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.

The Many Faces of a Software Engineer in a Research Community

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

Marinovici, Maria C.; Kirkham, Harold

2013-10-14

The ability to gather, analyze and make decisions based on real world data is changing nearly every field of human endeavor. These changes are particularly challenging for software engineers working in a scientific community, designing and developing large, complex systems. To avoid the creation of a communications gap (almost a language barrier), the software engineers should possess an ‘adaptive’ skill. In the science and engineering research community, the software engineers must be responsible for more than creating mechanisms for storing and analyzing data. They must also develop a fundamental scientific and engineering understanding of the data. This paper looks atmore » the many faces that a software engineer should have: developer, domain expert, business analyst, security expert, project manager, tester, user experience professional, etc. Observations made during work on a power-systems scientific software development are analyzed and extended to describe more generic software development projects.« less

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.

Publishing Platform for Scientific Software - Lessons Learned

NASA Astrophysics Data System (ADS)

Hammitzsch, Martin; Fritzsch, Bernadette; Reusser, Dominik; Brembs, Björn; Deinzer, Gernot; Loewe, Peter; Fenner, Martin; van Edig, Xenia; Bertelmann, Roland; Pampel, Heinz; Klump, Jens; Wächter, Joachim

2015-04-01

Scientific software has become an indispensable commodity for the production, processing and analysis of empirical data but also for modelling and simulation of complex processes. Software has a significant influence on the quality of research results. For strengthening the recognition of the academic performance of scientific software development, for increasing its visibility and for promoting the reproducibility of research results, concepts for the publication of scientific software have to be developed, tested, evaluated, and then transferred into operations. For this, the publication and citability of scientific software have to fulfil scientific criteria by means of defined processes and the use of persistent identifiers, similar to data publications. The SciForge project is addressing these challenges. Based on interviews a blueprint for a scientific software publishing platform and a systematic implementation plan has been designed. In addition, the potential of journals, software repositories and persistent identifiers have been evaluated to improve the publication and dissemination of reusable software solutions. It is important that procedures for publishing software as well as methods and tools for software engineering are reflected in the architecture of the platform, in order to improve the quality of the software and the results of research. In addition, it is necessary to work continuously on improving specific conditions that promote the adoption and sustainable utilization of scientific software publications. Among others, this would include policies for the development and publication of scientific software in the institutions but also policies for establishing the necessary competencies and skills of scientists and IT personnel. To implement the concepts developed in SciForge a combined bottom-up / top-down approach is considered that will be implemented in parallel in different scientific domains, e.g. in earth sciences, climate research and the life sciences. Based on the developed blueprints a scientific software publishing platform will be iteratively implemented, tested, and evaluated. Thus the platform should be developed continuously on the basis of gained experiences and results. The platform services will be extended one by one corresponding to the requirements of the communities. Thus the implemented platform for the publication of scientific software can be improved and stabilized incrementally as a tool with software, science, publishing, and user oriented features.

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.

Optimel: Software for selecting the optimal method

NASA Astrophysics Data System (ADS)

Popova, Olga; Popov, Boris; Romanov, Dmitry; Evseeva, Marina

Optimel: software for selecting the optimal method automates the process of selecting a solution method from the optimization methods domain. Optimel features practical novelty. It saves time and money when conducting exploratory studies if its objective is to select the most appropriate method for solving an optimization problem. Optimel features theoretical novelty because for obtaining the domain a new method of knowledge structuring was used. In the Optimel domain, extended quantity of methods and their properties are used, which allows identifying the level of scientific studies, enhancing the user's expertise level, expand the prospects the user faces and opening up new research objectives. Optimel can be used both in scientific research institutes and in educational institutions.

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.

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.

Planetary Data Workshop, Part 2

NASA Technical Reports Server (NTRS)

1984-01-01

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

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.

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.

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;…

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.

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

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.

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.

Integration of an expert system into a user interface language demonstration

NASA Technical Reports Server (NTRS)

Stclair, D. C.

1986-01-01

The need for a User Interface Language (UIL) has been recognized by the Space Station Program Office as a necessary tool to aid in minimizing the cost of software generation by multiple users. Previous history in the Space Shuttle Program has shown that many different areas of software generation, such as operations, integration, testing, etc., have each used a different user command language although the types of operations being performed were similar in many respects. Since the Space Station represents a much more complex software task, a common user command language--a user interface language--is required to support the large spectrum of space station software developers and users. To assist in the selection of an appropriate set of definitions for a UIL, a series of demonstration programs was generated with which to test UIL concepts against specific Space Station scenarios using operators for the astronaut and scientific community. Because of the importance of expert system in the space station, it was decided that an expert system should be embedded in the UIL. This would not only provide insight into the UIL components required but would indicate the effectiveness with which an expert system could function in such an environment.

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

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.

The microcomputer scientific software series 4: testing prediction accuracy.

Treesearch

H. Michael Rauscher

1986-01-01

A computer program, ATEST, is described in this combination user's guide / programmer's manual. ATEST provides users with an efficient and convenient tool to test the accuracy of predictors. As input ATEST requires observed-predicted data pairs. The output reports the two components of accuracy, bias and precision.

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.

Promoting Science Software Best Practices: A Scientist's Perspective (Invited)

NASA Astrophysics Data System (ADS)

Blanton, B. O.

2013-12-01

Software is at the core of most modern scientific activities, and as societal awareness of, and impacts from, extreme weather, disasters, and climate and global change continue to increase, the roles that scientific software play in analyses and decision-making are brought more to the forefront. Reproducibility of research results (particularly those that enter into the decision-making arena) and open access to the software is essential for scientific and scientists' credibility. This has been highlighted in a recent article by Joppa et al (Troubling Trends in Scientific Software Use, Science Magazine, May 2013) that describes reasons for particular software being chosen by scientists, including that the "developer is well-respected" and on "recommendation from a close colleague". This reliance on recommendation, Joppa et al conclude, is fraught with risks to both sciences and scientists. Scientists must frequently take software for granted, assuming that it performs as expected and advertised and that the software itself has been validated and results verified. This is largely due to the manner in which much software is written and developed; in an ad hoc manner, with an inconsistent funding stream, and with little application of core software engineering best practices. Insufficient documentation, limited test cases, and code unavailability are significant barriers to informed and intelligent science software usage. This situation is exacerbated when the scientist becomes the software developer out of necessity due to resource constraints. Adoption of, and adherence to, best practices in scientific software development will substantially increase intelligent software usage and promote a sustainable evolution of the science as encoded in the software. We describe a typical scientist's perspective on using and developing scientific software in the context of storm surge research and forecasting applications that have real-time objectives and regulatory constraints. This include perspectives on what scientists/users of software can contribute back to the software development process and examples of successful scientist/developer interactions, and the competition between "getting it done" and "getting it done right".

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

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.

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.

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.

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.

Introduction to the LaRC central scientific computing complex

NASA Technical Reports Server (NTRS)

Shoosmith, John N.

1993-01-01

The computers and associated equipment that make up the Central Scientific Computing Complex of the Langley Research Center are briefly described. The electronic networks that provide access to the various components of the complex and a number of areas that can be used by Langley and contractors staff for special applications (scientific visualization, image processing, software engineering, and grid generation) are also described. Flight simulation facilities that use the central computers are described. Management of the complex, procedures for its use, and available services and resources are discussed. This document is intended for new users of the complex, for current users who wish to keep appraised of changes, and for visitors who need to understand the role of central scientific computers at Langley.

A Scientific Software Product Line for the Bioinformatics domain.

PubMed

Costa, Gabriella Castro B; Braga, Regina; David, José Maria N; Campos, Fernanda

2015-08-01

Most specialized users (scientists) that use bioinformatics applications do not have suitable training on software development. Software Product Line (SPL) employs the concept of reuse considering that it is defined as a set of systems that are developed from a common set of base artifacts. In some contexts, such as in bioinformatics applications, it is advantageous to develop a collection of related software products, using SPL approach. If software products are similar enough, there is the possibility of predicting their commonalities, differences and then reuse these common features to support the development of new applications in the bioinformatics area. This paper presents the PL-Science approach which considers the context of SPL and ontology in order to assist scientists to define a scientific experiment, and to specify a workflow that encompasses bioinformatics applications of a given experiment. This paper also focuses on the use of ontologies to enable the use of Software Product Line in biological domains. In the context of this paper, Scientific Software Product Line (SSPL) differs from the Software Product Line due to the fact that SSPL uses an abstract scientific workflow model. This workflow is defined according to a scientific domain and using this abstract workflow model the products (scientific applications/algorithms) are instantiated. Through the use of ontology as a knowledge representation model, we can provide domain restrictions as well as add semantic aspects in order to facilitate the selection and organization of bioinformatics workflows in a Scientific Software Product Line. The use of ontologies enables not only the expression of formal restrictions but also the inferences on these restrictions, considering that a scientific domain needs a formal specification. This paper presents the development of the PL-Science approach, encompassing a methodology and an infrastructure, and also presents an approach evaluation. This evaluation presents case studies in bioinformatics, which were conducted in two renowned research institutions in Brazil. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

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.

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

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.

The IUE Science Operations Ground System

NASA Technical Reports Server (NTRS)

Pitts, Ronald E.; Arquilla, Richard

1994-01-01

The International Ultraviolet Explorer (IUE) Science Operations System provides full realtime operations capabilities and support to the operations staff and astronomer users. The components of this very diverse and extremely flexible hardware and software system have played a major role in maintaining the scientific efficiency and productivity of the IUE. The software provides the staff and user with all the tools necessary for pre-visit and real-time planning and operations analysis for any day of the year. Examples of such tools include the effects of spacecraft constraints on target availability, maneuver times between targets, availability of guide stars, target identification, coordinate transforms, e-mail transfer of Observatory forms and messages, and quick-look analysis of image data. Most of this extensive software package can also be accessed remotely by individual users for information, scheduling of shifts, pre-visit planning, and actual observing program execution. Astronomers, with a modest investment in hardware and software, may establish remote observing sites. We currently have over 20 such sites in our remote observers' network.

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

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.

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

Accelerating Science with the NERSC Burst Buffer Early User Program

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

Bhimji, Wahid; Bard, Debbie; Romanus, Melissa

NVRAM-based Burst Buffers are an important part of the emerging HPC storage landscape. The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory recently installed one of the first Burst Buffer systems as part of its new Cori supercomputer, collaborating with Cray on the development of the DataWarp software. NERSC has a diverse user base comprised of over 6500 users in 700 different projects spanning a wide variety of scientific computing applications. The use-cases of the Burst Buffer at NERSC are therefore also considerable and diverse. We describe here performance measurements and lessons learned from the Burstmore » Buffer Early User Program at NERSC, which selected a number of research projects to gain early access to the Burst Buffer and exercise its capability to enable new scientific advancements. To the best of our knowledge this is the first time a Burst Buffer has been stressed at scale by diverse, real user workloads and therefore these lessons will be of considerable benefit to shaping the developing use of Burst Buffers at HPC centers.« less

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

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)

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.

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.

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

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

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

PubMed

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee

2014-09-22

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-dockings" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

MONTE: the next generation of mission design and navigation software

NASA Astrophysics Data System (ADS)

Evans, Scott; Taber, William; Drain, Theodore; Smith, Jonathon; Wu, Hsi-Cheng; Guevara, Michelle; Sunseri, Richard; Evans, James

2018-03-01

The Mission analysis, Operations and Navigation Toolkit Environment (MONTE) (Sunseri et al. in NASA Tech Briefs 36(9), 2012) is an astrodynamic toolkit produced by the Mission Design and Navigation Software Group at the Jet Propulsion Laboratory. It provides a single integrated environment for all phases of deep space and Earth orbiting missions. Capabilities include: trajectory optimization and analysis, operational orbit determination, flight path control, and 2D/3D visualization. MONTE is presented to the user as an importable Python language module. This allows a simple but powerful user interface via CLUI or script. In addition, the Python interface allows MONTE to be used seamlessly with other canonical scientific programming tools such as SciPy, NumPy, and Matplotlib. MONTE is the prime operational orbit determination software for all JPL navigated missions.

Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

PubMed

Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

2012-01-01

Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging.

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

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.

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

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.

