream economics: (i) the justification of public funding for basic research and (ii) persistent international differences in investment in research and development and related activities. In addition, one major gap is now emerging in our systems of empirical measurement—the development of software technology, especially in the service sector. There are therefore dangers of diminishing returns to the usefulness of economic research, which continues to rely completely on established theory and established statistical sources. Alternative propositions that deserve serious consideration are: (i) the economic usefulness of basic research is in the provision of (mainly tacit) skills rather than codified and applicable information; (ii) in developing and exploiting technological opportunities, institutional competencies are just as important as the incentive structures that they face; and (iii) software technology developed in traditional service sectors may now be a more important locus of technical change than software technology developed in “high-tech” manufacturing. PMID:8917481

Computer networks for financial activity management, control and statistics of databases of economic administration at the Joint Institute for Nuclear Research

NASA Astrophysics Data System (ADS)

Tyupikova, T. V.; Samoilov, V. N.

2003-04-01

Modern information technologies urge natural sciences to further development. But it comes together with evaluation of infrastructures, to spotlight favorable conditions for the development of science and financial base in order to prove and protect legally new research. Any scientific development entails accounting and legal protection. In the report, we consider a new direction in software, organization and control of common databases on the example of the electronic document handling, which functions in some departments of the Joint Institute for Nuclear Research.

Astronomy Aid

NASA Technical Reports Server (NTRS)

1995-01-01

As a Jet Propulsion Laboratory astronomer, John D. Callahan developed a computer program called Multimission Interactive Planner (MIP) to help astronomers analyze scientific and optical data collected on the Voyager's Grand Tour. The commercial version of the program called XonVu is published by XonTech, Inc. Callahan has since developed two more advanced programs based on MIP technology, Grand Tour and Jovian Traveler, which simulate Voyager and Giotto missions. The software allows astronomers and space novices to view the objects seen by the spacecraft, manipulating perspective, distance and field of vision.

BRAVO (Brazilian Astrophysical Virtual Observatory): data mining development

NASA Astrophysics Data System (ADS)

De Carvalho, R. R.; Capelato, H. V.; Velho, H. C.

2007-08-01

The primary goal of the BRAVO project is to generate investment in information technology, with particular emphasis on datamining and statistical analysis. From a scientific standpoint, the participants assembled to date are engaged in several scientific projects in various fields of cosmology, astrophysics, and data analysis, with significant contributions from international partners. These scientists conduct research on clusters of galaxies, small groups of galaxies, elliptical galaxies, population synthesis, N-body simulations, and a variety of studies in stellar astrophysics. One of the main aspects of this project is the incorporation of these disparate areas of astrophysical research within the context of the coherent development of database technology.Observational cosmology is one of the branches of science experiencing the largest growth in the past few decades. large photometric and spectroscopic surveys have been carried out in both hemispheres. As a result, an extraordinary amount of data in all portions of the electromagnetic spectrum exists, but without standard techniques for storage and distribution. This project will utilize several specific astronomical databases, created to store data generated by several instruments (including SOAR, Gemini, BDA, etc), uniting them within a common framework and with standard interfaces. We are inviting members of the entire Brazilian astronomical community to partake in this effort. This will certainly impact both education and outreach efforts, as well as the future development of astrophysical research. Finally, this project will provide a constant investment in human resources. First, it will do so by stimulating ongoing short technical visits to Johns Hopkins University and Caltech. These will allow us to bring software technology and expertise in datamining back to Brazil. Second, we will organize the Summer School on Software Technology in Astrophysics, which will be designed to ensure that the Brazilian scientific community can take full advantage of the benefits offered by the VO project

High performance computing and communications: Advancing the frontiers of information technology

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

NONE

1997-12-31

This report, which supplements the President`s Fiscal Year 1997 Budget, describes the interagency High Performance Computing and Communications (HPCC) Program. The HPCC Program will celebrate its fifth anniversary in October 1996 with an impressive array of accomplishments to its credit. Over its five-year history, the HPCC Program has focused on developing high performance computing and communications technologies that can be applied to computation-intensive applications. Major highlights for FY 1996: (1) High performance computing systems enable practical solutions to complex problems with accuracies not possible five years ago; (2) HPCC-funded research in very large scale networking techniques has been instrumental inmore » the evolution of the Internet, which continues exponential growth in size, speed, and availability of information; (3) The combination of hardware capability measured in gigaflop/s, networking technology measured in gigabit/s, and new computational science techniques for modeling phenomena has demonstrated that very large scale accurate scientific calculations can be executed across heterogeneous parallel processing systems located thousands of miles apart; (4) Federal investments in HPCC software R and D support researchers who pioneered the development of parallel languages and compilers, high performance mathematical, engineering, and scientific libraries, and software tools--technologies that allow scientists to use powerful parallel systems to focus on Federal agency mission applications; and (5) HPCC support for virtual environments has enabled the development of immersive technologies, where researchers can explore and manipulate multi-dimensional scientific and engineering problems. Educational programs fostered by the HPCC Program have brought into classrooms new science and engineering curricula designed to teach computational science. This document contains a small sample of the significant HPCC Program accomplishments in FY 1996.« less

Adaptation of XMM-Newton SAS to GRID and VO architectures via web

NASA Astrophysics Data System (ADS)

Ibarra, A.; de La Calle, I.; Gabriel, C.; Salgado, J.; Osuna, P.

2008-10-01

The XMM-Newton Scientific Analysis Software (SAS) is a robust software that has allowed users to produce good scientific results since the beginning of the mission. This has been possible given the SAS capability to evolve with the advent of new technologies and adapt to the needs of the scientific community. The prototype of the Remote Interface for Science Analysis (RISA) presented here, is one such example, which provides remote analysis of XMM-Newton data with access to all the existing SAS functionality, while making use of GRID computing technology. This new technology has recently emerged within the astrophysical community to tackle the ever lasting problem of computer power for the reduction of large amounts of data.

OMPC: an Open-Source MATLAB®-to-Python Compiler

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

Combinatorial Algorithms to Enable Computational Science and Engineering: Work from the CSCAPES Institute

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

Boman, Erik G.; Catalyurek, Umit V.; Chevalier, Cedric

2015-01-16

This final progress report summarizes the work accomplished at the Combinatorial Scientific Computing and Petascale Simulations Institute. We developed Zoltan, a parallel mesh partitioning library that made use of accurate hypergraph models to provide load balancing in mesh-based computations. We developed several graph coloring algorithms for computing Jacobian and Hessian matrices and organized them into a software package called ColPack. We developed parallel algorithms for graph coloring and graph matching problems, and also designed multi-scale graph algorithms. Three PhD students graduated, six more are continuing their PhD studies, and four postdoctoral scholars were advised. Six of these students and Fellowsmore » have joined DOE Labs (Sandia, Berkeley), as staff scientists or as postdoctoral scientists. We also organized the SIAM Workshop on Combinatorial Scientific Computing (CSC) in 2007, 2009, and 2011 to continue to foster the CSC community.« less

Computer sciences

NASA Technical Reports Server (NTRS)

Smith, Paul H.

1988-01-01

The Computer Science Program provides advanced concepts, techniques, system architectures, algorithms, and software for both space and aeronautics information sciences and computer systems. The overall goal is to provide the technical foundation within NASA for the advancement of computing technology in aerospace applications. The research program is improving the state of knowledge of fundamental aerospace computing principles and advancing computing technology in space applications such as software engineering and information extraction from data collected by scientific instruments in space. The program includes the development of special algorithms and techniques to exploit the computing power provided by high performance parallel processors and special purpose architectures. Research is being conducted in the fundamentals of data base logic and improvement techniques for producing reliable computing systems.

Grid Stability Awareness System (GSAS) Final Scientific/Technical Report

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

Feuerborn, Scott; Ma, Jian; Black, Clifton

The project team developed a software suite named Grid Stability Awareness System (GSAS) for power system near real-time stability monitoring and analysis based on synchrophasor measurement. The software suite consists of five analytical tools: an oscillation monitoring tool, a voltage stability monitoring tool, a transient instability monitoring tool, an angle difference monitoring tool, and an event detection tool. These tools have been integrated into one framework to provide power grid operators with both real-time or near real-time stability status of a power grid and historical information about system stability status. These tools are being considered for real-time use in themore » operation environment.« less

Research on Safety Monitoring System of Tailings Dam Based on Internet of Things

NASA Astrophysics Data System (ADS)

Wang, Ligang; Yang, Xiaocong; He, Manchao

2018-03-01

The paper designed and implemented the safety monitoring system of tailings dam based on Internet of things, completed the hardware and software design of sensor nodes, routing nodes and coordinator node by using ZigBee wireless sensor chip CC2630 and 3G/4G data transmission module, developed the software platform integrated with geographic information system. The paper achieved real-time monitoring and data collection of tailings dam dam deformation, seepage line, water level and rainfall for all-weather, the stability of tailings dam based on the Internet of things monitoring is analyzed, and realized intelligent and scientific management of tailings dam under the guidance of the remote expert system.