PI in the sky: The astronaut science advisor on SLS-2

NASA Technical Reports Server (NTRS)

Hazelton, Lyman R.; Groleau, Nicolas; Frainier, Richard J.; Compton, Michael M.; Colombano, Silvano P.; Szolovits, Peter

1994-01-01

The Astronaut Science Advisor (ASA, also known as Principal-Investigator-in-a-Box) is an advanced engineering effort to apply expert systems technology to experiment monitoring and control. Its goal is to increase the scientific value of information returned from experiments on manned space missions. The first in-space test of the system will be in conjunction with Professor Larry Young's (MIT) vestibulo-ocular 'Rotating Dome' experiment on the Spacelab Life Sciences 2 mission (STS-58) in the Fall of 1993. In a cost-saving effort, off-the-shelf equipment was employed wherever possible. Several modifications were necessary in order to make the system flight-worthy. The software consists of three interlocking modules. A real-time data acquisition system digitizes and stores all experiment data and then characterizes the signals in symbolic form; a rule-based expert system uses the symbolic signal characteristics to make decisions concerning the experiment; and a highly graphic user interface requiring a minimum of user intervention presents information to the astronaut operator. Much has been learned about the design of software and user interfaces for interactive computing in space. In addition, we gained a great deal of knowledge about building relatively inexpensive hardware and software for use in space. New technologies are being assessed to make the system a much more powerful ally in future scientific research in space and on the ground.

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.

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.

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.

Design of web platform for science and engineering in the model of open market

NASA Astrophysics Data System (ADS)

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

2016-09-01

This paper presents a design and operation algorithms of a web-platform for convenient, secure and effective remote interaction on the principles of the open market of users and providers of scientific application software and databases.

PixelLearn

NASA Technical Reports Server (NTRS)

Mazzoni, Dominic; Wagstaff, Kiri; Bornstein, Benjamin; Tang, Nghia; Roden, Joseph

2006-01-01

PixelLearn is an integrated user-interface computer program for classifying pixels in scientific images. Heretofore, training a machine-learning algorithm to classify pixels in images has been tedious and difficult. PixelLearn provides a graphical user interface that makes it faster and more intuitive, leading to more interactive exploration of image data sets. PixelLearn also provides image-enhancement controls to make it easier to see subtle details in images. PixelLearn opens images or sets of images in a variety of common scientific file formats and enables the user to interact with several supervised or unsupervised machine-learning pixel-classifying algorithms while the user continues to browse through the images. The machinelearning algorithms in PixelLearn use advanced clustering and classification methods that enable accuracy much higher than is achievable by most other software previously available for this purpose. PixelLearn is written in portable C++ and runs natively on computers running Linux, Windows, or Mac OS X.

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.

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.

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.

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.

Acquisition, use, and archiving of real-time data

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

Leach, M.J.; Bernstein, H.J.; Tichler, J.L.

Meteorological information is needed by scientific personnel at Brookhaven National Laboratory (BNL) for various purposes. An automated system, used to acquire, archive, and provide users with weather data, is described. Hardware, software, and some of the examples of the uses of the system are detailed.

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

User Interface Technology Transfer to NASA's Virtual Wind Tunnel System

NASA Technical Reports Server (NTRS)

vanDam, Andries

1998-01-01

Funded by NASA grants for four years, the Brown Computer Graphics Group has developed novel 3D user interfaces for desktop and immersive scientific visualization applications. This past grant period supported the design and development of a software library, the 3D Widget Library, which supports the construction and run-time management of 3D widgets. The 3D Widget Library is a mechanism for transferring user interface technology from the Brown Graphics Group to the Virtual Wind Tunnel system at NASA Ames as well as the public domain.

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.

The Scientific Uplink and User Support System for SIRTF

NASA Astrophysics Data System (ADS)

Heinrichsen, I.; Chavez, J.; Hartley, B.; Mei, Y.; Potts, S.; Roby, T.; Turek, G.; Valjavec, E.; Wu, X.

The Space Infrared Telescope Facility (SIRTF) is one of NASA's Great Observatory missions, scheduled for launch in 2001. As such its ground segment design is driven by the requirement to provide strong support for the entire astronomical community starting with the call for Legacy Proposals in early 2000. In this contribution, we present the astronomical user interface and the design of the server software that comprises the Scientific Uplink System for SIRTF. The software architecture is split into three major parts: A front-end Java application deployed to the astronomical community providing the capabilities to visualize and edit proposals and the associated lists of observations. This observer toolkit provides templates to define all parameters necessary to carry out the required observations. A specialized version of this software, based on the same overall architecture, is used internal to the SIRTF Science Center to prepare calibration and engineering observations. A Weblogic (TM) based middleware component brokers the transactions with the servers, astronomical image and catalog sources as well as the SIRTF operational databases. Several server systems perform the necessary computations, to obtain resource estimates, target visibilities and to access the instrument models for signal to noise calculations. The same server software is used internally at a later stage to derive the detailed command sequences needed by the SIRTF instruments and spacecraft to execute a given observation.

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.

BASIC Data Manipulation And Display System (BDMADS)

NASA Technical Reports Server (NTRS)

Szuch, J. R.

1983-01-01

BDMADS, a BASIC Data Manipulation and Display System, is a collection of software programs that run on an Apple II Plus personal computer. BDMADS provides a user-friendly environment for the engineer in which to perform scientific data processing. The computer programs and their use are described. Jet engine performance calculations are used to illustrate the use of BDMADS. Source listings of the BDMADS programs are provided and should permit users to customize the programs for their particular applications.

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).

Visualizer: 3D Gridded Data Visualization Software for Geoscience Education and Research

NASA Astrophysics Data System (ADS)

Harwood, C.; Billen, M. I.; Kreylos, O.; Jadamec, M.; Sumner, D. Y.; Kellogg, L. H.; Hamann, B.

2008-12-01

In both research and education learning is an interactive and iterative process of exploring and analyzing data or model results. However, visualization software often presents challenges on the path to learning because it assumes the user already knows the locations and types of features of interest, instead of enabling flexible and intuitive examination of results. We present examples of research and teaching using the software, Visualizer, specifically designed to create an effective and intuitive environment for interactive, scientific analysis of 3D gridded data. Visualizer runs in a range of 3D virtual reality environments (e.g., GeoWall, ImmersaDesk, or CAVE), but also provides a similar level of real-time interactivity on a desktop computer. When using Visualizer in a 3D-enabled environment, the software allows the user to interact with the data images as real objects, grabbing, rotating or walking around the data to gain insight and perspective. On the desktop, simple features, such as a set of cross-bars marking the plane of the screen, provide extra 3D spatial cues that allow the user to more quickly understand geometric relationships within the data. This platform portability allows the user to more easily integrate research results into classroom demonstrations and exercises, while the interactivity provides an engaging environment for self-directed and inquiry-based learning by students. Visualizer software is freely available for download (www.keckcaves.org) and runs on Mac OSX and Linux platforms.

3DVEM Software Modules for Efficient Management of Point Clouds and Photorealistic 3d Models

NASA Astrophysics Data System (ADS)

Fabado, S.; Seguí, A. E.; Cabrelles, M.; Navarro, S.; García-De-San-Miguel, D.; Lerma, J. L.

2013-07-01

Cultural heritage managers in general and information users in particular are not usually used to deal with high-technological hardware and software. On the contrary, information providers of metric surveys are most of the times applying latest developments for real-life conservation and restoration projects. This paper addresses the software issue of handling and managing either 3D point clouds or (photorealistic) 3D models to bridge the gap between information users and information providers as regards the management of information which users and providers share as a tool for decision-making, analysis, visualization and management. There are not many viewers specifically designed to handle, manage and create easily animations of architectural and/or archaeological 3D objects, monuments and sites, among others. 3DVEM - 3D Viewer, Editor & Meter software will be introduced to the scientific community, as well as 3DVEM - Live and 3DVEM - Register. The advantages of managing projects with both sets of data, 3D point cloud and photorealistic 3D models, will be introduced. Different visualizations of true documentation projects in the fields of architecture, archaeology and industry will be presented. Emphasis will be driven to highlight the features of new userfriendly software to manage virtual projects. Furthermore, the easiness of creating controlled interactive animations (both walkthrough and fly-through) by the user either on-the-fly or as a traditional movie file will be demonstrated through 3DVEM - Live.

NASA's Global Imagery Browse Services - Technologies for Visualizing Earth Science Data

NASA Astrophysics Data System (ADS)

Cechini, M. F.; Boller, R. A.; Baynes, K.; Schmaltz, J. E.; Thompson, C. K.; Roberts, J. T.; Rodriguez, J.; Wong, M. M.; King, B. A.; King, J.; De Luca, A. P.; Pressley, N. N.

2017-12-01

For more than 20 years, the NASA Earth Observing System (EOS) has collected earth science data for thousands of scientific parameters now totaling nearly 15 Petabytes of data. In 2013, NASA's Global Imagery Browse Services (GIBS) formed its vision to "transform how end users interact and discover [EOS] data through visualizations." This vision included leveraging scientific and community best practices and standards to provide a scalable, compliant, and authoritative source for EOS earth science data visualizations. Since that time, GIBS has grown quickly and now services millions of daily requests for over 500 imagery layers representing hundreds of earth science parameters to a broad community of users. For many of these parameters, visualizations are available within hours of acquisition from the satellite. For others, visualizations are available for the entire mission of the satellite. The GIBS system is built upon the OnEarth and MRF open source software projects, which are provided by the GIBS team. This software facilitates standards-based access for compliance with existing GIS tools. The GIBS imagery layers are predominantly rasterized images represented in two-dimensional coordinate systems, though multiple projections are supported. The OnEarth software also supports the GIBS ingest pipeline to facilitate low latency updates to new or updated visualizations. This presentation will focus on the following topics: Overview of GIBS visualizations and user community Current benefits and limitations of the OnEarth and MRF software projects and related standards GIBS access methods and their in/compatibilities with existing GIS libraries and applications Considerations for visualization accuracy and understandability Future plans for more advanced visualization concepts including Vertical Profiles and Vector-Based Representations Future plans for Amazon Web Service support and deployments

The microcomputer scientific software series 2: general linear model--regression.

Treesearch

Harold M. Rauscher

1983-01-01

The general linear model regression (GLMR) program provides the microcomputer user with a sophisticated regression analysis capability. The output provides a regression ANOVA table, estimators of the regression model coefficients, their confidence intervals, confidence intervals around the predicted Y-values, residuals for plotting, a check for multicollinearity, a...

PharmTeX: a LaTeX-Based Open-Source Platform for Automated Reporting Workflow.

PubMed

Rasmussen, Christian Hove; Smith, Mike K; Ito, Kaori; Sundararajan, Vijayakumar; Magnusson, Mats O; Niclas Jonsson, E; Fostvedt, Luke; Burger, Paula; McFadyen, Lynn; Tensfeldt, Thomas G; Nicholas, Timothy

2018-03-16

Every year, the pharmaceutical industry generates a large number of scientific reports related to drug research, development, and regulatory submissions. Many of these reports are created using text processing tools such as Microsoft Word. Given the large number of figures, tables, references, and other elements, this is often a tedious task involving hours of copying and pasting and substantial efforts in quality control (QC). In the present article, we present the LaTeX-based open-source reporting platform, PharmTeX, a community-based effort to make reporting simple, reproducible, and user-friendly. The PharmTeX creators put a substantial effort into simplifying the sometimes complex elements of LaTeX into user-friendly functions that rely on advanced LaTeX and Perl code running in the background. Using this setup makes LaTeX much more accessible for users with no prior LaTeX experience. A software collection was compiled for users not wanting to manually install the required software components. The PharmTeX templates allow for inclusion of tables directly from mathematical software output as well and figures from several formats. Code listings can be included directly from source. No previous experience and only a few hours of training are required to start writing reports using PharmTeX. PharmTeX significantly reduces the time required for creating a scientific report fully compliant with regulatory and industry expectations. QC is made much simpler, since there is a direct link between analysis output and report input. PharmTeX makes available to report authors the strengths of LaTeX document processing without the need for extensive training. Graphical Abstract ᅟ.

Web Services Provide Access to SCEC Scientific Research Application Software

NASA Astrophysics Data System (ADS)

Gupta, N.; Gupta, V.; Okaya, D.; Kamb, L.; Maechling, P.

2003-12-01

Web services offer scientific communities a new paradigm for sharing research codes and communicating results. While there are formal technical definitions of what constitutes a web service, for a user community such as the Southern California Earthquake Center (SCEC), we may conceptually consider a web service to be functionality provided on-demand by an application which is run on a remote computer located elsewhere on the Internet. The value of a web service is that it can (1) run a scientific code without the user needing to install and learn the intricacies of running the code; (2) provide the technical framework which allows a user's computer to talk to the remote computer which performs the service; (3) provide the computational resources to run the code; and (4) bundle several analysis steps and provide the end results in digital or (post-processed) graphical form. Within an NSF-sponsored ITR project coordinated by SCEC, we are constructing web services using architectural protocols and programming languages (e.g., Java). However, because the SCEC community has a rich pool of scientific research software (written in traditional languages such as C and FORTRAN), we also emphasize making existing scientific codes available by constructing web service frameworks which wrap around and directly run these codes. In doing so we attempt to broaden community usage of these codes. Web service wrapping of a scientific code can be done using a "web servlet" construction or by using a SOAP/WSDL-based framework. This latter approach is widely adopted in IT circles although it is subject to rapid evolution. Our wrapping framework attempts to "honor" the original codes with as little modification as is possible. For versatility we identify three methods of user access: (A) a web-based GUI (written in HTML and/or Java applets); (B) a Linux/OSX/UNIX command line "initiator" utility (shell-scriptable); and (C) direct access from within any Java application (and with the correct API interface from within C++ and/or C/Fortran). This poster presentation will provide descriptions of the following selected web services and their origin as scientific application codes: 3D community velocity models for Southern California, geocoordinate conversions (latitude/longitude to UTM), execution of GMT graphical scripts, data format conversions (Gocad to Matlab format), and implementation of Seismic Hazard Analysis application programs that calculate hazard curve and hazard map data sets.

Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

NASA Astrophysics Data System (ADS)

Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

AXAF user interfaces for heterogeneous analysis environments

NASA Technical Reports Server (NTRS)

Mandel, Eric; Roll, John; Ackerman, Mark S.

1992-01-01

The AXAF Science Center (ASC) will develop software to support all facets of data center activities and user research for the AXAF X-ray Observatory, scheduled for launch in 1999. The goal is to provide astronomers with the ability to utilize heterogeneous data analysis packages, that is, to allow astronomers to pick the best packages for doing their scientific analysis. For example, ASC software will be based on IRAF, but non-IRAF programs will be incorporated into the data system where appropriate. Additionally, it is desired to allow AXAF users to mix ASC software with their own local software. The need to support heterogeneous analysis environments is not special to the AXAF project, and therefore finding mechanisms for coordinating heterogeneous programs is an important problem for astronomical software today. The approach to solving this problem has been to develop two interfaces that allow the scientific user to run heterogeneous programs together. The first is an IRAF-compatible parameter interface that provides non-IRAF programs with IRAF's parameter handling capabilities. Included in the interface is an application programming interface to manipulate parameters from within programs, and also a set of host programs to manipulate parameters at the command line or from within scripts. The parameter interface has been implemented to support parameter storage formats other than IRAF parameter files, allowing one, for example, to access parameters that are stored in data bases. An X Windows graphical user interface called 'agcl' has been developed, layered on top of the IRAF-compatible parameter interface, that provides a standard graphical mechanism for interacting with IRAF and non-IRAF programs. Users can edit parameters and run programs for both non-IRAF programs and IRAF tasks. The agcl interface allows one to communicate with any command line environment in a transparent manner and without any changes to the original environment. For example, the authors routinely layer the GUI on top of IRAF, ksh, SMongo, and IDL. The agcl, based on the facilities of a system called Answer Garden, also has sophisticated support for examining documentation and help files, asking questions of experts, and developing a knowledge base of frequently required information. Thus, the GUI becomes a total environment for running programs, accessing information, examining documents, and finding human assistance. Because the agcl can communicate with any command-line environment, most projects can make use of it easily. New applications are continually being found for these interfaces. It is the authors' intention to evolve the GUI and its underlying parameter interface in response to these needs - from users as well as developers - throughout the astronomy community. This presentation describes the capabilities and technology of the above user interface mechanisms and tools. It also discusses the design philosophies guiding the work, as well as hopes for the future.

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

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.

MAGSAT for geomagnetic studies over Indian region

NASA Technical Reports Server (NTRS)

Rastogi, R. G.; Bhargava, B. N.; Singh, B. P.; Rao, D. R. K.; Rangarajan, G. K.; Rajaram, R.; Roy, M.; Arora, B. R.; Seth, A. (Principal Investigator)

1981-01-01

Progress in the preparation of software for converting data tapes produced on an IBM system to data readable on a DEC-10 system, in the creation of awareness of the utility of MAGSAT data among users in India, and in making computer programs supplied by NASA operational on the DEC-10 system is reported. Papers presented to Indian users, at the IAGA fourth scientific assembly, at a symposium on interdisciplinary approaches to geomagnetism, and a paper published in Science Today are included.

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

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

The microcomputer scientific software series 6: ECOPHYS user's manual.

Treesearch

George E. Host; H. Michael Rauscher; J. G. Isebrands; Donald I. Dickmann; Richard E. Dickson; Thomas R. Crow; D.A. Michael

1990-01-01

ECOPHYS is an ecophysiological whole-tree growth process model designed to simulate the growth of poplar in the establishment year. This microcomputer-based model may be used to test the influence of genetically determined physiological or morphological attributes on plant growth. This manual describes the installation, file structures, and operational procedures for...

The microcomputer scientific software series 5: the BIOMASS user's guide.

Treesearch

George E. Host; Stephen C. Westin; William G. Cole; Kurt S. Pregitzer

1989-01-01

BIOMASS is an interactive microcomputer program that uses allometric regression equations to calculate aboveground biomass of common tree species of the Lake States. The equations are species-specific and most use both diameter and height as independent variables. The program accommodates fixed area and variable radius sample designs and produces both individual tree...

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.

High-throughput neuroimaging-genetics computational infrastructure

PubMed Central

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D.; Franco, Joseph; Toga, Arthur W.

2014-01-01

Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize diverse suites of software tools and web-services. These pipeline workflows are represented as portable XML objects which transfer the execution instructions and user specifications from the client user machine to remote pipeline servers for distributed computing. Using Alzheimer's and Parkinson's data, we provide several examples of translational applications using this infrastructure1. PMID:24795619

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.

PubMed

de Matos, Paula; Cham, Jennifer A; Cao, Hong; Alcántara, Rafael; Rowland, Francis; Lopez, Rodrigo; Steinbeck, Christoph

2013-03-20

User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users' requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, 'canvas sort' card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.

Earth Science Data Education through Cooking Up Recipes

NASA Astrophysics Data System (ADS)

Weigel, A. M.; Maskey, M.; Smith, T.; Conover, H.

2016-12-01

One of the major challenges in Earth science research and applications is understanding and applying the proper methods, tools, and software for using scientific data. These techniques are often difficult and time consuming to identify, requiring novel users to conduct extensive research, take classes, and reach out for assistance, thus hindering scientific discovery and real-world applications. To address these challenges, the Global Hydrology Resource Center (GHRC) DAAC has developed a series of data recipes that novel users such as students, decision makers, and general Earth scientists can leverage to learn how to use Earth science datasets. Once the data recipe content had been finalized, GHRC computer and Earth scientists collaborated with a web and graphic designer to ensure the content is both attractively presented to data users, and clearly communicated to promote the education and use of Earth science data. The completed data recipes include, but are not limited to, tutorials, iPython Notebooks, resources, and tools necessary for addressing key difficulties in data use across a broad user base. These recipes enable non-traditional users to learn how to use data, but also curates and communicates common methods and approaches that may be difficult and time consuming for these users to identify.

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

Geodetic Strain Analysis Tool

NASA Technical Reports Server (NTRS)

Kedar, Sharon; Baxter, Sean C.; Parker, Jay W.; Webb, Frank H.; Owen, Susan E.; Sibthorpe, Anthony J.; Dong, Danan

2011-01-01

A geodetic software analysis tool enables the user to analyze 2D crustal strain from geodetic ground motion, and create models of crustal deformation using a graphical interface. Users can use any geodetic measurements of ground motion and derive the 2D crustal strain interactively. This software also provides a forward-modeling tool that calculates a geodetic velocity and strain field for a given fault model, and lets the user compare the modeled strain field with the strain field obtained from the user s data. Users may change parameters on-the-fly and obtain a real-time recalculation of the resulting strain field. Four data products are computed: maximum shear, dilatation, shear angle, and principal components. The current view and data dependencies are processed first. The remaining data products and views are then computed in a round-robin fashion to anticipate view changes. When an analysis or display parameter is changed, the affected data products and views are invalidated and progressively re-displayed as available. This software is designed to facilitate the derivation of the strain fields from the GPS and strain meter data that sample it to facilitate the understanding of the strengths and weaknesses of the strain field derivation from continuous GPS (CGPS) and other geodetic data from a variety of tectonic settings, to converge on the "best practices" strain derivation strategy for the Solid Earth Science ESDR System (SESES) project given the CGPS station distribution in the western U.S., and to provide SESES users with a scientific and educational tool to explore the strain field on their own with user-defined parameters.

Pandora Operation and Analysis Software

NASA Technical Reports Server (NTRS)

Herman, Jay; Cede, Alexander; Abuhassan, Nader

2012-01-01

Pandora Operation and Analysis Software controls the Pandora Sun- and sky-pointing optical head and built-in filter wheels (neutral density, UV bandpass, polarization filters, and opaque). The software also controls the attached spectrometer exposure time and thermoelectric cooler to maintain the spectrometer temperature to within 1 C. All functions are available through a GUI so as to be easily accessible by the user. The data are automatically stored on a miniature computer (netbook) for automatic download to a designated server at user defined intervals (once per day, once per week, etc.), or to a USB external device. An additional software component reduces the raw data (spectrometer counts) to preliminary scientific products for quick-view purposes. The Pandora systems are built from off-the-shelf commercial parts and from mechanical parts machined using electronic machine shop drawings. The Pandora spectrometer system is designed to look at the Sun (tracking to within 0.1 ), or to look at the sky at any zenith or azimuth angle, to gather information about the amount of trace gases or aerosols that are present.

User Interface Technology for Formal Specification Development

NASA Technical Reports Server (NTRS)

Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

Formal specification development and modification are an essential component of the knowledge-based software life cycle. User interface technology is needed to empower end-users to create their own formal specifications. This paper describes the advanced user interface for AMPHION1 a knowledge-based software engineering system that targets scientific subroutine libraries. AMPHION is a generic, domain-independent architecture that is specialized to an application domain through a declarative domain theory. Formal specification development and reuse is made accessible to end-users through an intuitive graphical interface that provides semantic guidance in creating diagrams denoting formal specifications in an application domain. The diagrams also serve to document the specifications. Automatic deductive program synthesis ensures that end-user specifications are correctly implemented. The tables that drive AMPHION's user interface are automatically compiled from a domain theory; portions of the interface can be customized by the end-user. The user interface facilitates formal specification development by hiding syntactic details, such as logical notation. It also turns some of the barriers for end-user specification development associated with strongly typed formal languages into active sources of guidance, without restricting advanced users. The interface is especially suited for specification modification. AMPHION has been applied to the domain of solar system kinematics through the development of a declarative domain theory. Testing over six months with planetary scientists indicates that AMPHION's interactive specification acquisition paradigm enables users to develop, modify, and reuse specifications at least an order of magnitude more rapidly than manual program development.

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.

The microcomputer scientific software series 8: the SYCOOR users manual.

Treesearch

Edgar E. Gutierrez-Espeleta; Gary J. Brand

1993-01-01

Describes how to use SYCOOR, an interactive Macintosh program written in BASIC for computing and adjusting synecological coordinates. Site synecological coordinates are indices of moisture, nutrients, heat, and light computed from lists of plant species present at the site. Graphs of a species` distribution in moisture-nutrient and heat-light space are also displayed...

SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows.

PubMed

Brun, Francesco; Massimi, Lorenzo; Fratini, Michela; Dreossi, Diego; Billé, Fulvio; Accardo, Agostino; Pugliese, Roberto; Cedola, Alessia

2017-01-01

When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction workflow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the reconstructed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images. Through an example of application, this article presents SYRMEP Tomo Project (STP), an open-source software tool conceived to let users design custom CT reconstruction workflows. STP has been designed for post-beamtime (off-line use) and for a new reconstruction of past archived data at user's home institution where simple computing resources are available. Releases of the software can be downloaded at the Elettra Scientific Computing group GitHub repository https://github.com/ElettraSciComp/STP-Gui.

ShakeMap manual: technical manual, user's guide, and software guide

USGS Publications Warehouse

Wald, David J.; Worden, Bruce C.; Quitoriano, Vincent; Pankow, Kris L.

2005-01-01

ShakeMap (http://earthquake.usgs.gov/shakemap) --rapidly, automatically generated shaking and intensity maps--combines instrumental measurements of shaking with information about local geology and earthquake location and magnitude to estimate shaking variations throughout a geographic area. The results are rapidly available via the Web through a variety of map formats, including Geographic Information System (GIS) coverages. These maps have become a valuable tool for emergency response, public information, loss estimation, earthquake planning, and post-earthquake engineering and scientific analyses. With the adoption of ShakeMap as a standard tool for a wide array of users and uses came an impressive demand for up-to-date technical documentation and more general guidelines for users and software developers. This manual is meant to address this need. ShakeMap, and associated Web and data products, are rapidly evolving as new advances in communications, earthquake science, and user needs drive improvements. As such, this documentation is organic in nature. We will make every effort to keep it current, but undoubtedly necessary changes in operational systems take precedence over producing and making documentation publishable.

Customizable scientific web-portal for DIII-D nuclear fusion experiment

NASA Astrophysics Data System (ADS)

Abla, G.; Kim, E. N.; Schissel, D. P.