Transdisciplinary integration and interfacing software in mechatronic system for carbon sequestration and harvesting energy in the agricultural soils for rewarding farmers through green certificates

NASA Astrophysics Data System (ADS)

Pop, P. P.; Pop-Vadean, A.; Barz, C.; Latinovic, T.

2017-01-01

In this article we will present a transdisciplinary approach to carbon sequestration in agricultural soils. The software provides a method proposed to measure the amount of carbon that can be captured from different soil types and different crop. The application has integrated an intuitive interface, is portable and calculate the number of green certificates as a reward for farmers financial support for environmental protection. We plan to initiate a scientific approach to environmental protection through financial incentives for agriculture fits in EU rules by taxing big polluters and rewarding those who maintain a suitable environment for the development of ecological and competitive agriculture.

Application of SLURM, BOINC, and GlusterFS as Software System for Sustainable Modeling and Data Analytics

NASA Astrophysics Data System (ADS)

Kashansky, Vladislav V.; Kaftannikov, Igor L.

2018-02-01

Modern numerical modeling experiments and data analytics problems in various fields of science and technology reveal a wide variety of serious requirements for distributed computing systems. Many scientific computing projects sometimes exceed the available resource pool limits, requiring extra scalability and sustainability. In this paper we share the experience and findings of our own on combining the power of SLURM, BOINC and GlusterFS as software system for scientific computing. Especially, we suggest a complete architecture and highlight important aspects of systems integration.

The Common Data Acquisition Platform in the Helmholtz Association

NASA Astrophysics Data System (ADS)

Kaever, P.; Balzer, M.; Kopmann, A.; Zimmer, M.; Rongen, H.

2017-04-01

Various centres of the German Helmholtz Association (HGF) started in 2012 to develop a modular data acquisition (DAQ) platform, covering the entire range from detector readout to data transfer into parallel computing environments. This platform integrates generic hardware components like the multi-purpose HGF-Advanced Mezzanine Card or a smart scientific camera framework, adding user value with Linux drivers and board support packages. Technically the scope comprises the DAQ-chain from FPGA-modules to computing servers, notably frontend-electronics-interfaces, microcontrollers and GPUs with their software plus high-performance data transmission links. The core idea is a generic and component-based approach, enabling the implementation of specific experiment requirements with low effort. This so called DTS-platform will support standards like MTCA.4 in hard- and software to ensure compatibility with commercial components. Its capability to deploy on other crate standards or FPGA-boards with PCI express or Ethernet interfaces remains an essential feature. Competences of the participating centres are coordinated in order to provide a solid technological basis for both research topics in the Helmholtz Programme ``Matter and Technology'': ``Detector Technology and Systems'' and ``Accelerator Research and Development''. The DTS-platform aims at reducing costs and development time and will ensure access to latest technologies for the collaboration. Due to its flexible approach, it has the potential to be applied in other scientific programs.

Reusable Rack Interface Controller Common Software for Various Science Research Racks on the International Space Station

NASA Technical Reports Server (NTRS)

Lu, George C.

2003-01-01

The purpose of the EXPRESS (Expedite the PRocessing of Experiments to Space Station) rack project is to provide a set of predefined interfaces for scientific payloads which allow rapid integration into a payload rack on International Space Station (ISS). VxWorks' was selected as the operating system for the rack and payload resource controller, primarily based on the proliferation of VME (Versa Module Eurocard) products. These products provide needed flexibility for future hardware upgrades to meet everchanging science research rack configuration requirements. On the International Space Station, there are multiple science research rack configurations, including: 1) Human Research Facility (HRF); 2) EXPRESS ARIS (Active Rack Isolation System); 3) WORF (Window Observational Research Facility); and 4) HHR (Habitat Holding Rack). The RIC (Rack Interface Controller) connects payloads to the ISS bus architecture for data transfer between the payload and ground control. The RIC is a general purpose embedded computer which supports multiple communication protocols, including fiber optic communication buses, Ethernet buses, EIA-422, Mil-Std-1553 buses, SMPTE (Society Motion Picture Television Engineers)-170M video, and audio interfaces to payloads and the ISS. As a cost saving and software reliability strategy, the Boeing Payload Software Organization developed reusable common software where appropriate. These reusable modules included a set of low-level driver software interfaces to 1553B. RS232, RS422, Ethernet buses, HRDL (High Rate Data Link), video switch functionality, telemetry processing, and executive software hosted on the FUC computer. These drivers formed the basis for software development of the HRF, EXPRESS, EXPRESS ARIS, WORF, and HHR RIC executable modules. The reusable RIC common software has provided extensive benefits, including: 1) Significant reduction in development flow time; 2) Minimal rework and maintenance; 3) Improved reliability; and 4) Overall reduction in software life cycle cost. Due to the limited number of crew hours available on ISS for science research, operational efficiency is a critical customer concern. The current method of upgrading RIC software is a time consuming process; thus, an improved methodology for uploading RIC software is currently under evaluation.

Software Framework for Controlling Unsupervised Scientific Instruments.

PubMed

Schmid, Benjamin; Jahr, Wiebke; Weber, Michael; Huisken, Jan

2016-01-01

Science outreach and communication are gaining more and more importance for conveying the meaning of today's research to the general public. Public exhibitions of scientific instruments can provide hands-on experience with technical advances and their applications in the life sciences. The software of such devices, however, is oftentimes not appropriate for this purpose. In this study, we describe a software framework and the necessary computer configuration that is well suited for exposing a complex self-built and software-controlled instrument such as a microscope to laymen under limited supervision, e.g. in museums or schools. We identify several aspects that must be met by such software, and we describe a design that can simultaneously be used to control either (i) a fully functional instrument in a robust and fail-safe manner, (ii) an instrument that has low-cost or only partially working hardware attached for illustration purposes or (iii) a completely virtual instrument without hardware attached. We describe how to assess the educational success of such a device, how to monitor its operation and how to facilitate its maintenance. The introduced concepts are illustrated using our software to control eduSPIM, a fluorescent light sheet microscope that we are currently exhibiting in a technical museum.

Software for the EVLA

NASA Astrophysics Data System (ADS)

Butler, Bryan J.; van Moorsel, Gustaaf; Tody, Doug

2004-09-01

The Expanded Very Large Array (EVLA) project is the next generation instrument for high resolution long-millimeter to short-meter wavelength radio astronomy. It is currently funded by NSF, with completion scheduled for 2012. The EVLA will upgrade the VLA with new feeds, receivers, data transmission hardware, correlator, and a new software system to enable the instrument to achieve its full potential. This software includes both that required for controlling and monitoring the instrument and that involved with the scientific dataflow. We concentrate here on a portion of the dataflow software, including: proposal preparation, submission, and handling; observation preparation, scheduling, and remote monitoring; data archiving; and data post-processing, including both automated (pipeline) and manual processing. The primary goals of the software are: to maximize the scientific return of the EVLA; provide ease of use, for both novices and experts; exploit commonality amongst all NRAO telescopes where possible. This last point is both a bane and a blessing: we are not at liberty to do whatever we want in the software, but on the other hand we may borrow from other projects (notably ALMA and GBT) where appropriate. The software design methodology includes detailed initial use-cases and requirements from the scientists, intimate interaction between the scientists and the programmers during design and implementation, and a thorough testing and acceptance plan.

Labview Interface Concepts Used in NASA Scientific Investigations and Virtual Instruments

NASA Technical Reports Server (NTRS)

Roth, Don J.; Parker, Bradford H.; Rapchun, David A.; Jones, Hollis H.; Cao, Wei

2001-01-01

This article provides an overview of several software control applications developed for NASA using LabVIEW. The applications covered here include (1) an Ultrasonic Measurement System for nondestructive evaluation of advanced structural materials, an Xray Spectral Mapping System for characterizing the quality and uniformity of developing photon detector materials, (2) a Life Testing System for these same materials, (3) and the instrument panel for an aircraft mounted Cloud Absorption Radiometer that measures the light scattered by clouds in multiple spectral bands. Many of the software interface concepts employed are explained. Panel layout and block diagram (code) strategies for each application are described. In particular, some of the more unique features of the applications' interfaces and source code are highlighted. This article assumes that the reader has a beginner-to-intermediate understanding of LabVIEW methods.