2010-04-01

Increasing utilization of the Internet and convenient web technologies has made the web-portal a major application interface for remote participation and control of scientific instruments. While web-portals have provided a centralized gateway for multiple computational services, the amount of visual output often is overwhelming due to the high volume of data generated by complex scientific instruments and experiments. Since each scientist may have different priorities and areas of interest in the experiment, filtering and organizing information based on the individual user's need can increase the usability and efficiency of a web-portal. DIII-D is the largest magnetic nuclear fusion device in the US. A web-portal has been designed to support the experimental activities of DIII-D researchers worldwide. It offers a customizable interface with personalized page layouts and list of services for users to select. Each individual user can create a unique working environment to fit his own needs and interests. Customizable services are: real-time experiment status monitoring, diagnostic data access, interactive data analysis and visualization. The web-portal also supports interactive collaborations by providing collaborative logbook, and online instant announcement services. The DIII-D web-portal development utilizes multi-tier software architecture, and Web 2.0 technologies and tools, such as AJAX and Django, to develop a highly-interactive and customizable user interface.

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 new Planetary Science Archive (PSA): Exploration and discovery of scientific datasets from ESA's planetary missions

NASA Astrophysics Data System (ADS)

Martinez, Santa; Besse, Sebastien; Heather, Dave; Barbarisi, Isa; Arviset, Christophe; De Marchi, Guido; Barthelemy, Maud; Docasal, Ruben; Fraga, Diego; Grotheer, Emmanuel; Lim, Tanya; Macfarlane, Alan; Rios, Carlos; Vallejo, Fran; Saiz, Jaime; ESDC (European Space Data Centre) Team

2016-10-01

The Planetary Science Archive (PSA) is the European Space Agency's (ESA) repository of science data from all planetary science and exploration missions. The PSA provides access to scientific datasets through various interfaces at http://archives.esac.esa.int/psa. All datasets are scientifically peer-reviewed by independent scientists, and are compliant with the Planetary Data System (PDS) standards. The PSA is currently implementing a number of significant improvements, mostly driven by the evolution of the PDS standard, and the growing need for better interfaces and advanced applications to support science exploitation. The newly designed PSA will enhance the user experience and will significantly reduce the complexity for users to find their data promoting one-click access to the scientific datasets with more specialised views when needed. This includes a better integration with Planetary GIS analysis tools and Planetary interoperability services (search and retrieve data, supporting e.g. PDAP, EPN-TAP). It will be also up-to-date with versions 3 and 4 of the PDS standards, as PDS4 will be used for ESA's ExoMars and upcoming BepiColombo missions. Users will have direct access to documentation, information and tools that are relevant to the scientific use of the dataset, including ancillary datasets, Software Interface Specification (SIS) documents, and any tools/help that the PSA team can provide. A login mechanism will provide additional functionalities to the users to aid / ease their searches (e.g. saving queries, managing default views). This contribution will introduce the new PSA, its key features and access interfaces.

Open access for ALICE analysis based on virtualization technology

NASA Astrophysics Data System (ADS)

Buncic, P.; Gheata, M.; Schutz, Y.

2015-12-01

Open access is one of the important leverages for long-term data preservation for a HEP experiment. To guarantee the usability of data analysis tools beyond the experiment lifetime it is crucial that third party users from the scientific community have access to the data and associated software. The ALICE Collaboration has developed a layer of lightweight components built on top of virtualization technology to hide the complexity and details of the experiment-specific software. Users can perform basic analysis tasks within CernVM, a lightweight generic virtual machine, paired with an ALICE specific contextualization. Once the virtual machine is launched, a graphical user interface is automatically started without any additional configuration. This interface allows downloading the base ALICE analysis software and running a set of ALICE analysis modules. Currently the available tools include fully documented tutorials for ALICE analysis, such as the measurement of strange particle production or the nuclear modification factor in Pb-Pb collisions. The interface can be easily extended to include an arbitrary number of additional analysis modules. We present the current status of the tools used by ALICE through the CERN open access portal, and the plans for future extensions of this system.

Automation and hypermedia technology applications

NASA Technical Reports Server (NTRS)

Jupin, Joseph H.; Ng, Edward W.; James, Mark L.

1993-01-01

This paper represents a progress report on HyLite (Hypermedia Library technology): a research and development activity to produce a versatile system as part of NASA's technology thrusts in automation, information sciences, and communications. HyLite can be used as a system or tool to facilitate the creation and maintenance of large distributed electronic libraries. The contents of such a library may be software components, hardware parts or designs, scientific data sets or databases, configuration management information, etc. Proliferation of computer use has made the diversity and quantity of information too large for any single user to sort, process, and utilize effectively. In response to this information deluge, we have created HyLite to enable the user to process relevant information into a more efficient organization for presentation, retrieval, and readability. To accomplish this end, we have incorporated various AI techniques into the HyLite hypermedia engine to facilitate parameters and properties of the system. The proposed techniques include intelligent searching tools for the libraries, intelligent retrievals, and navigational assistance based on user histories. HyLite itself is based on an earlier project, the Encyclopedia of Software Components (ESC) which used hypermedia to facilitate and encourage software reuse.

Spacelab data analysis and interactive control study

NASA Technical Reports Server (NTRS)

Tarbell, T. D.; Drake, J. F.

1980-01-01

The study consisted of two main tasks, a series of interviews of Spacelab users and a survey of data processing and display equipment. Findings from the user interviews on questions of interactive control, downlink data formats, and Spacelab computer software development are presented. Equipment for quick look processing and display of scientific data in the Spacelab Payload Operations Control Center (POCC) was surveyed. Results of this survey effort are discussed in detail, along with recommendations for NASA development of several specific display systems which meet common requirements of many Spacelab experiments.

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

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

2015-01-01

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

A Student-Friendly Graphical User Interface to Extract Data from Remote Sensing Level-2 Products.

NASA Astrophysics Data System (ADS)

Bernardello, R.

2016-02-01

Remote sensing era has provided an unprecedented amount of publicly available data. The United States National Aeronautics and Space Administration Goddard Space Flight Center (NASA-GSFC) has achieved remarkable results in the distribution of these data to the scientific community through the OceanColor web page (http://oceancolor.gsfc.nasa.gov/). However, the access to these data, is not straightforward and needs a certain investment of time in learning the use of existing software. Satellite sensors acquire raw data that are processed through several steps towards a format usable by the scientific community. These products are distributed in Hierarchical Data Format (HDF) which often represents the first obstacle for students, teachers and scientists not used to deal with extensive matrices. We present here SATellite data PROcessing (SATPRO) a newly developed Graphical User Interface (GUI) designed in MATLAB environment to provide an easy, immediate yet reliable way to select and extract Level-2 data from NASA SeaWIFS and MODIS-Aqua databases for oceanic surface temperature and chlorophyll. Since no previous experience with MATLAB is required, SATPRO allows the user to explore the available dataset without investing any software-learning time. SATPRO is an ideal tool to introduce undergraduate students to the use of remote sensing data in oceanography and can also be useful for research projects at the graduate level.

CIAO: A Modern Data Analysis System for X-Ray Astronomy

NASA Astrophysics Data System (ADS)

Fruscione, Antonella

2017-08-01

It is now eighteen years after launch and Chandra continues to produce spectacular results!A portion of the success is to be attributed to the data analysis software CIAO (Chandra Interactive Analysis of Observations) that the Chandra X-Ray Center (CXC) continues to improve and release year after year.CIAO is downloaded more than 1200 times a year and it is used by a wide variety of users around the world: from novice to experienced X-ray astronomers, high school, undergraduate and graduate students, archival users (many new to X-ray or Chandra data), users with extensive resources and others from smaller countries and institutions.The scientific goals and kinds of datasets and analysis cover a wide range: observations spanning from days to years, different instrument configurations and different kinds of targets, from pointlike stars and quasars, to fuzzy galaxies and clusters, to moving solar objects. These different needs and goals require a variety of specialized software and careful and detailed documentation which is what the CIAO software provides. In general, we strive to build a software system which is easy for beginners, yet powerful for advanced users.The complexity of the Chandra data require a flexible data analysis system which provides an environment where the users can apply our tools, but can also explore and construct their own applications. The main purpose of this talk is to present CIAO as a modern data analysis system for X-ray data analysis.CIAO has grown tremendously over the years and we will highlight (a) the most recent advancements with a particular emphasis on the newly developed high-level scripts which simplify the analysis steps for the most common cases making CIAO more accessible to all users - including beginners and users who are not X-ray astronomy specialists, (b) the python-based Sherpa modelling and fitting application and the new stand-alone version openly developed and distributed on Github and (c) progress on methods to characterize the Chandra PSF.

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

Social Tagging of Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

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.

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.

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

PubMed Central

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V.; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-01-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfra­structure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities. PMID:22514186

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology.

PubMed

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-05-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

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.

Recording the LHCb data and software dependencies

NASA Astrophysics Data System (ADS)

Trisovic, Ana; Couturier, Ben; Gibson, Val; Jones, Chris

2017-10-01

In recent years awareness of the importance of preserving the experimental data and scientific software at CERN has been rising. To support this effort, we are presenting a novel approach to structure dependencies of the LHCb data and software to make it more accessible in the long-term future. In this paper, we detail the implementation of a graph database of these dependencies. We list the implications that can be deduced from the graph mining (such as a search for the legacy software), with emphasis on data preservation. Furthermore, we introduce a methodology of recreating the LHCb data, thus supporting reproducible research and data stewardship. Finally, we describe how this information is made available to the users on a web portal that promotes data and analysis preservation and good practise with analysis documentation.

Digital Repositories and the Question of Data Usefulness

NASA Astrophysics Data System (ADS)

Hughes, J. S.; Downs, R. R.

2017-12-01

The advent of ISO standards for trustworthy long-term digital repositories provides both a set of principles to develop long-term data repositories and the instruments to assess them for trustworthiness. Such mandatory high-level requirements are broad enough to be achievable, to some extent, by many scientific data centers, archives, and other repositories. But the requirement that the data be useful in the future, the requirement that is usually considered to be most relevant to the value of the repository for its user communities, largely remains subject to various interpretations and misunderstanding. However, current and future users will be relying on repositories to preserve and disseminate the data and information needed to discover, understand, and utilize these resources to support their research, learning, and decision-making objectives. Therefore, further study is needed to determine the approaches that can be adopted by repositories to make data useful to future communities of users. This presentation will describe approaches for enabling scientific data and related information, such as software, to be useful for current and potential future user communities and will present the methodology chosen to make one science discipline's data useful for both current and future users. The method uses an ontology-based information model to define and capture the information necessary to make the data useful for contemporary and future users.

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).

A land-surface Testbed for EOSDIS

NASA Technical Reports Server (NTRS)

Emery, William; Kelley, Tim

1994-01-01

The main objective of the Testbed project was to deliver satellite images via the Internet to scientific and educational users free of charge. The main method of operations was to store satellite images on a low cost tape library system, visually browse the raw satellite data, access the raw data filed, navigate the imagery through 'C' programming and X-Windows interface software, and deliver the finished image to the end user over the Internet by means of file transfer protocol methods. The conclusion is that the distribution of satellite imagery by means of the Internet is feasible, and the archiving of large data sets can be accomplished with low cost storage systems allowing multiple users.

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.

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 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

PQLX: A seismic data quality control system description, applications, and users manual

USGS Publications Warehouse

McNamara, Daniel E.; Boaz, Richard I.

2011-01-01

We present a detailed description and users manual for a new tool to evaluate seismic station performance and characteristics by providing quick and easy transitions between visualizations of the frequency and time domains. The software is based on the probability density functions (PDF) of power spectral densities (PSD) (McNamara and Buland, 2004) and builds on the original development of the PDF stand-alone software system (McNamara and Boaz, 2005) and the seismological data viewer application PQL (IRIS-PASSCAL Quick Look) and PQLII (available through the IRIS PASSCAL program: http://www.passcal.nmt.edu/content/pql-ii-program-viewing-data). With PQLX (PQL eXtended), computed PSDs are stored in a MySQL database, allowing a user to access specific time periods of PSDs (PDF subsets) and time series segments through a GUI-driven interface. The power of the method and software lies in the fact that there is no need to screen the data for system transients, earthquakes, or general data artifacts, because they map into a background probability level. In fact, examination of artifacts related to station operation and episodic cultural noise allow us to estimate both the overall station quality and a baseline level of Earth noise at each site. The output of this analysis tool is useful for both operational and scientific applications. Operationally, it is useful for characterizing the current and past performance of existing broadband stations, for conducting tests on potential new seismic station locations, for evaluating station baseline noise levels (McNamara and others, 2009), for detecting problems with the recording system or sensors, and for evaluating the overall quality of data and metadata. Scientifically, the tool allows for mining of PSDs for investigations on the evolution of seismic noise (for example, Aster and others, 2008; and Aster and others, 2010) and other phenomena. Currently, PQLX is operational at several organizations including the USGS National Earthquake Information Center (NEIC), the USGS Albuquerque Seismological Laboratory (ASL), and the Incorporated Research Institutions in Seismology (IRIS) Data Management Center (DMC) for station monitoring and instrument response quality control. The PQLX system is available to the community at large through the U.S. Geological Survey (USGS) (http://ehpm-earthquake.wr.usgs.gov/research/software/pqlx.php) and IRIS (http://www.iris.edu/software/pqlx). Also provided is a fully searchable website for bug reporting and enhancement requests (http://wush.net/bugzilla/PQLX). The first part of this document aims to describe and illustrate some of the features and capabilities of the software. The second part of this document is a detailed users manual that covers installation procedures, system requirements, operations, bug reporting, and software components (Appendix).