Development of Self-made LSM Software using in Neuroscience

NASA Astrophysics Data System (ADS)

Doronin, Maxim; Makovkin, Sergey; Popov, Alexander

2017-07-01

One of the main and modern visualization method in neuroscience is two-photon microscopy. However, scientists need to upgrade their microscopy system so regular because they are interested to get more specific data. Self-developed microscopy system allows to modify the construction of microscope in not-complicated manner depending on specialized experimental models and scientific tasks. Earlier we reported about building of self-made laser scanning microscope (LSM) using in neuroscience both for in vivo and in vitro experiments. Here we will report how to create software AMAScan for LSM controlling in MATLAB. The work was performed with financial support of the government represented by the Ministry of Education and Science of the Russian Federation, the unique identifier of the project is RFMEFI58115X0016, the agreement on granting a subsidy №14.581.21.0016 dated 14.10.2015.

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

NASA Astrophysics Data System (ADS)

Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

2017-10-01

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks. Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.

Enhanced Training for Cyber Situational Awareness in Red versus Blue Team Exercises

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

Carbajal, Armida J.; Stevens-Adams, Susan Marie; Silva, Austin Ray

This report summarizes research conducted through the Sandia National Laboratories Enhanced Training for Cyber Situational Awareness in Red Versus Blue Team Exercises Laboratory Directed Research and Development project. The objective of this project was to advance scientific understanding concerning how to best structure training for cyber defenders. Two modes of training were considered. The baseline training condition (Tool-Based training) was based on current practices where classroom instruction focuses on the functions of a software tool with various exercises in which students apply those functions. In the second training condition (Narrative-Based training), classroom instruction addressed software functions, but in the contextmore » of adversary tactics and techniques. It was hypothesized that students receiving narrative-based training would gain a deeper conceptual understanding of the software tools and this would be reflected in better performance within a red versus blue team exercise.« less

Interactive graphics for the Macintosh: software review of FlexiGraphs.

PubMed

Antonak, R F

1990-01-01

While this product is clearly unique, its usefulness to individuals outside small business environments is somewhat limited. FlexiGraphs is, however, a reasonable first attempt to design a microcomputer software package that controls data through interactive editing within a graph. Although the graphics capabilities of mainframe programs such as MINITAB (Ryan, Joiner, & Ryan, 1981) and the graphic manipulations available through exploratory data analysis (e.g., Velleman & Hoaglin, 1981) will not be surpassed anytime soon by this program, a researcher may want to add this program to a software library containing other Macintosh statistics, drawing, and graphics programs if only to obtain the easy-to-obtain curve fitting and line smoothing options. I welcome the opportunity to review the enhanced "scientific" version of FlexiGraphs that the author of the program indicates is currently under development. An MS-DOS version of the program should be available within the year.

Security Risks of Cloud Computing and Its Emergence as 5th Utility Service

NASA Astrophysics Data System (ADS)

Ahmad, Mushtaq

Cloud Computing is being projected by the major cloud services provider IT companies such as IBM, Google, Yahoo, Amazon and others as fifth utility where clients will have access for processing those applications and or software projects which need very high processing speed for compute intensive and huge data capacity for scientific, engineering research problems and also e- business and data content network applications. These services for different types of clients are provided under DASM-Direct Access Service Management based on virtualization of hardware, software and very high bandwidth Internet (Web 2.0) communication. The paper reviews these developments for Cloud Computing and Hardware/Software configuration of the cloud paradigm. The paper also examines the vital aspects of security risks projected by IT Industry experts, cloud clients. The paper also highlights the cloud provider's response to cloud security risks.

Preliminary design of the HARMONI science software

NASA Astrophysics Data System (ADS)

Piqueras, Laure; Jarno, Aurelien; Pécontal-Rousset, Arlette; Loupias, Magali; Richard, Johan; Schwartz, Noah; Fusco, Thierry; Sauvage, Jean-François; Neichel, Benoît; Correia, Carlos M.

2016-08-01

This paper introduces the science software of HARMONI. The Instrument Numerical Model simulates the instrument from the optical point of view and provides synthetic exposures simulating detector readouts from data-cubes containing astrophysical scenes. The Data Reduction Software converts raw-data frames into a fully calibrated, scientifically usable data cube. We present the functionalities and the preliminary design of this software, describe some of the methods and algorithms used and highlight the challenges that we will have to face.

SpectraCAM SPM: a camera system with high dynamic range for scientific and medical applications

NASA Astrophysics Data System (ADS)

Bhaskaran, S.; Baiko, D.; Lungu, G.; Pilon, M.; VanGorden, S.

2005-08-01

A scientific camera system having high dynamic range designed and manufactured by Thermo Electron for scientific and medical applications is presented. The newly developed CID820 image sensor with preamplifier-per-pixel technology is employed in this camera system. The 4 Mega-pixel imaging sensor has a raw dynamic range of 82dB. Each high-transparent pixel is based on a preamplifier-per-pixel architecture and contains two photogates for non-destructive readout of the photon-generated charge (NDRO). Readout is achieved via parallel row processing with on-chip correlated double sampling (CDS). The imager is capable of true random pixel access with a maximum operating speed of 4MHz. The camera controller consists of a custom camera signal processor (CSP) with an integrated 16-bit A/D converter and a PowerPC-based CPU running a Linux embedded operating system. The imager is cooled to -40C via three-stage cooler to minimize dark current. The camera housing is sealed and is designed to maintain the CID820 imager in the evacuated chamber for at least 5 years. Thermo Electron has also developed custom software and firmware to drive the SpectraCAM SPM camera. Included in this firmware package is the new Extreme DRTM algorithm that is designed to extend the effective dynamic range of the camera by several orders of magnitude up to 32-bit dynamic range. The RACID Exposure graphical user interface image analysis software runs on a standard PC that is connected to the camera via Gigabit Ethernet.

Data archiving and serving system implementation in CLEP's GRAS Core System

NASA Astrophysics Data System (ADS)

Zuo, Wei; Zeng, Xingguo; Zhang, Zhoubin; Geng, Liang; Li, Chunlai

2017-04-01

The Ground Research & Applications System(GRAS) is one of the five systems of China's Lunar Exploration Project(CLEP), it is responsible for data acquisition, processing, management and application, and it is also the operation control center during satellite in-orbit and payload operation management. Chang'E-1, Chang'E-2 and Chang'E-3 have collected abundant lunar exploration data. The aim of this work is to present the implementation of data archiving and Serving in CLEP's GRAS Core System software. This first approach provides a client side API and server side software allowing the creation of a simplified version of CLEPDB data archiving software, and implements all required elements to complete data archiving flow from data acquisition until its persistent storage technology. The client side includes all necessary components that run on devices that acquire or produce data, distributing and streaming to configure remote archiving servers. The server side comprises an archiving service that stores into PDS files all received data. The archiving solution aims at storing data coming for the Data Acquisition Subsystem, the Operation Management Subsystem, the Data Preprocessing Subsystem and the Scientific Application & Research Subsystem. The serving solution aims at serving data for the various business systems, scientific researchers and public users. The data-driven and component clustering methods was adopted in this system, the former is used to solve real-time data archiving and data persistence services; the latter is used to keep the continuous supporting ability of archive and service to new data from Chang'E Mission. Meanwhile, it can save software development cost as well.

ANL statement of site strategy for computing workstations

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

Fenske, K.R.; Boxberger, L.M.; Amiot, L.W.