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.

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.

Program status

NASA Technical Reports Server (NTRS)

Smith, P.

1986-01-01

The Pilot Climate Data System (PCDS) was designed to support a variety of users that have been arbitrarily categorized into four groups: researchers, data producers, occasional users, and management. The expanding capabilities of the system are attracting the attention of both academic and other scientific institutions worldwide. Highlighted by progress in networking capabilities, hardware acquisitions, software developments, data set additions, and tutorial developments, exciting advances have taken place since the First PCDS Workshop. In the plans for the 1986 fiscal year, recommendations from an ad hoc users' group meeting in May 1985 and from the First PCDS workshop are apparent. This year's plans are listed, along with comments made at the users' group meeting. Although the PCDS is presently considered to be in a developmental phase, plans for making the transition to an operational phase are being implemented.

Netlib services and resources

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

Browne, S.V.; Green, S.C.; Moore, K.

1994-04-01

The Netlib repository, maintained by the University of Tennessee and Oak Ridge National Laboratory, contains freely available software, documents, and databases of interest to the numerical, scientific computing, and other communities. This report includes both the Netlib User`s Guide and the Netlib System Manager`s Guide, and contains information about Netlib`s databases, interfaces, and system implementation. The Netlib repository`s databases include the Performance Database, the Conferences Database, and the NA-NET mail forwarding and Whitepages Databases. A variety of user interfaces enable users to access the Netlib repository in the manner most convenient and compatible with their networking capabilities. These interfaces includemore » the Netlib email interface, the Xnetlib X Windows client, the netlibget command-line TCP/IP client, anonymous FTP, anonymous RCP, and gopher.« less

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.

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

Debian/meterology is a project to integrate climate tools and analysis software into the mainstream Debian/Ubuntu Linux distributions. This work describes lessons learnt, and recommends practices for scientific software to be adopted and maintained in OS distributions. In addition to standard analysis tools (cdo,, grads, ferret, metview, ncl, etc.), software used by the Earth System Grid Federation was chosen for integraion, to enable ESGF portals to be built on this base; however exposing scientific codes via web APIs enables security weaknesses, normally ignorable, to be exposed. How tools are hardened, and what changes are required to handle security upgrades, are described. Secondly, to enable libraries and components (e.g. Python modules) to be integrated requires planning by writers: it is not sufficient to assume users can upgrade their code when you make incompatible changes. Here, practices are recommended to enable upgrades and co-installability of C, C++, Fortran and Python codes. Finally, software packages such as NetCDF and HDF5 can be built in multiple configurations. Tools may then expect incompatible versions of these libraries (e.g. serial and parallel) to be simultaneously available; how this was solved in Debian using "pkg-config" and shared library interfaces is described, and best practices for software writers to enable this are summarised.

Internet-to-orbit gateway and virtual ground station: A tool for space research and scientific outreach

NASA Astrophysics Data System (ADS)

Jaffer, Ghulam; Nader, Ronnie; Koudelka, Otto

2011-09-01

Students in higher education, and scientific and technological researchers want to communicate with the International Space Station (ISS), download live satellite images, and receive telemetry, housekeeping and science/engineering data from nano-satellites and larger spacecrafts. To meet this need the Ecuadorian Civilian Space Agency (EXA) has recently provided the civilian world with an internet-to-orbit gateway (Hermes-A/Minotaur) Space Flight Control Center (SFCC) available for public use. The gateway has a maximum range of tracking and detection of 22,000 km and sensitivity such that it can receive and discriminate the signals from a satellite transmitter with power˜0.1 W. The capability is enough to receive the faintest low-earth-orbit (LEO) satellites. This gateway virtually connects participating internet clients around the world to a remote satellite ground station (GS), providing a broad community for multinational cooperation. The goal of the GS is to lower financial and engineering barriers that hinder access to science and engineering data from orbit. The basic design of the virtual GS on a user side is based on free software suites. Using these and other software tools the GS is able to provide access to orbit for a multitude of users without each having to go through the costly setups. We present the design and implementation of the virtual GS in a higher education and scientific outreach settings. We also discuss the basic architecture of the single existing system and the benefits of a proposed distributed system. Details of the software tools and their applicability to synchronous round-the-world tracking, monitoring and processing performed by students and teams at Graz University of Technology, Austria, EXA-Ecuador, University of Michigan, USA and JAXA who have participated in various mission operations and have investigated real-time satellite data download and image acquisition and processing. Students and other remote users at these institutions undergo training with in orbit satellites in preparation for their own use with future university-class nano-satellites' post launch space operations. The exclusive ability of Hermes-A/Minotaur to act as a gateway between remote users (internet) and satellites (in orbit) makes the virtual GS at user-end more feasible for the long-term real-time nano/cubesats space operations. The only requirement is to have a mutual agreement between EXA and participating university/research organization and broadband internet connection at user-end. With successful and remote satellite tracking and downloading of real-time data from many operational satellites, the Hermes has been found a reliable potential GS for current and future university missions and a training platform for individuals pursuing space operations.

Modeling Guru: Knowledge Base for NASA Modelers

NASA Astrophysics Data System (ADS)

Seablom, M. S.; Wojcik, G. S.; van Aartsen, B. H.

2009-05-01

Modeling Guru is an on-line knowledge-sharing resource for anyone involved with or interested in NASA's scientific models or High End Computing (HEC) systems. Developed and maintained by the NASA's Software Integration and Visualization Office (SIVO) and the NASA Center for Computational Sciences (NCCS), Modeling Guru's combined forums and knowledge base for research and collaboration is becoming a repository for the accumulated expertise of NASA's scientific modeling and HEC communities. All NASA modelers and associates are encouraged to participate and provide knowledge about the models and systems so that other users may benefit from their experience. Modeling Guru is divided into a hierarchy of communities, each with its own set forums and knowledge base documents. Current modeling communities include those for space science, land and atmospheric dynamics, atmospheric chemistry, and oceanography. In addition, there are communities focused on NCCS systems, HEC tools and libraries, and programming and scripting languages. Anyone may view most of the content on Modeling Guru (available at http://modelingguru.nasa.gov/), but you must log in to post messages and subscribe to community postings. The site offers a full range of "Web 2.0" features, including discussion forums, "wiki" document generation, document uploading, RSS feeds, search tools, blogs, email notification, and "breadcrumb" links. A discussion (a.k.a. forum "thread") is used to post comments, solicit feedback, or ask questions. If marked as a question, SIVO will monitor the thread, and normally respond within a day. Discussions can include embedded images, tables, and formatting through the use of the Rich Text Editor. Also, the user can add "Tags" to their thread to facilitate later searches. The "knowledge base" is comprised of documents that are used to capture and share expertise with others. The default "wiki" document lets users edit within the browser so others can easily collaborate on the same document, even allowing the author to select those who may edit and approve the document. To maintain knowledge integrity, all documents are moderated before they are visible to the public. Modeling Guru, running on Clearspace by Jive Software, has been an active resource to the NASA modeling and HEC communities for more than a year and currently has more than 100 active users. SIVO will soon install live instant messaging support, as well as a user-customizable homepage with social-networking features. In addition, SIVO plans to implement a large dataset/file storage capability so that users can quickly and easily exchange datasets and files with one another. Continued active community participation combined with periodic software updates and improved features will ensure that Modeling Guru remains a vibrant, effective, easy-to-use tool for the NASA scientific community.

Collaborative Planetary GIS with JMARS

NASA Astrophysics Data System (ADS)

Dickenshied, S.; Christensen, P. R.; Edwards, C. S.; Prashad, L. C.; Anwar, S.; Engle, E.; Noss, D.; Jmars Development Team

2010-12-01

Traditional GIS tools have allowed users to work locally with their own datasets in their own computing environment. More recently, data providers have started offering online repositories of preprocessed data which helps minimize the learning curve required to access new datasets. The ideal collaborative GIS tool provides the functionality of a traditional GIS and easy access to preprocessed data repositories while also enabling users to contribute data, analysis, and ideas back into the very tools they're using. JMARS (Java Mission-planning and Analysis for Remote Sensing) is a suite of geospatial applications developed by the Mars Space Flight Facility at Arizona State University. This software is used for mission planning and scientific data analysis by several NASA missions, including Mars Odyssey, Mars Reconnaissance Orbiter, and the Lunar Reconnaissance Orbiter. It is used by scientists, researchers and students of all ages from more than 40 countries around the world. In addition to offering a rich set of global and regional maps and publicly released orbiter images, the JMARS software development team has been working on ways to encourage the creation of collaborative datasets. Bringing together users from diverse teams and backgrounds allows new features to be developed with an interest in making the application useful and accessible to as wide a potential audience as possible. Actively engaging the scientific community in development strategy and hands on tasks allows the creation of user driven data content that would not otherwise be possible. The first community generated dataset to result from this effort is a tool mapping peer-reviewed papers to the locations they relate to on Mars with links to ancillary data. This allows users of JMARS to browse to an area of interest and then quickly locate papers corresponding to that area. Alternately, users can search for published papers over a specified time interval and visually see what areas of Mars have received the most attention over the requested time span.

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.

Hypertext and Multimedia for Functional Enhancement of USARIEM Medical Handbooks and Biomedical Simulation Software.

DTIC Science & Technology

1994-12-01

complex Internet addresses. Hypertext and hypermedia documents have logical and physical structure (Shneiderman, 1993). The logical structure delineates...Rubra, Miliaria Profunda , Anhidrotic Heat Exhaustion, Heat Syncope, Heat Edema, Sunburn, and Heat Tetany. The user may return to the main document...military or scientific organizations via digital communications networks such as the Internet . Access clearance would first be obtained from the USARIEM

Public-domain-software solution to data-access problems for numerical modelers

USGS Publications Warehouse

Jenter, Harry; Signell, Richard

1992-01-01

Unidata's network Common Data Form, netCDF, provides users with an efficient set of software for scientific-data-storage, retrieval, and manipulation. The netCDF file format is machine-independent, direct-access, self-describing, and in the public domain, thereby alleviating many problems associated with accessing output from large hydrodynamic models. NetCDF has programming interfaces in both the Fortran and C computer language with an interface to C++ planned for release in the future. NetCDF also has an abstract data type that relieves users from understanding details of the binary file structure; data are written and retrieved by an intuitive, user-supplied name rather than by file position. Users are aided further by Unidata's inclusion of the Common Data Language, CDL, a printable text-equivalent of the contents of a netCDF file. Unidata provides numerous operators and utilities for processing netCDF files. In addition, a number of public-domain and proprietary netCDF utilities from other sources are available at this time or will be available later this year. The U.S. Geological Survey has produced and is producing a number of public-domain netCDF utilities.

Performance of the engineering analysis and data system 2 common file system

NASA Technical Reports Server (NTRS)

Debrunner, Linda S.

1993-01-01

The Engineering Analysis and Data System (EADS) was used from April 1986 to July 1993 to support large scale scientific and engineering computation (e.g. computational fluid dynamics) at Marshall Space Flight Center. The need for an updated system resulted in a RFP in June 1991, after which a contract was awarded to Cray Grumman. EADS II was installed in February 1993, and by July 1993 most users were migrated. EADS II is a network of heterogeneous computer systems supporting scientific and engineering applications. The Common File System (CFS) is a key component of this system. The CFS provides a seamless, integrated environment to the users of EADS II including both disk and tape storage. UniTree software is used to implement this hierarchical storage management system. The performance of the CFS suffered during the early months of the production system. Several of the performance problems were traced to software bugs which have been corrected. Other problems were associated with hardware. However, the use of NFS in UniTree UCFM software limits the performance of the system. The performance issues related to the CFS have led to a need to develop a greater understanding of the CFS organization. This paper will first describe the EADS II with emphasis on the CFS. Then, a discussion of mass storage systems will be presented, and methods of measuring the performance of the Common File System will be outlined. Finally, areas for further study will be identified and conclusions will be drawn.

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.

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.

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics

PubMed Central

2013-01-01

User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users’ requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios. For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature. We employed several UCD techniques, including: persona development, interviews, ‘canvas sort’ card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience. PMID:23514033

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.

SEDA: A software package for the Statistical Earthquake Data Analysis

NASA Astrophysics Data System (ADS)

Lombardi, A. M.

2017-03-01

In this paper, the first version of the software SEDA (SEDAv1.0), designed to help seismologists statistically analyze earthquake data, is presented. The package consists of a user-friendly Matlab-based interface, which allows the user to easily interact with the application, and a computational core of Fortran codes, to guarantee the maximum speed. The primary factor driving the development of SEDA is to guarantee the research reproducibility, which is a growing movement among scientists and highly recommended by the most important scientific journals. SEDAv1.0 is mainly devoted to produce accurate and fast outputs. Less care has been taken for the graphic appeal, which will be improved in the future. The main part of SEDAv1.0 is devoted to the ETAS modeling. SEDAv1.0 contains a set of consistent tools on ETAS, allowing the estimation of parameters, the testing of model on data, the simulation of catalogs, the identification of sequences and forecasts calculation. The peculiarities of routines inside SEDAv1.0 are discussed in this paper. More specific details on the software are presented in the manual accompanying the program package.

2MASS Catalog Server Kit Version 2.1

NASA Astrophysics Data System (ADS)

Yamauchi, C.

2013-10-01

The 2MASS Catalog Server Kit is open source software for use in easily constructing a high performance search server for important astronomical catalogs. This software utilizes the open source RDBMS PostgreSQL, therefore, any users can setup the database on their local computers by following step-by-step installation guide. The kit provides highly optimized stored functions for positional searchs similar to SDSS SkyServer. Together with these, the powerful SQL environment of PostgreSQL will meet various user's demands. We released 2MASS Catalog Server Kit version 2.1 in 2012 May, which supports the latest WISE All-Sky catalog (563,921,584 rows) and 9 major all-sky catalogs. Local databases are often indispensable for observatories with unstable or narrow-band networks or severe use, such as retrieving large numbers of records within a small period of time. This software is the best for such purposes, and increasing supported catalogs and improvements of version 2.1 can cover a wider range of applications including advanced calibration system, scientific studies using complicated SQL queries, etc. Official page: http://www.ir.isas.jaxa.jp/~cyamauch/2masskit/

SEDA: A software package for the Statistical Earthquake Data Analysis

PubMed Central

Lombardi, A. M.

2017-01-01

In this paper, the first version of the software SEDA (SEDAv1.0), designed to help seismologists statistically analyze earthquake data, is presented. The package consists of a user-friendly Matlab-based interface, which allows the user to easily interact with the application, and a computational core of Fortran codes, to guarantee the maximum speed. The primary factor driving the development of SEDA is to guarantee the research reproducibility, which is a growing movement among scientists and highly recommended by the most important scientific journals. SEDAv1.0 is mainly devoted to produce accurate and fast outputs. Less care has been taken for the graphic appeal, which will be improved in the future. The main part of SEDAv1.0 is devoted to the ETAS modeling. SEDAv1.0 contains a set of consistent tools on ETAS, allowing the estimation of parameters, the testing of model on data, the simulation of catalogs, the identification of sequences and forecasts calculation. The peculiarities of routines inside SEDAv1.0 are discussed in this paper. More specific details on the software are presented in the manual accompanying the program package. PMID:28290482

Air Markets Program Data (AMPD)

EPA Pesticide Factsheets

The Air Markets Program Data tool allows users to search EPA data to answer scientific, general, policy, and regulatory questions about industry emissions. Air Markets Program Data (AMPD) is a web-based application that allows users easy access to both current and historical data collected as part of EPA's emissions trading programs. This site allows you to create and view reports and to download emissions data for further analysis. AMPD provides a query tool so users can create custom queries of industry source emissions data, allowance data, compliance data, and facility attributes. In addition, AMPD provides interactive maps, charts, reports, and pre-packaged datasets. AMPD does not require any additional software, plug-ins, or security controls and can be accessed using a standard web browser.

Viewing ISS Data in Real Time via the Internet

NASA Technical Reports Server (NTRS)

Myers, Gerry; Chamberlain, Jim

2004-01-01

EZStream is a computer program that enables authorized users at diverse terrestrial locations to view, in real time, data generated by scientific payloads aboard the International Space Station (ISS). The only computation/communication resource needed for use of EZStream is a computer equipped with standard Web-browser software and a connection to the Internet. EZStream runs in conjunction with the TReK software, described in a prior NASA Tech Briefs article, that coordinates multiple streams of data for the ground communication system of the ISS. EZStream includes server components that interact with TReK within the ISS ground communication system and client components that reside in the users' remote computers. Once an authorized client has logged in, a server component of EZStream pulls the requested data from a TReK application-program interface and sends the data to the client. Future EZStream enhancements will include (1) extensions that enable the server to receive and process arbitrary data streams on its own and (2) a Web-based graphical-user-interface-building subprogram that enables a client who lacks programming expertise to create customized display Web pages.

The INDIGO-Datacloud Authentication and Authorization Infrastructure

NASA Astrophysics Data System (ADS)

Ceccanti, A.; Hardt, M.; Wegh, B.; Millar, AP; Caberletti, M.; Vianello, E.; Licehammer, S.

2017-10-01

Contemporary distributed computing infrastructures (DCIs) are not easily and securely accessible by scientists. These computing environments are typically hard to integrate due to interoperability problems resulting from the use of different authentication mechanisms, identity negotiation protocols and access control policies. Such limitations have a big impact on the user experience making it hard for user communities to port and run their scientific applications on resources aggregated from multiple providers. The INDIGO-DataCloud project wants to provide the services and tools needed to enable a secure composition of resources from multiple providers in support of scientific applications. In order to do so, a common AAI architecture has to be defined that supports multiple authentication mechanisms, support delegated authorization across services and can be easily integrated in off-the-shelf software. In this contribution we introduce the INDIGO Authentication and Authorization Infrastructure, describing its main components and their status and how authentication, delegation and authorization flows are implemented across services.

Minutes of the CD-ROM Workshop

NASA Technical Reports Server (NTRS)

King, Joseph H.; Grayzeck, Edwin J.

1989-01-01

The workshop described in this document had two goals: (1) to establish guidelines for the CD-ROM as a tool to distribute datasets; and (2) to evaluate current scientific CD-ROM projects as an archive. Workshop attendees were urged to coordinate with European groups to develop CD-ROM, which is already available at low cost in the U.S., as a distribution medium for astronomical datasets. It was noted that NASA has made the CD Publisher at the National Space Science Data Center (NSSDC) available to the scientific community when the Publisher is not needed for NASA work. NSSDC's goal is to provide the Publisher's user with the hardware and software tools needed to design a user's dataset for distribution. This includes producing a master CD and copies. The prerequisite premastering process is described, as well as guidelines for CD-ROM construction. The production of discs was evaluated. CD-ROM projects, guidelines, and problems of the technology were discussed.

Mac OS X for Astronomy

NASA Astrophysics Data System (ADS)

Pierfederici, F.; Pirzkal, N.; Hook, R. N.

Mac OS X is the new Unix based version of the Macintosh operating system. It combines a high performance DisplayPDF user interface with a standard BSD UNIX subsystem and provides users with simultaneous access to a broad range of applications which were not previously available on a single system such as Microsoft Office and Adobe Photoshop, as well as legacy X11-based scientific tools and packages like IRAF, SuperMongo, MIDAS, etc. The combination of a modern GUI layered on top of a familiar UNIX environment paves the way for new, more flexible and powerful astronomical tools to be developed while assuring compatibility with already existing, older programs. In this paper, we outline the strengths of the Mac OS X platform in a scientific environment, astronomy in particular, and point to the numerous astronomical software packages available for this platform; most notably the Scisoft collection which we have compiled.

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.

Sustainability of Open-Source Software Organizations as Underpinning for Sustainable Interoperability on Large Scales

NASA Astrophysics Data System (ADS)

Fulker, D. W.; Gallagher, J. H. R.

2015-12-01

OPeNDAP's Hyrax data server is an open-source framework fostering interoperability via easily-deployed Web services. Compatible with solutions listed in the (PA001) session description—federation, rigid standards and brokering/mediation—the framework can support tight or loose coupling, even with dependence on community-contributed software. Hyrax is a Web-services framework with a middleware-like design and a handler-style architecture that together reduce the interoperability challenge (for N datatypes and M user contexts) to an O(N+M) problem, similar to brokering. Combined with an open-source ethos, this reduction makes Hyrax a community tool for gaining interoperability. E.g., in its response to the Big Earth Data Initiative (BEDI), NASA references OPeNDAP-based interoperability. Assuming its suitability, the question becomes: how sustainable is OPeNDAP, a small not-for-profit that produces open-source software, i.e., has no software-sales? In other words, if geoscience interoperability depends on OPeNDAP and similar organizations, are those entities in turn sustainable? Jim Collins (in Good to Great) highlights three questions that successful companies can answer (paraphrased here): What is your passion? Where is your world-class excellence? What drives your economic engine? We attempt to shed light on OPeNDAP sustainability by examining these. Passion: OPeNDAP has a focused passion for improving the effectiveness of scientific data sharing and use, as deeply-cooperative community endeavors. Excellence: OPeNDAP has few peers in remote, scientific data access. Skills include computer science with experience in data science, (operational, secure) Web services, and software design (for servers and clients, where the latter vary from Web pages to standalone apps and end-user programs). Economic Engine: OPeNDAP is an engineering services organization more than a product company, despite software being key to OPeNDAP's reputation. In essence, provision of engineering expertise, via contracts and grants, is the economic engine. Hence sustainability, as needed to address global grand challenges in geoscience, depends on agencies' and others' abilities and willingness to offer grants and let contracts for continually upgrading open-source software from OPeNDAP and others.

Database Design and Management in Engineering Optimization.

DTIC Science & Technology

1988-02-01

scientific and engineer- Q.- ’ method In the mid-19SOs along with modern digital com- ing applications. The paper highlights the difference puters, have made...is continuously tion software can call standard subroutines from the DBMS redefined in an application program, DDL must have j libary to define...operations. .. " type data usually encountered in engineering applications. GFDGT: Computes the number of digits needed to display " "’ A user

The microcomputer scientific software series 9: user's guide to Geo-CLM: geostatistical interpolation of the historical climatic record in the Lake States.

Treesearch

Margaret R. Holdaway

1994-01-01

Describes Geo-CLM, a computer application (for Mac or DOS) whose primary aim is to perform multiple kriging runs to interpolate the historic climatic record at research plots in the Lake States. It is an exploration and analysis tool. Addition capabilities include climatic databases, a flexible test mode, cross validation, lat/long conversion, English/metric units,...

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.

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.

AstrodyToolsWeb an e-Science project in Astrodynamics and Celestial Mechanics fields

NASA Astrophysics Data System (ADS)

López, R.; San-Juan, J. F.

2013-05-01

Astrodynamics Web Tools, AstrodyToolsWeb (http://tastrody.unirioja.es), is an ongoing collaborative Web Tools computing infrastructure project which has been specially designed to support scientific computation. AstrodyToolsWeb provides project collaborators with all the technical and human facilities in order to wrap, manage, and use specialized noncommercial software tools in Astrodynamics and Celestial Mechanics fields, with the aim of optimizing the use of resources, both human and material. However, this project is open to collaboration from the whole scientific community in order to create a library of useful tools and their corresponding theoretical backgrounds. AstrodyToolsWeb offers a user-friendly web interface in order to choose applications, introduce data, and select appropriate constraints in an intuitive and easy way for the user. After that, the application is executed in real time, whenever possible; then the critical information about program behavior (errors and logs) and output, including the postprocessing and interpretation of its results (graphical representation of data, statistical analysis or whatever manipulation therein), are shown via the same web interface or can be downloaded to the user's computer.

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.

Beyond the Renderer: Software Architecture for Parallel Graphics and Visualization

NASA Technical Reports Server (NTRS)

Crockett, Thomas W.

1996-01-01

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

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

A workflow learning model to improve geovisual analytics utility

PubMed Central

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

2011-01-01

Introduction This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. Objectives The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. Methodology The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. Results/Conclusions In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009. PMID:21983545

A workflow learning model to improve geovisual analytics utility.

PubMed

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

2009-01-01

INTRODUCTION: This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. OBJECTIVES: The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. METHODOLOGY: The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. RESULTS/CONCLUSIONS: In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009.