1991-11-01

This Statement of Site Strategy describes the procedure at Argonne National Laboratory for defining, acquiring, using, and evaluating scientific and office workstations and related equipment and software in accord with DOE Order 1360.1A (5-30-85), and Laboratory policy. It is Laboratory policy to promote the installation and use of computing workstations to improve productivity and communications for both programmatic and support personnel, to ensure that computing workstations acquisitions meet the expressed need in a cost-effective manner, and to ensure that acquisitions of computing workstations are in accord with Laboratory and DOE policies. The overall computing site strategy at ANL is tomore » develop a hierarchy of integrated computing system resources to address the current and future computing needs of the laboratory. The major system components of this hierarchical strategy are: Supercomputers, Parallel computers, Centralized general purpose computers, Distributed multipurpose minicomputers, and Computing workstations and office automation support systems. Computing workstations include personal computers, scientific and engineering workstations, computer terminals, microcomputers, word processing and office automation electronic workstations, and associated software and peripheral devices costing less than $25,000 per item.« less

Strengthening Software Authentication with the ROSE Software Suite

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

White, G

2006-06-15

Many recent nonproliferation and arms control software projects include a software authentication regime. These include U.S. Government-sponsored projects both in the United States and in the Russian Federation (RF). This trend toward requiring software authentication is only accelerating. Demonstrating assurance that software performs as expected without hidden ''backdoors'' is crucial to a project's success. In this context, ''authentication'' is defined as determining that a software package performs only its intended purpose and performs said purpose correctly and reliably over the planned duration of an agreement. In addition to visual inspections by knowledgeable computer scientists, automated tools are needed to highlightmore » suspicious code constructs, both to aid visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary and not extensible. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool has to be based on a complete language compiler. ROSE is precisely such a compiler infrastructure developed within the Department of Energy (DOE) and targeted at the optimization of scientific applications and user-defined libraries within large-scale applications (typically applications of a million lines of code). ROSE is a robust, source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C and C++ (handling the full C, C99, C++ languages and with current collaborations to support Fortran90). We propose to extend ROSE to address a number of security-specific requirements, and apply it to software authentication for nonproliferation and arms control projects.« less

Identification of New Potential Scientific and Technology Areas for DoD Application. Summary of Activities

DTIC Science & Technology

1986-07-31

designer will be able to more rapid- ly assemble a total software package from perfected modules that can be easily de - bugged or replaced with more...antinuclear interactions e. gravitational effects of antimatter 2. possible machine parameters and lattice design 3. electron and stochastic cooling needs 4...implementation, reliability requirements; development of design environments and of experimental methodology; technology transfer methods from

Theoretical and experimental fundamentals of designing promising technological equipment to improve efficiency and environmental safety of highly viscous oil recovery from deep oil reservoirs

NASA Astrophysics Data System (ADS)

Moiseyev, V. A.; Nazarov, V. P.; Zhuravlev, V. Y.; Zhuykov, D. A.; Kubrikov, M. V.; Klokotov, Y. N.

2016-12-01

The development of new technological equipment for the implementation of highly effective methods of recovering highly viscous oil from deep reservoirs is an important scientific and technical challenge. Thermal recovery methods are promising approaches to solving the problem. It is necessary to carry out theoretical and experimental research aimed at developing oil-well tubing (OWT) with composite heatinsulating coatings on the basis of basalt and glass fibers. We used the method of finite element analysis in Nastran software, which implements complex scientific and engineering calculations, including the calculation of the stress-strain state of mechanical systems, the solution of problems of heat transfer, the study of nonlinear static, the dynamic transient analysis of frequency characteristics, etc. As a result, we obtained a mathematical model of thermal conductivity which describes the steady-state temperature and changes in the fibrous highly porous material with the heat loss by Stefan-Boltzmann's radiation. It has been performed for the first time using the method of computer modeling in Nastran software environments. The results give grounds for further implementation of the real design of the OWT when implementing thermal methods for increasing the rates of oil production and mitigating environmental impacts.

Scientific Assistant Virtual Laboratory (SAVL)

NASA Astrophysics Data System (ADS)

Alaghband, Gita; Fardi, Hamid; Gnabasik, David

2007-03-01

The Scientific Assistant Virtual Laboratory (SAVL) is a scientific discovery environment, an interactive simulated virtual laboratory, for learning physics and mathematics. The purpose of this computer-assisted intervention is to improve middle and high school student interest, insight and scores in physics and mathematics. SAVL develops scientific and mathematical imagination in a visual, symbolic, and experimental simulation environment. It directly addresses the issues of scientific and technological competency by providing critical thinking training through integrated modules. This on-going research provides a virtual laboratory environment in which the student directs the building of the experiment rather than observing a packaged simulation. SAVL: * Engages the persistent interest of young minds in physics and math by visually linking simulation objects and events with mathematical relations. * Teaches integrated concepts by the hands-on exploration and focused visualization of classic physics experiments within software. * Systematically and uniformly assesses and scores students by their ability to answer their own questions within the context of a Master Question Network. We will demonstrate how the Master Question Network uses polymorphic interfaces and C# lambda expressions to manage simulation objects.

Computational Science in Armenia (Invited Talk)

NASA Astrophysics Data System (ADS)

Marandjian, H.; Shoukourian, Yu.

This survey is devoted to the development of informatics and computer science in Armenia. The results in theoretical computer science (algebraic models, solutions to systems of general form recursive equations, the methods of coding theory, pattern recognition and image processing), constitute the theoretical basis for developing problem-solving-oriented environments. As examples can be mentioned: a synthesizer of optimized distributed recursive programs, software tools for cluster-oriented implementations of two-dimensional cellular automata, a grid-aware web interface with advanced service trading for linear algebra calculations. In the direction of solving scientific problems that require high-performance computing resources, examples of completed projects include the field of physics (parallel computing of complex quantum systems), astrophysics (Armenian virtual laboratory), biology (molecular dynamics study of human red blood cell membrane), meteorology (implementing and evaluating the Weather Research and Forecast Model for the territory of Armenia). The overview also notes that the Institute for Informatics and Automation Problems of the National Academy of Sciences of Armenia has established a scientific and educational infrastructure, uniting computing clusters of scientific and educational institutions of the country and provides the scientific community with access to local and international computational resources, that is a strong support for computational science in Armenia.

How can we cope with the complexity of the environment? A "Learning by modelling" approach using qualitative reasoning for developing causal models and simulations with focus on Sustainable River Catchment Management

NASA Astrophysics Data System (ADS)

Poppe, Michaela; Zitek, Andreas; Salles, Paulo; Bredeweg, Bert; Muhar, Susanne

2010-05-01

The education system needs strategies to attract future scientists and practitioners. There is an alarming decline in the number of students choosing science subjects. Reasons for this include the perceived complexity and the lack of effective cognitive tools that enable learners to acquire the expertise in a way that fits its qualitative nature. The DynaLearn project utilises a "Learning by modelling" approach to deliver an individualised and engaging cognitive tool for acquiring conceptual knowledge. The modelling approach is based on qualitative reasoning, a research area within artificial intelligence, and allows for capturing and simulating qualitative systems knowledge. Educational activities within the DynaLearn software address topics at different levels of complexity, depending on the educational goals and settings. DynaLearn uses virtual characters in the learning environment as agents for engaging and motivating the students during their modelling exercise. The DynaLearn software represents an interactive learning environment in which learners are in control of their learning activities. The software is able to coach them individually based on their current progress, their knowledge needs and learning goals. Within the project 70 expert models on different environmental issues covering seven core topics (Earth Systems and Resources, The Living World, Human population, Land and Water Use, Energy Resources and Consumption, Pollution, and Global Changes) will be delivered. In the context of the core topic "Land and Water Use" the Institute of Hydrobiology and Aquatic Ecosystem Management has developed a model on Sustainable River Catchment Management. River systems with their catchments have been tremendously altered due to human pressures with serious consequences for the ecological integrity of riverine landscapes. The operation of hydropower plants, the implementation of flood protection measures, the regulation of flow and sediment regime and intensive land use in the catchments have created ecological problems. A sustainable, catchment-wide management of riverine landscapes is needed and stated by water right acts, e.g. the European Water Framework and Floods Directive. This interdisciplinary approach needs the integration of natural riverine processes, flood protection, resource management, landscape planning, and social and political aspects to achieve a sustainable development. Therefore the model shows the effects of different management strategies concerning flood protection, restoration measures and land use. The model illustrates the wide range of ecosystem services of riverine landscapes that contribute to human well-being such as water supply, hydropower generation, flood regulation, and recreational opportunities. The effects of different land use strategies in the catchment are highlighted by means of the Driver-Pressure-State-Impact-Response (DPSIR) framework. The model is used to support activities of students at the University as well as at High School within the DynaLearn Software to promote scientific culture in the secondary education system. Model fragments allow learners to re-use parts of the existing model at different levels of complexity. But learners can also construct their own conceptual system knowledge, either individually or in a collaborative setting, and using the model as a reference for comparisons of their own understanding. Of special interest for the DynaLearn project is the intended development of interdisciplinary and social skills like cooperative working, cross-linked thinking, problem solving, decision-making, and the identification of the conflicts between environment, economy, legislation, science, technology, and society. A comprehensive evaluation of the DynaLearn software is part of the project. To be effective, science education should focus on understanding scientific concepts and on application of scientific knowledge to everyday life. Conceptual knowledge of systems behaviour is crucial for society to understand and successfully interact with its environment. The transfer of environmental-scientific knowledge by means of the DynaLearn software to wide parts of the society can be regarded as an important contribution to that, and contributes to foster a life-long learning process.

Using R for large spatiotemporal data sets

NASA Astrophysics Data System (ADS)

Pebesma, Edzer

2017-04-01

Writing and sharing scientific software is a means to communicate scientific ideas for finding scientific consensus, no more and no less than writing and sharing scientific papers is. Important factors for successful communication are adopting an open source environment, and using a language that is understood by many. For many scientist, R's combination of rich data abstraction and highly exposed data structures makes it an attractive communication tool. This paper discusses the development of spatial and spatiotemporal data handling and analysis with R since 2000, and will point to some of R's strengths and weaknesses in a historical perspective. We will also discuss a new, S3-based package for feature data ("Simple Features for R"), and point to a way forward into the data science realm, where pipeline-based workflows are assumed. Finally, we will discuss how, in a similar vein, massive satellite or climate model data sets, potentially held in a cloud environment, can be handled and analyzed with R.

Experiences Supporting the Lunar Reconnaissance Orbiter Camera: the Devops Model

NASA Astrophysics Data System (ADS)

Licht, A.; Estes, N. M.; Bowman-Cisnesros, E.; Hanger, C. D.

2013-12-01

Introduction: The Lunar Reconnaissance Orbiter Camera (LROC) Science Operations Center (SOC) is responsible for instrument targeting, product processing, and archiving [1]. The LROC SOC maintains over 1,000,000 observations with over 300 TB of released data. Processing challenges compound with the acquisition of over 400 Gbits of observations daily creating the need for a robust, efficient, and reliable suite of specialized software. Development Environment: The LROC SOC's software development methodology has evolved over time. Today, the development team operates in close cooperation with the systems administration team in a model known in the IT industry as DevOps. The DevOps model enables a highly productive development environment that facilitates accomplishment of key goals within tight schedules[2]. The LROC SOC DevOps model incorporates industry best practices including prototyping, continuous integration, unit testing, code coverage analysis, version control, and utilizing existing open source software. Scientists and researchers at LROC often prototype algorithms and scripts in a high-level language such as MATLAB or IDL. After the prototype is functionally complete the solution is implemented as production ready software by the developers. Following this process ensures that all controls and requirements set by the LROC SOC DevOps team are met. The LROC SOC also strives to enhance the efficiency of the operations staff by way of weekly presentations and informal mentoring. Many small scripting tasks are assigned to the cognizant operations personnel (end users), allowing for the DevOps team to focus on more complex and mission critical tasks. In addition to leveraging open source software the LROC SOC has also contributed to the open source community by releasing Lunaserv [3]. Findings: The DevOps software model very efficiently provides smooth software releases and maintains team momentum. Scientists prototyping their work has proven to be very efficient as developers do not need to spend time iterating over small changes. Instead, these changes are realized in early prototypes and implemented before the task is seen by developers. The development practices followed by the LROC SOC DevOps team help facilitate a high level of software quality that is necessary for LROC SOC operations. Application to the Scientific Community: There is no replacement for having software developed by professional developers. While it is beneficial for scientists to write software, this activity should be seen as prototyping, which is then made production ready by professional developers. When constructed properly, even a small development team has the ability to increase the rate of software development for a research group while creating more efficient, reliable, and maintainable products. This strategy allows scientists to accomplish more, focusing on teamwork, rather than software development, which may not be their primary focus. 1. Robinson et al. (2010) Space Sci. Rev. 150, 81-124 2. DeGrandis. (2011) Cutter IT Journal. Vol 24, No. 8, 34-39 3. Estes, N.M.; Hanger, C.D.; Licht, A.A.; Bowman-Cisneros, E.; Lunaserv Web Map Service: History, Implementation Details, Development, and Uses, http://adsabs.harvard.edu/abs/2013LPICo1719.2609E.

Confronting prospective teachers' ideas of evolution and scientific inquiry using technology and inquiry-based tasks

NASA Astrophysics Data System (ADS)

Crawford, Barbara A.; Zembal-Saul, Carla; Munford, Danusa; Friedrichsen, Patricia

2005-08-01

This study addresses the need for research in three areas: (1) teachers' understandings of scientific inquiry; (2) conceptual understandings of evolutionary processes; and (3) technology-enhanced instruction using an inquiry approach. The purpose of this study was to determine in what ways The Galapagos Finches software-based materials created a context for learning and teaching about the nature of scientific knowledge and evolutionary concepts. The research used a design experiment in which researchers significantly modified a secondary science methods course. The multiple data sources included: audiotaped conversations of two focus pairs of participants as they interacted with the software; written pre- and posttests on concepts of natural selection of the 21 prospective teachers; written pre- and posttests on views of the nature of science; three e-mail journal questions; and videotaped class discussions. Findings indicate that prospective teachers initially demonstrated alternative understandings of evolutionary concepts; there were uninformed understandings of the nature of scientific inquiry; there was little correlation between understandings and disciplines; and even the prospective teachers with research experience failed to understand the diverse methods used by scientists. Following the module there was evidence of enhanced understandings through metacognition, and the potential for interactive software to provide promising context for enhancing content understandings.

High performance compression of science data

NASA Technical Reports Server (NTRS)

Storer, James A.; Cohn, Martin

1992-01-01

In the future, NASA expects to gather over a tera-byte per day of data requiring space for levels of archival storage. Data compression will be a key component in systems that store this data (e.g., optical disk and tape) as well as in communications systems (both between space and Earth and between scientific locations on Earth). We propose to develop algorithms that can be a basis for software and hardware systems that compress a wide variety of scientific data with different criteria for fidelity/bandwidth tradeoffs. The algorithmic approaches we consider are specially targeted for parallel computation where data rates of over 1 billion bits per second are achievable with current technology.

High performance compression of science data

NASA Technical Reports Server (NTRS)

Storer, James A.; Cohn, Martin

1993-01-01

In the future, NASA expects to gather over a tera-byte per day of data requiring space for levels of archival storage. Data compression will be a key component in systems that store this data (e.g., optical disk and tape) as well as in communications systems (both between space and Earth and between scientific locations on Earth). We propose to develop algorithms that can be a basis for software and hardware systems that compress a wide variety of scientific data with different criteria for fidelity/bandwidth tradeoffs. The algorithmic approaches we consider are specially targeted for parallel computation where data rates of over 1 billion bits per second are achievable with current technology.

Rebuilding the space technology base

NASA Technical Reports Server (NTRS)

Povinelli, Frederick P.; Stephenson, Frank W.; Sokoloski, Martin M.; Montemerlo, Melvin D.; Venneri, Samuel L.; Mulville, Daniel R.; Hirschbein, Murray S.; Smith, Paul H.; Schnyer, A. Dan; Lum, Henry

1989-01-01

NASA's Civil Space Technology Initiative (CSTI) will not only develop novel technologies for space exploration and exploitation, but also take mature technologies into their demonstration phase in earth orbit. In the course of five years, CSTI will pay off in ground- and space-tested hardware, software, processes, methods for low-orbit transport and operation, and fundamental scientific research on the orbital environment. Attention is given to LOX/hydrogen and LOX/hydrocarbon reusable engines, liquid/solid fuel hybrid boosters, and aeroassist flight experiments for the validation of aerobraking with atmospheric friction. Also discussed are advanced scientific sensors, systems autonomy and telerobotics, control of flexible structures, precise segmented reflectors, high-rate high-capacity data handling, and advanced nuclear power systems.

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

Ayer, Vidya M.; Miguez, Sheila; Toby, Brian H.