The EPOS e-Infrastructure

NASA Astrophysics Data System (ADS)

Jeffery, Keith; Bailo, Daniele

2014-05-01

The European Plate Observing System (EPOS) is integrating geoscientific information concerning earth movements in Europe. We are approaching the end of the PP (Preparatory Project) phase and in October 2014 expect to continue with the full project within ESFRI (European Strategic Framework for Research Infrastructures). The key aspects of EPOS concern providing services to allow homogeneous access by end-users over heterogeneous data, software, facilities, equipment and services. The e-infrastructure of EPOS is the heart of the project since it integrates the work on organisational, legal, economic and scientific aspects. Following the creation of an inventory of relevant organisations, persons, facilities, equipment, services, datasets and software (RIDE) the scale of integration required became apparent. The EPOS e-infrastructure architecture has been developed systematically based on recorded primary (user) requirements and secondary (interoperation with other systems) requirements through Strawman, Woodman and Ironman phases with the specification - and developed confirmatory prototypes - becoming more precise and progressively moving from paper to implemented system. The EPOS architecture is based on global core services (Integrated Core Services - ICS) which access thematic nodes (domain-specific European-wide collections, called thematic Core Services - TCS), national nodes and specific institutional nodes. The key aspect is the metadata catalog. In one dimension this is described in 3 levels: (1) discovery metadata using well-known and commonly used standards such as DC (Dublin Core) to enable users (via an intelligent user interface) to search for objects within the EPOS environment relevant to their needs; (2) contextual metadata providing the context of the object described in the catalog to enable a user or the system to determine the relevance of the discovered object(s) to their requirement - the context includes projects, funding, organisations involved, persons involved, related publications, facilities, equipment and others, and utilises CERIF (Common European Research Information Format) standard (see www.eurocris.org); (3) detailed metadata which is specific to a domain or to a particular object and includes the schema describing the object to processing software. The other dimension of the metadata concerns the objects described. These are classified into users, services (including software), data and resources (computing, data storage, instruments and scientific equipment). An alternative architecture has been considered: using brokering. This technique has been used especially in North America geoscience projects to interoperate datasets. The technique involves writing software to interconvert between any two node datasets. Given n nodes this implies writing n*(n-1) convertors. EPOS Working Group 7 (e-infrastructures and virtual community) which deals with the design and implementation of a prototype of the EPOS services, chose to use an approach which endows the system with an extreme flexibility and sustainability. It is called the Metadata Catalogue approach. With the use of the catalogue the EPOS system can: 1. interoperate with software, services, users, organisations, facilities, equipment etc. as well as datasets; 2. avoid to write n*(n-1) software convertors and generate as much as possible, through the information contained in the catalogue only n convertors. This is a huge saving - especially in maintenance as the datasets (or other node resources) evolve. We are working on (semi-) automation of convertor generation by metadata mapping - this is leading-edge computer science research; 3. make large use of contextual metadata which enable a user or a machine to: (i) improve discovery of resources at nodes; (ii) improve precision and recall in search; (iii) drive the systems for identification, authentication, authorisation, security and privacy recording the relevant attributes of the node resources and of the user; (iv) manage provenance and long-term digital preservation; The linkage between the Integrated Services, which provide the integration of data and services, with the diverse Thematic Services Nodes is provided by means of a compatibility layer, which includes the aforementioned metadata catalogue. This layer provides 'connectors' to make local data, software and services available through the EPOS Integrated Services layer. In conclusion, we believe the EPOS e-infrastructure architecture is fit for purpose including long-term sustainability and pan-European access to data and services.

'Tagger' - a Mac OS X Interactive Graphical Application for Data Inference and Analysis of N-Dimensional Datasets in the Natural Physical Sciences.

NASA Astrophysics Data System (ADS)

Morse, P. E.; Reading, A. M.; Lueg, C.

2014-12-01

Pattern-recognition in scientific data is not only a computational problem but a human-observer problem as well. Human observation of - and interaction with - data visualization software can augment, select, interrupt and modify computational routines and facilitate processes of pattern and significant feature recognition for subsequent human analysis, machine learning, expert and artificial intelligence systems.'Tagger' is a Mac OS X interactive data visualisation tool that facilitates Human-Computer interaction for the recognition of patterns and significant structures. It is a graphical application developed using the Quartz Composer framework. 'Tagger' follows a Model-View-Controller (MVC) software architecture: the application problem domain (the model) is to facilitate novel ways of abstractly representing data to a human interlocutor, presenting these via different viewer modalities (e.g. chart representations, particle systems, parametric geometry) to the user (View) and enabling interaction with the data (Controller) via a variety of Human Interface Devices (HID). The software enables the user to create an arbitrary array of tags that may be appended to the visualised data, which are then saved into output files as forms of semantic metadata. Three fundamental problems that are not strongly supported by conventional scientific visualisation software are addressed:1] How to visually animate data over time, 2] How to rapidly deploy unconventional parametrically driven data visualisations, 3] How to construct and explore novel interaction models that capture the activity of the end-user as semantic metadata that can be used to computationally enhance subsequent interrogation. Saved tagged data files may be loaded into Tagger, so that tags may be tagged, if desired. Recursion opens up the possibility of refining or overlapping different types of tags, tagging a variety of different POIs or types of events, and of capturing different types of specialist observations of important or noticeable events. Other visualisations and modes of interaction will also be demonstrated, with the aim of discovering knowledge in large datasets in the natural, physical sciences. Fig.1 Wave height data from an oceanographic Wave Rider Buoy. Colors/radii are driven by wave height data.

The Chandra X-ray Center data system: supporting the mission of the Chandra X-ray Observatory

NASA Astrophysics Data System (ADS)

Evans, Janet D.; Cresitello-Dittmar, Mark; Doe, Stephen; Evans, Ian; Fabbiano, Giuseppina; Germain, Gregg; Glotfelty, Kenny; Hall, Diane; Plummer, David; Zografou, Panagoula

2006-06-01

The Chandra X-ray Center Data System provides end-to-end scientific software support for Chandra X-ray Observatory mission operations. The data system includes the following components: (1) observers' science proposal planning tools; (2) science mission planning tools; (3) science data processing, monitoring, and trending pipelines and tools; and (4) data archive and database management. A subset of the science data processing component is ported to multiple platforms and distributed to end-users as a portable data analysis package. Web-based user tools are also available for data archive search and retrieval. We describe the overall architecture of the data system and its component pieces, and consider the design choices and their impacts on maintainability. We discuss the many challenges involved in maintaining a large, mission-critical software system with limited resources. These challenges include managing continually changing software requirements and ensuring the integrity of the data system and resulting data products while being highly responsive to the needs of the project. We describe our use of COTS and OTS software at the subsystem and component levels, our methods for managing multiple release builds, and adapting a large code base to new hardware and software platforms. We review our experiences during the life of the mission so-far, and our approaches for keeping a small, but highly talented, development team engaged during the maintenance phase of a mission.

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.

Gpufit: An open-source toolkit for GPU-accelerated curve fitting.

PubMed

Przybylski, Adrian; Thiel, Björn; Keller-Findeisen, Jan; Stock, Bernd; Bates, Mark

2017-11-16

We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of up to 42 times when comparing Gpufit with an identical CPU-based algorithm, with no loss of precision or accuracy. Gpufit is designed such that it is easily incorporated into existing applications or adapted for new ones. Multiple software interfaces, including to C, Python, and Matlab, ensure that Gpufit is accessible from most programming environments. The full source code is published as an open source software repository, making its function transparent to the user and facilitating future improvements and extensions. As a demonstration, we used Gpufit to accelerate an existing scientific image analysis package, yielding significantly improved processing times for super-resolution fluorescence microscopy datasets.

DB90: A Fortran Callable Relational Database Routine for Scientific and Engineering Computer Programs

NASA Technical Reports Server (NTRS)

Wrenn, Gregory A.

2005-01-01

This report describes a database routine called DB90 which is intended for use with scientific and engineering computer programs. The software is written in the Fortran 90/95 programming language standard with file input and output routines written in the C programming language. These routines should be completely portable to any computing platform and operating system that has Fortran 90/95 and C compilers. DB90 allows a program to supply relation names and up to 5 integer key values to uniquely identify each record of each relation. This permits the user to select records or retrieve data in any desired order.

Prowess - A Software Model for the Ooty Wide Field Array

NASA Astrophysics Data System (ADS)

Marthi, Visweshwar Ram

2017-03-01

One of the scientific objectives of the Ooty Wide Field Array (OWFA) is to observe the redshifted H i emission from z ˜ 3.35. Although predictions spell out optimistic outcomes in reasonable integration times, these studies were based purely on analytical assumptions, without accounting for limiting systematics. A software model for OWFA has been developed with a view to understanding the instrument-induced systematics, by describing a complete software model for the instrument. This model has been implemented through a suite of programs, together called Prowess, which has been conceived with the dual role of an emulator as well as observatory data analysis software. The programming philosophy followed in building Prowess enables a general user to define an own set of functions and add new functionality. This paper describes a co-ordinate system suitable for OWFA in which the baselines are defined. The foregrounds are simulated from their angular power spectra. The visibilities are then computed from the foregrounds. These visibilities are then used for further processing, such as calibration and power spectrum estimation. The package allows for rich visualization features in multiple output formats in an interactive fashion, giving the user an intuitive feel for the data. Prowess has been extensively used for numerical predictions of the foregrounds for the OWFA H i experiment.

InSAR Scientific Computing Environment

NASA Astrophysics Data System (ADS)

Gurrola, E. M.; Rosen, P. A.; Sacco, G.; Zebker, H. A.; Simons, M.; Sandwell, D. T.

2010-12-01

The InSAR Scientific Computing Environment (ISCE) is a software development effort in its second year within the NASA Advanced Information Systems and Technology program. The ISCE will provide a new computing environment for geodetic image processing for InSAR sensors that will enable scientists to reduce measurements directly from radar satellites and aircraft to new geophysical products without first requiring them to develop detailed expertise in radar processing methods. The environment can serve as the core of a centralized processing center to bring Level-0 raw radar data up to Level-3 data products, but is adaptable to alternative processing approaches for science users interested in new and different ways to exploit mission data. The NRC Decadal Survey-recommended DESDynI mission will deliver data of unprecedented quantity and quality, making possible global-scale studies in climate research, natural hazards, and Earth's ecosystem. The InSAR Scientific Computing Environment is planned to become a key element in processing DESDynI data into higher level data products and it is expected to enable a new class of analyses that take greater advantage of the long time and large spatial scales of these new data, than current approaches. At the core of ISCE is both legacy processing software from the JPL/Caltech ROI_PAC repeat-pass interferometry package as well as a new InSAR processing package containing more efficient and more accurate processing algorithms being developed at Stanford for this project that is based on experience gained in developing processors for missions such as SRTM and UAVSAR. Around the core InSAR processing programs we are building object-oriented wrappers to enable their incorporation into a more modern, flexible, extensible software package that is informed by modern programming methods, including rigorous componentization of processing codes, abstraction and generalization of data models, and a robust, intuitive user interface with graduated exposure to the levels of sophistication, allowing novices to apply it readily for common tasks and experienced users to mine data with great facility and flexibility. The environment is designed to easily allow user contributions, enabling an open source community to extend the framework into the indefinite future. In this paper we briefly describe both the legacy and the new core processing algorithms and their integration into the new computing environment. We describe the ISCE component and application architecture and the features that permit the desired flexibility, extensibility and ease-of-use. We summarize the state of progress of the environment and the plans for completion of the environment and for its future introduction into the radar processing community.

JHelioviewer. Time-dependent 3D visualisation of solar and heliospheric data

NASA Astrophysics Data System (ADS)

Müller, D.; Nicula, B.; Felix, S.; Verstringe, F.; Bourgoignie, B.; Csillaghy, A.; Berghmans, D.; Jiggens, P.; García-Ortiz, J. P.; Ireland, J.; Zahniy, S.; Fleck, B.

2017-09-01

Context. Solar observatories are providing the world-wide community with a wealth of data, covering wide time ranges (e.g. Solar and Heliospheric Observatory, SOHO), multiple viewpoints (Solar TErrestrial RElations Observatory, STEREO), and returning large amounts of data (Solar Dynamics Observatory, SDO). In particular, the large volume of SDO data presents challenges; the data are available only from a few repositories, and full-disk, full-cadence data for reasonable durations of scientific interest are difficult to download, due to their size and the download rates available to most users. From a scientist's perspective this poses three problems: accessing, browsing, and finding interesting data as efficiently as possible. Aims: To address these challenges, we have developed JHelioviewer, a visualisation tool for solar data based on the JPEG 2000 compression standard and part of the open source ESA/NASA Helioviewer Project. Since the first release of JHelioviewer in 2009, the scientific functionality of the software has been extended significantly, and the objective of this paper is to highlight these improvements. Methods: The JPEG 2000 standard offers useful new features that facilitate the dissemination and analysis of high-resolution image data and offers a solution to the challenge of efficiently browsing petabyte-scale image archives. The JHelioviewer software is open source, platform independent, and extendable via a plug-in architecture. Results: With JHelioviewer, users can visualise the Sun for any time period between September 1991 and today; they can perform basic image processing in real time, track features on the Sun, and interactively overlay magnetic field extrapolations. The software integrates solar event data and a timeline display. Once an interesting event has been identified, science quality data can be accessed for in-depth analysis. As a first step towards supporting science planning of the upcoming Solar Orbiter mission, JHelioviewer offers a virtual camera model that enables users to set the vantage point to the location of a spacecraft or celestial body at any given time.