Scientists have been central to the historical development of the computer industry, but the importance of software only continues to grow for all areas of scientific research and in particular for powder diffraction. Knowing how to program a computer is a basic and useful skill for scientists. The article introduces the three types of programming languages and why scripting languages are now preferred for scientists. Of them, the authors assert Python is the most useful and easiest to learn. Python is introduced. Also presented is an overview to a few of the many add-on packages available to extend the capabilitiesmore » of Python, for example, for numerical computations, scientific graphics and graphical user interface programming.« less

Development of high performance scientific components for interoperability of computing packages

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

Gulabani, Teena Pratap

2008-01-01

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achievedmore » by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.« less

Algorithms for Coastal-Zone Color-Scanner Data

NASA Technical Reports Server (NTRS)

1986-01-01

Software for Nimbus-7 Coastal-Zone Color-Scanner (CZCS) derived products consists of set of scientific algorithms for extracting information from CZCS-gathered data. Software uses CZCS-generated Calibrated RadianceTemperature (CRT) tape as input and outputs computer-compatible tape and film product.

Position Paper: Applying Machine Learning to Software Analysis to Achieve Trusted, Repeatable Scientific Computing

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

Prowell, Stacy J; Symons, Christopher T

2015-01-01

Producing trusted results from high-performance codes is essential for policy and has significant economic impact. We propose combining rigorous analytical methods with machine learning techniques to achieve the goal of repeatable, trustworthy scientific computing.

A Unique Digital Electrocardiographic Repository for the Development of Quantitative Electrocardiography and Cardiac Safety: The Telemetric and Holter ECG Warehouse (THEW)

PubMed Central

Couderc, Jean-Philippe

2010-01-01

The sharing of scientific data reinforces open scientific inquiry; it encourages diversity of analysis and opinion while promoting new research and facilitating the education of next generations of scientists. In this article, we present an initiative for the development of a repository containing continuous electrocardiographic information and their associated clinical information. This information is shared with the worldwide scientific community in order to improve quantitative electrocardiology and cardiac safety. First, we present the objectives of the initiative and its mission. Then, we describe the resources available in this initiative following three components: data, expertise and tools. The Data available in the Telemetric and Holter ECG Warehouse (THEW) includes continuous ECG signals and associated clinical information. The initiative attracted various academic and private partners whom expertise covers a large list of research arenas related to quantitative electrocardiography; their contribution to the THEW promotes cross-fertilization of scientific knowledge, resources, and ideas that will advance the field of quantitative electrocardiography. Finally, the tools of the THEW include software and servers to access and review the data available in the repository. To conclude, the THEW is an initiative developed to benefit the scientific community and to advance the field of quantitative electrocardiography and cardiac safety. It is a new repository designed to complement the existing ones such as Physionet, the AHA-BIH Arrhythmia Database, and the CSE database. The THEW hosts unique datasets from clinical trials and drug safety studies that, so far, were not available to the worldwide scientific community. PMID:20863512

PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments.

PubMed

Mohammed, Yassene; Domański, Dominik; Jackson, Angela M; Smith, Derek S; Deelder, André M; Palmblad, Magnus; Borchers, Christoph H

2014-06-25

One challenge in Multiple Reaction Monitoring (MRM)-based proteomics is to select the most appropriate surrogate peptides to represent a target protein. We present here a software package to automatically generate these most appropriate surrogate peptides for an LC/MRM-MS analysis. Our method integrates information about the proteins, their tryptic peptides, and the suitability of these peptides for MRM which is available online in UniProtKB, NCBI's dbSNP, ExPASy, PeptideAtlas, PRIDE, and GPMDB. The scoring algorithm reflects our knowledge in choosing the best candidate peptides for MRM, based on the uniqueness of the peptide in the targeted proteome, its physiochemical properties, and whether it previously has been observed. The modularity of the workflow allows further extension and additional selection criteria to be incorporated. We have developed a simple Web interface where the researcher provides the protein accession number, the subject organism, and peptide-specific options. Currently, the software is designed for human and mouse proteomes, but additional species can be easily be added. Our software improved the peptide selection by eliminating human error, considering multiple data sources and all of the isoforms of the protein, and resulted in faster peptide selection - approximately 50 proteins per hour compared to 8 per day. Compiling a list of optimal surrogate peptides for target proteins to be analyzed by LC/MRM-MS has been a cumbersome process, in which expert researchers retrieved information from different online repositories and used their own reasoning to find the most appropriate peptides. Our scientific workflow automates this process by integrating information from different data sources including UniProt, Global Proteome Machine, NCBI's dbSNP, and PeptideAtlas, simulating the researchers' reasoning, and incorporating their knowledge of how to select the best proteotypic peptides for an MRM analysis. The developed software can help to standardize the selection of peptides, eliminate human error, and increase productivity. Copyright © 2014 Elsevier B.V. All rights reserved.

GHEP-ISFG collaborative exercise on mixture profiles (GHEP-MIX06). Reporting conclusions: Results and evaluation.

PubMed

Barrio, P A; Crespillo, M; Luque, J A; Aler, M; Baeza-Richer, C; Baldassarri, L; Carnevali, E; Coufalova, P; Flores, I; García, O; García, M A; González, R; Hernández, A; Inglés, V; Luque, G M; Mosquera-Miguel, A; Pedrosa, S; Pontes, M L; Porto, M J; Posada, Y; Ramella, M I; Ribeiro, T; Riego, E; Sala, A; Saragoni, V G; Serrano, A; Vannelli, S

2018-07-01

One of the main goals of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the field of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise on analysis and interpretation of autosomal short tandem repeat (STR) mixture profiles. Until now, six exercises have been organized. At the present edition (GHEP-MIX06), with 25 participant laboratories, the exercise main aim was to assess mixture profiles results by issuing a report, from the proposal of a complex mock case. One of the conclusions obtained from this exercise is the increasing tendency of participating laboratories to validate DNA mixture profiles analysis following international recommendations. However, the results have shown some differences among them regarding the edition and also the interpretation of mixture profiles. Besides, although the last revision of ISO/IEC 17025:2017 gives indications of how results should be reported, not all laboratories strictly follow their recommendations. Regarding the statistical aspect, all those laboratories that have performed statistical evaluation of the data have employed the likelihood ratio (LR) as a parameter to evaluate the statistical compatibility. However, LR values obtained show a wide range of variation. This fact could not be attributed to the software employed, since the vast majority of laboratories that performed LR calculation employed the same software (LRmixStudio). Thus, the final allelic composition of the edited mixture profile and the parameters employed in the software could explain this data dispersion. This highlights the need, for each laboratory, to define through internal validations its criteria for editing and interpreting mixtures, and to continuous train in software handling. Copyright © 2018 Elsevier B.V. All rights reserved.

The New Cloud Absorption Radiometer (CAR) Software: One Model for NASA Remote Sensing Virtual Instruments

NASA Technical Reports Server (NTRS)

Roth, Don J.; Rapchun, David A.; Jones, Hollis H.

2001-01-01

The Cloud Absorption Radiometer (CAR) instrument has been the most frequently used airborne instrument built in-house at NASA Goddard Space Flight Center, having flown scientific research missions on-board various aircraft to many locations in the United States, Azores, Brazil, and Kuwait since 1983. The CAR instrument is capable of measuring scattered light by clouds in fourteen spectral bands in UV, visible and near-infrared region. This document describes the control, data acquisition, display, and file storage software for the new version of CAR. This software completely replaces the prior CAR Data System and Control Panel with a compact and robust virtual instrument computer interface. Additionally, the instrument is now usable for the first time for taking data in an off-aircraft mode. The new instrument is controlled via a LabVIEW v5. 1.1-developed software interface that utilizes, (1) serial port writes to write commands to the controller module of the instrument, and (2) serial port reads to acquire data from the controller module of the instrument. Step-by-step operational procedures are provided in this document. A suite of other software programs has been developed to complement the actual CAR virtual instrument. These programs include: (1) a simulator mode that allows pretesting of new features that might be added in the future, as well as demonstrations to CAR customers, and development at times when the instrument/hardware is off-location, and (2) a post-experiment data viewer that can be used to view all segments of individual data cycles and to locate positions where 'start' and stop' byte sequences were incorrectly formulated by the instrument controller. The CAR software described here is expected to be the basis for CAR operation for many missions and many years to come.

Bringing the Unidata IDV to the Cloud

NASA Astrophysics Data System (ADS)

Fisher, W. I.; Oxelson Ganter, J.

2015-12-01

Maintaining software compatibility across new computing environments and the associated underlying hardware is a common problem for software engineers and scientific programmers. While traditional software engineering provides a suite of tools and methodologies which may mitigate this issue, they are typically ignored by developers lacking a background in software engineering. Causing further problems, these methodologies are best applied at the start of project; trying to apply them to an existing, mature project can require an immense effort. Visualization software is particularly vulnerable to this problem, given the inherent dependency on particular graphics hardware and software API's. As a result of these issues, there exists a large body of software which is simultaneously critical to the scientists who are dependent upon it, and yet increasingly difficult to maintain.The solution to this problem was partially provided with the advent of Cloud Computing; Application Streaming. This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations, with little-to-no re-engineering required. When coupled with containerization technology such as Docker, we are able to easily bring the same visualization software to a desktop, a netbook, a smartphone, and the next generation of hardware, whatever it may be.Unidata has been able to harness Application Streaming to provide a tablet-compatible version of our visualization software, the Integrated Data Viewer (IDV). This work will examine the challenges associated with adapting the IDV to an application streaming platform, and include a brief discussion of the underlying technologies involved.

Data and Analysis Center for Software: An IAC in Transition.

DTIC Science & Technology

1983-06-01

reviewed and is approved for publication. * APPROVEDt Proj ect Engineer . JOHN J. MARCINIAK, Colonel, USAF Chief, Command and Control Division . FOR THE CO...SUPPLEMENTARY NOTES RADC Project Engineer : John Palaimo (COEE) It. KEY WORDS (Conilnuo n rever*e aide if necessary and identify by block numober...Software Engineering Software Technology Information Analysis Center Database Scientific and Technical Information 20. ABSTRACT (Continue on reverse side It

Supporting Middle School Students' Online Reading of Scientific Resources: Moving beyond Cursory, Fragmented, and Opportunistic Reading

ERIC Educational Resources Information Center

Zhang, M.

2013-01-01

The abundant scientific resources on the Web provide great opportunities for students to expand their science learning, yet easy access to information does not ensure learning. Prior research has found that middle school students tend to read Web-based scientific resources in a shallow, superficial manner. A software tool was designed to support…

Constructing Scientific Applications from Heterogeneous Resources

NASA Technical Reports Server (NTRS)

Schichting, Richard D.

1995-01-01

A new model for high-performance scientific applications in which such applications are implemented as heterogeneous distributed programs or, equivalently, meta-computations, is investigated. The specific focus of this grant was a collaborative effort with researchers at NASA and the University of Toledo to test and improve Schooner, a software interconnection system, and to explore the benefits of increased user interaction with existing scientific applications.

Operations Manager Tim Miller checks out software for the Airborne Synthetic Aperature Radar (AIRSAR

NASA Technical Reports Server (NTRS)

1998-01-01

Tim Miller checks out software for the Airborne Synthetic Aperture Radar (AIRSAR). He was the AIRSAR operations manager for NASA's Jet Propulsion Laboratory. The AIRSAR produces imaging data for a range of studies conducted by the DC-8. NASA is using a DC-8 aircraft as a flying science laboratory. The platform aircraft, based at NASA's Dryden Flight Research Center, Edwards, Calif., collects data for many experiments in support of scientific projects serving the world scientific community. Included in this community are NASA, federal, state, academic and foreign investigators. Data gathered by the DC-8 at flight altitude and by remote sensing have been used for scientific studies in archeology, ecology, geography, hydrology, meteorology, oceanography, volcanology, atmospheric chemistry, soil science and biology.

The Science and Technology of Future Space Missions

NASA Astrophysics Data System (ADS)

Bonati, A.; Fusi, R.; Longoni, F.

1999-12-01

The future space missions span over a wide range of scientific objectives. After different successful scientific missions, other international cornerstone experiments are planned to study of the evolution of the universe and of the primordial stellar systems, and our solar system. Space missions for the survey of the microwave cosmic background radiation, deep-field search in the near and mid-infrared region and planetary exploration will be carried out. Several fields are open for research and development in the space business. Three major categories can be found: detector technology in different areas, electronics, and software. At LABEN, a Finmeccanica Company, we are focusing the technologies to respond to this challenging scientific demands. Particle trackers based on silicon micro-strips supported by lightweight structures (CFRP) are studied. In the X-ray field, CCD's are investigated with pixels of very small size so as to increase the spatial resolution of the focal plane detectors. High-efficiency and higly miniaturized high-voltage power supplies are developed for detectors with an increasingly large number of phototubes. Material research is underway to study material properties at extreme temperatures. Low-temperature mechanical structures are designed for cryogenic ( 20 K) detectors in order to maintain the high precision in pointing the instrument. Miniaturization of front end electronics with low power consumption and high number of signal processing channels is investigated; silicon-based microchips (ASIC's) are designed and developed using state-of-the-art technology. Miniaturized instruments to investigate the planets surface using X-Ray and Gamma-Ray scattering techniques are developed. The data obtained from the detectors have to be processed, compressed, formatted and stored before their transmission to ground. These tasks open up additional strategic areas of development such as microprocessor-based electronics for high-speed and parallel data processing. Powerful computers with customized architectures are designed and developed. High-speed intercommunication networks are studied and tested. In parallel to the hardware research activities, software development is undertaken for several purposes: digital and video compression algorithms, payload and spacecraft control and diagnostics, scientific processing algorithms, etc. Besides, embedded Java virtual machines are studied for tele-science applications (direct link between scientist console and scientific payload). At system engineering level, the demand for spacecraft autonomy is increased for planetology missions: reliable intelligent systems that can operate for long periods of time without human intervention from ground are requested and investigated. A technologically challenging but less glamorous area of development is represented by the laboratory equipment for end-to-end testing (on ground) of payload instruments. The main fields are cryogenics, laser and X-ray optics, microwave radiometry, UV and infrared testing systems.

MememxGATE: Unearthing Latent Content Features for Improved Search and Relevancy Ranking Across Scientific Literature

NASA Astrophysics Data System (ADS)

Wilson, B. D.; McGibbney, L. J.; Mattmann, C. A.; Ramirez, P.; Joyce, M.; Whitehall, K. D.

2015-12-01

Quantifying scientific relevancy is of increasing importance to NASA and the research community. Scientific relevancy may be defined by mapping the impacts of a particular NASA mission, instrument, and/or retrieved variables to disciplines such as climate predictions, natural hazards detection and mitigation processes, education, and scientific discoveries. Related to relevancy, is the ability to expose data with similar attributes. This in turn depends upon the ability for us to extract latent, implicit document features from scientific data and resources and make them explicit, accessible and useable for search activities amongst others. This paper presents MemexGATE; a server side application, command line interface and computing environment for running large scale metadata extraction, general architecture text engineering, document classification and indexing tasks over document resources such as social media streams, scientific literature archives, legal documentation, etc. This work builds on existing experiences using MemexGATE (funded, developed and validated through the DARPA Memex Progrjam PI Mattmann) for extracting and leveraging latent content features from document resources within the Materials Research domain. We extend the software functionality capability to the domain of scientific literature with emphasis on the expansion of gazetteer lists, named entity rules, natural language construct labeling (e.g. synonym, antonym, hyponym, etc.) efforts to enable extraction of latent content features from data hosted by wide variety of scientific literature vendors (AGU Meeting Abstract Database, Springer, Wiley Online, Elsevier, etc.) hosting earth science literature. Such literature makes both implicit and explicit references to NASA datasets and relationships between such concepts stored across EOSDIS DAAC's hence we envisage that a significant part of this effort will also include development and understanding of relevancy signals which can ultimately be utilized for improved search and relevancy ranking across scientific literature.

The Diamond Beamline Controls and Data Acquisition Software Architecture

NASA Astrophysics Data System (ADS)

Rees, N.

2010-06-01

The software for the Diamond Light Source beamlines[1] is based on two complementary software frameworks: low level control is provided by the Experimental Physics and Industrial Control System (EPICS) framework[2][3] and the high level user interface is provided by the Java based Generic Data Acquisition or GDA[4][5]. EPICS provides a widely used, robust, generic interface across a wide range of hardware where the user interfaces are focused on serving the needs of engineers and beamline scientists to obtain detailed low level views of all aspects of the beamline control systems. The GDA system provides a high-level system that combines an understanding of scientific concepts, such as reciprocal lattice coordinates, a flexible python syntax scripting interface for the scientific user to control their data acquisition, and graphical user interfaces where necessary. This paper describes the beamline software architecture in more detail, highlighting how these complementary frameworks provide a flexible system that can accommodate a wide range of requirements.

The Production Data Approach for Full Lifecycle Management

NASA Astrophysics Data System (ADS)

Schopf, J.

2012-04-01

The amount of data generated by scientists is growing exponentially, and studies have shown [Koe04] that un-archived data sets have a resource half-life that is only a fraction of those resources that are electronically archived. Most groups still lack standard approaches and procedures for data management. Arguably, however, scientists know something about building software. A recent article in Nature [Mer10] stated that 45% of research scientists spend more time now developing software than they did 5 years ago, and 38% spent at least 1/5th of their time developing software. Fox argues [Fox10] that a simple release of data is not the correct approach to data curation. In addition, just as software is used in a wide variety of ways never initially envisioned by its developers, we're seeing this even to a greater extent with data sets. In order to address the need for better data preservation and access, we propose that data sets should be managed in a similar fashion to building production quality software. These production data sets are not simply published once, but go through a cyclical process, including phases such as design, development, verification, deployment, support, analysis, and then development again, thereby supporting the full lifecycle of a data set. The process involved in academically-produced software changes over time with respect to issues such as how much it is used outside the development group, but factors in aspects such as knowing who is using the code, enabling multiple developers to contribute to code development with common procedures, formal testing and release processes, developing documentation, and licensing. When we work with data, either as a collection source, as someone tagging data, or someone re-using it, many of the lessons learned in building production software are applicable. Table 1 shows a comparison of production software elements to production data elements. Table 1: Comparison of production software and production data. Production Software Production Data End-user considerations End-user considerations Multiple Coders: Repository with check-in procedures Coding standards Multiple producers/collectors Local archive with check-in procedure Metadata Standards Formal testing Formal testing Bug tracking and fixes Bug tracking and fixes, QA/QC Documentation Documentation Formal Release Process Formal release process to external archive License Citation/usage statement The full presentation of this abstract will include a detailed discussion of these issues so that researchers can produce usable and accessible data sets as a first step toward reproducible science. By creating production-quality data sets, we extend the potential of our data, both in terms of usability and usefulness to ourselves and other researchers. The more we treat data with formal processes and release cycles, the more relevant and useful it can be to the scientific community.

Adapting astronomical source detection software to help detect animals in thermal images obtained by unmanned aerial systems

NASA Astrophysics Data System (ADS)

Longmore, S. N.; Collins, R. P.; Pfeifer, S.; Fox, S. E.; Mulero-Pazmany, M.; Bezombes, F.; Goodwind, A.; de Juan Ovelar, M.; Knapen, J. H.; Wich, S. A.

2017-02-01

In this paper we describe an unmanned aerial system equipped with a thermal-infrared camera and software pipeline that we have developed to monitor animal populations for conservation purposes. Taking a multi-disciplinary approach to tackle this problem, we use freely available astronomical source detection software and the associated expertise of astronomers, to efficiently and reliably detect humans and animals in aerial thermal-infrared footage. Combining this astronomical detection software with existing machine learning algorithms into a single, automated, end-to-end pipeline, we test the software using aerial video footage taken in a controlled, field-like environment. We demonstrate that the pipeline works reliably and describe how it can be used to estimate the completeness of different observational datasets to objects of a given type as a function of height, observing conditions etc. - a crucial step in converting video footage to scientifically useful information such as the spatial distribution and density of different animal species. Finally, having demonstrated the potential utility of the system, we describe the steps we are taking to adapt the system for work in the field, in particular systematic monitoring of endangered species at National Parks around the world.

Net-VISA used as a complement to standard software at the CTBTO: initial operational experience with next-generation software.

NASA Astrophysics Data System (ADS)

Le Bras, R. J.; Arora, N. S.; Kushida, N.; Kebede, F.; Feitio, P.; Tomuta, E.

2017-12-01

The International Monitoring System of the Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO) has reached out to the broader scientific community through a series of conferences, the later one of which took place in June 2017 in Vienna, Austria. Stemming out of this outreach effort, after the inception of research and development efforts in 2009, the NET-VISA software, following a Bayesian modelling approach, has been elaborated to improve on the key step of automatic association of joint seismic, hydro-acoustic, and infrasound detections. When compared with the current operational system, it has been consistently shown on off-line tests to improve the overlap with the analyst-reviewed Reviewed Event Bulletin (REB) by ten percent for an average of 85% overlap, while the inconsistency rate is essentially the same at about 50%. Testing by analysts in realistic conditions on a few days of data has also demonstrated the software performance in finding additional events which qualify for publication in the REB. Starting in August 2017, the automatic events produced by the software will be reviewed by analysts at the CTBTO, and we report on the initial evaluation of this introduction into operations.

The Cherenkov Telescope Array Observatory: top level use cases

NASA Astrophysics Data System (ADS)

Bulgarelli, A.; Kosack, K.; Hinton, J.; Tosti, G.; Schwanke, U.; Schwarz, J.; Colomé, P.; Conforti, V.; Khelifi, B.; Goullon, J.; Ong, R.; Markoff, S.; Contreras, J. L.; Lucarelli, F.; Antonelli, L. A.; Bigongiari, C.; Boisson, C.; Bosnjak, Z.; Brau-Nogué, S.; Carosi, A.; Chen, A.; Cotter, G.; Covino, S.; Daniel, M.; De Cesare, G.; de Ona Wilhelmi, E.; Della Volpe, M.; Di Pierro, F.; Fioretti, V.; Füßling, M.; Garczarczyk, M.; Gaug, M.; Glicenstein, J. F.; Goldoni, P.; Götz, D.; Grandi, P.; Heller, M.; Hermann, G.; Inoue, S.; Knödlseder, J.; Lenain, J.-P.; Lindfors, E.; Lombardi, S.; Luque-Escamilla, P.; Maier, G.; Marisaldi, M.; Mundell, C.; Neyroud, N.; Noda, K.; O'Brien, P.; Petrucci, P. O.; Martí Ribas, J.; Ribó, M.; Rodriguez, J.; Romano, P.; Schmid, J.; Serre, N.; Sol, H.; Schussler, F.; Stamerra, A.; Stolarczyk, T.; Vandenbrouck, J.; Vercellone, S.; Vergani, S.; Zech, A.; Zoli, A.

2016-08-01

Today the scientific community is facing an increasing complexity of the scientific projects, from both a technological and a management point of view. The reason for this is in the advance of science itself, where new experiments with unprecedented levels of accuracy, precision and coverage (time and spatial) are realised. Astronomy is one of the fields of the physical sciences where a strong interaction between the scientists, the instrument and software developers is necessary to achieve the goals of any Big Science Project. The Cherenkov Telescope Array (CTA) will be the largest ground-based very high-energy gamma-ray observatory of the next decades. To achieve the full potential of the CTA Observatory, the system must be put into place to enable users to operate the telescopes productively. The software will cover all stages of the CTA system, from the preparation of the observing proposals to the final data reduction, and must also fit into the overall system. Scientists, engineers, operators and others will use the system to operate the Observatory, hence they should be involved in the design process from the beginning. We have organised a workgroup and a workflow for the definition of the CTA Top Level Use Cases in the context of the Requirement Management activities of the CTA Observatory. Scientists, instrument and software developers are collaborating and sharing information to provide a common and general understanding of the Observatory from a functional point of view. Scientists that will use the CTA Observatory will provide mainly Science Driven Use Cases, whereas software engineers will subsequently provide more detailed Use Cases, comments and feedbacks. The main purposes are to define observing modes and strategies, and to provide a framework for the flow down of the Use Cases and requirements to check missing requirements and the already developed Use-Case models at CTA sub-system level. Use Cases will also provide the basis for the definition of the Acceptance Test Plan for the validation of the overall CTA system. In this contribution we present the organisation and the workflow of the Top Level Use Cases workgroup.

Non-linear mixed effects modeling - from methodology and software development to driving implementation in drug development science.

PubMed

Pillai, Goonaseelan Colin; Mentré, France; Steimer, Jean-Louis

2005-04-01

Few scientific contributions have made significant impact unless there was a champion who had the vision to see the potential for its use in seemingly disparate areas-and who then drove active implementation. In this paper, we present a historical summary of the development of non-linear mixed effects (NLME) modeling up to the more recent extensions of this statistical methodology. The paper places strong emphasis on the pivotal role played by Lewis B. Sheiner (1940-2004), who used this statistical methodology to elucidate solutions to real problems identified in clinical practice and in medical research and on how he drove implementation of the proposed solutions. A succinct overview of the evolution of the NLME modeling methodology is presented as well as ideas on how its expansion helped to provide guidance for a more scientific view of (model-based) drug development that reduces empiricism in favor of critical quantitative thinking and decision making.