Integrating Time-Synchronized Video with Other Geospatial and Temporal Data for Remote Science Operations

NASA Technical Reports Server (NTRS)

Cohen, Tamar E.; Lees, David S.; Deans, Matthew C.; Lim, Darlene S. S.; Lee, Yeon Jin Grace

2018-01-01

Exploration Ground Data Systems (xGDS) supports rapid scientific decision making by synchronizing video in context with map, instrument data visualization, geo-located notes and any other collected data. xGDS is an open source web-based software suite developed at NASA Ames Research Center to support remote science operations in analog missions and prototype solutions for remote planetary exploration. (See Appendix B) Typical video systems are designed to play or stream video only, independent of other data collected in the context of the video. Providing customizable displays for monitoring live video and data as well as replaying recorded video and data helps end users build up a rich situational awareness. xGDS was designed to support remote field exploration with unreliable networks. Commercial digital recording systems operate under the assumption that there is a stable and reliable network between the source of the video and the recording system. In many field deployments and space exploration scenarios, this is not the case - there are both anticipated and unexpected network losses. xGDS' Video Module handles these interruptions, storing the available video, organizing and characterizing the dropouts, and presenting the video for streaming or replay to the end user including visualization of the dropouts. Scientific instruments often require custom or expensive software to analyze and visualize collected data. This limits the speed at which the data can be visualized and limits access to the data to those users with the software. xGDS' Instrument Module integrates with instruments that collect and broadcast data in a single snapshot or that continually collect and broadcast a stream of data. While seeing a visualization of collected instrument data is informative, showing the context for the collected data, other data collected nearby along with events indicating current status helps remote science teams build a better understanding of the environment. Further, sharing geo-located, tagged notes recorded by the scientists and others on the team spurs deeper analysis of the data.

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

PubMed Central

Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

2016-01-01

Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/. PMID:26882475

SysSon - A Framework for Systematic Sonification Design

NASA Astrophysics Data System (ADS)

Vogt, Katharina; Goudarzi, Visda; Holger Rutz, Hanns

2015-04-01

SysSon is a research approach on introducing sonification systematically to a scientific community where it is not yet commonly used - e.g., in climate science. Thereby, both technical and socio-cultural barriers have to be met. The approach was further developed with climate scientists, who participated in contextual inquiries, usability tests and a workshop of collaborative design. Following from these extensive user tests resulted our final software framework. As frontend, a graphical user interface allows climate scientists to parametrize standard sonifications with their own data sets. Additionally, an interactive shell allows to code new sonifications for users competent in sound design. The framework is a standalone desktop application, available as open source (for details see http://sysson.kug.ac.at/) and works with data in NetCDF format.

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.

Rapid access to information resources in clinical biochemistry: medical applications of Personal Digital Assistants (PDA).

PubMed

Serdar, Muhittin A; Turan, Mustafa; Cihan, Murat

2008-06-01

Laboratory specialists currently need to access scientific-based information at anytime and anywhere. A considerable period of time and too much effort are required to access this information through existing accumulated data. Personal digital assistants (PDA) are supposed to provide an effective solution with commercial software for this problem. In this study, 11 commercial software products (UpToDate, ePocrates, Inforetrive, Pepid, eMedicine, FIRST Consult, and 5 laboratory e-books released by Skyscape and/or Isilo) were selected and the benefits of their use were evaluated by seven laboratory specialists. The assessment of the software was performed based on the number of the tests included, the software content of detailed information for each test-like process, method, interpretation of results, reference ranges, critical values, interferences, equations, pathophysiology, supplementary technical details such as sample collection principles, and additional information such as linked references, evidence-based data, test cost, etc. In terms of technique, the following items are considered: the amount of memory required to run the software, the graphical user interface, which is a user-friendly instrument, and the frequency of new and/or up-date releases. There is still no perfect program, as we have anticipated. Interpretation of laboratory results may require software with an integrated program. However, methodological data are mostly not included in the software evaluated. It seems that these shortcomings will be fixed in the near future, and PDAs and relevant medical applications will also become indispensable for all physicians including laboratory specialists in the field of training/education and in patient care.

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.

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

The Virtual Geophysics Laboratory (VGL): Scientific Workflows Operating Across Organizations and Across Infrastructures

NASA Astrophysics Data System (ADS)

Cox, S. J.; Wyborn, L. A.; Fraser, R.; Rankine, T.; Woodcock, R.; Vote, J.; Evans, B.

2012-12-01

The Virtual Geophysics Laboratory (VGL) is web portal that provides geoscientists with an integrated online environment that: seamlessly accesses geophysical and geoscience data services from the AuScope national geoscience information infrastructure; loosely couples these data to a variety of gesocience software tools; and provides large scale processing facilities via cloud computing. VGL is a collaboration between CSIRO, Geoscience Australia, National Computational Infrastructure, Monash University, Australian National University and the University of Queensland. The VGL provides a distributed system whereby a user can enter an online virtual laboratory to seamlessly connect to OGC web services for geoscience data. The data is supplied in open standards formats using international standards like GeoSciML. A VGL user uses a web mapping interface to discover and filter the data sources using spatial and attribute filters to define a subset. Once the data is selected the user is not required to download the data. VGL collates the service query information for later in the processing workflow where it will be staged directly to the computing facilities. The combination of deferring data download and access to Cloud computing enables VGL users to access their data at higher resolutions and to undertake larger scale inversions, more complex models and simulations than their own local computing facilities might allow. Inside the Virtual Geophysics Laboratory, the user has access to a library of existing models, complete with exemplar workflows for specific scientific problems based on those models. For example, the user can load a geological model published by Geoscience Australia, apply a basic deformation workflow provided by a CSIRO scientist, and have it run in a scientific code from Monash. Finally the user can publish these results to share with a colleague or cite in a paper. This opens new opportunities for access and collaboration as all the resources (models, code, data, processing) are shared in the one virtual laboratory. VGL provides end users with access to an intuitive, user-centered interface that leverages cloud storage and cloud and cluster processing from both the research communities and commercial suppliers (e.g. Amazon). As the underlying data and information services are agnostic of the scientific domain, they can support many other data types. This fundamental characteristic results in a highly reusable virtual laboratory infrastructure that could also be used for example natural hazards, satellite processing, soil geochemistry, climate modeling, agriculture crop modeling.

Bridging the Gap Between Earth Science Open Data Producers and Consumers Using a Standards based approach

NASA Astrophysics Data System (ADS)

Stephan, E.; Sivaraman, C.

2016-12-01

The Web brought together science communities creating collaborative opportunities that were previously unimaginable. This was due to the novel ways technology enabled users to share information that would otherwise not be available. This means that data and software that previously could not be discovered without direct contact with data or software creators can now be downloaded with the click of a mouse button, and the same products can now outlive the lifespan of their research projects. While in many ways these technological advancements provide benefit to collaborating scientists, a critical producer-consumer knowledge gap is created when collaborating scientists rely solely on web sites, web browsers, or similar technology to exchange services, software, and data. Without some best practices and common approaches from Web publishers, collaborating scientific consumers have no inherent way to trust the results or other products being shared, producers have no way to convey their scientific credibility, and publishers risk obscurity where data is hidden in the deep Web. By leveraging recommendations from the W3C Data Activity, scientific communities can adopt best practices for data publication enabling consumers to explore, reuse, reproduce, and contribute their knowledge about the data. This talk will discuss the application of W3C Data on the Web Best Practices in support of published earth science data and feature the Data Usage Vocabulary.

OASIS: a data and software distribution service for Open Science Grid

NASA Astrophysics Data System (ADS)

Bockelman, B.; Caballero Bejar, J.; De Stefano, J.; Hover, J.; Quick, R.; Teige, S.

2014-06-01

The Open Science Grid encourages the concept of software portability: a user's scientific application should be able to run at as many sites as possible. It is necessary to provide a mechanism for OSG Virtual Organizations to install software at sites. Since its initial release, the OSG Compute Element has provided an application software installation directory to Virtual Organizations, where they can create their own sub-directory, install software into that sub-directory, and have the directory shared on the worker nodes at that site. The current model has shortcomings with regard to permissions, policies, versioning, and the lack of a unified, collective procedure or toolset for deploying software across all sites. Therefore, a new mechanism for data and software distributing is desirable. The architecture for the OSG Application Software Installation Service (OASIS) is a server-client model: the software and data are installed only once in a single place, and are automatically distributed to all client sites simultaneously. Central file distribution offers other advantages, including server-side authentication and authorization, activity records, quota management, data validation and inspection, and well-defined versioning and deletion policies. The architecture, as well as a complete analysis of the current implementation, will be described in this paper.

A Concept for the One Degree Imager (ODI) Data Reduction Pipeline and Archiving System

NASA Astrophysics Data System (ADS)

Knezek, Patricia; Stobie, B.; Michael, S.; Valdes, F.; Marru, S.; Henschel, R.; Pierce, M.

2010-05-01

The One Degree Imager (ODI), currently being built by the WIYN Observatory, will provide tremendous possibilities for conducting diverse scientific programs. ODI will be a complex instrument, using non-conventional Orthogonal Transfer Array (OTA) detectors. Due to its large field of view, small pixel size, use of OTA technology, and expected frequent use, ODI will produce vast amounts of astronomical data. If ODI is to achieve its full potential, a data reduction pipeline must be developed. Long-term archiving must also be incorporated into the pipeline system to ensure the continued value of ODI data. This paper presents a concept for an ODI data reduction pipeline and archiving system. To limit costs and development time, our plan leverages existing software and hardware, including existing pipeline software, Science Gateways, Computational Grid & Cloud Technology, Indiana University's Data Capacitor and Massive Data Storage System, and TeraGrid compute resources. Existing pipeline software will be augmented to add functionality required to meet challenges specific to ODI, enhance end-user control, and enable the execution of the pipeline on grid resources including national grid resources such as the TeraGrid and Open Science Grid. The planned system offers consistent standard reductions and end-user flexibility when working with images beyond the initial instrument signature removal. It also gives end-users access to computational and storage resources far beyond what are typically available at most institutions. Overall, the proposed system provides a wide array of software tools and the necessary hardware resources to use them effectively.

Metadata Wizard: an easy-to-use tool for creating FGDC-CSDGM metadata for geospatial datasets in ESRI ArcGIS Desktop

USGS Publications Warehouse

Ignizio, Drew A.; O'Donnell, Michael S.; Talbert, Colin B.

2014-01-01

Creating compliant metadata for scientific data products is mandated for all federal Geographic Information Systems professionals and is a best practice for members of the geospatial data community. However, the complexity of the The Federal Geographic Data Committee’s Content Standards for Digital Geospatial Metadata, the limited availability of easy-to-use tools, and recent changes in the ESRI software environment continue to make metadata creation a challenge. Staff at the U.S. Geological Survey Fort Collins Science Center have developed a Python toolbox for ESRI ArcDesktop to facilitate a semi-automated workflow to create and update metadata records in ESRI’s 10.x software. The U.S. Geological Survey Metadata Wizard tool automatically populates several metadata elements: the spatial reference, spatial extent, geospatial presentation format, vector feature count or raster column/row count, native system/processing environment, and the metadata creation date. Once the software auto-populates these elements, users can easily add attribute definitions and other relevant information in a simple Graphical User Interface. The tool, which offers a simple design free of esoteric metadata language, has the potential to save many government and non-government organizations a significant amount of time and costs by facilitating the development of The Federal Geographic Data Committee’s Content Standards for Digital Geospatial Metadata compliant metadata for ESRI software users. A working version of the tool is now available for ESRI ArcDesktop, version 10.0, 10.1, and 10.2 (downloadable at http:/www.sciencebase.gov/metadatawizard).

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

PubMed

Vetrovský, Tomáš; Baldrian, Petr; Morais, Daniel; Berger, Bonnie

2018-02-14

Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4GB of data. SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions. daniel.morais@biomed.cas.cz. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

Testing Scientific Software: A Systematic Literature Review.

PubMed

Kanewala, Upulee; Bieman, James M

2014-10-01

Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to retract publications due to errors caused by software faults. Systematic testing can identify such faults in code. This study aims to identify specific challenges, proposed solutions, and unsolved problems faced when testing scientific software. We conducted a systematic literature survey to identify and analyze relevant literature. We identified 62 studies that provided relevant information about testing scientific software. We found that challenges faced when testing scientific software fall into two main categories: (1) testing challenges that occur due to characteristics of scientific software such as oracle problems and (2) testing challenges that occur due to cultural differences between scientists and the software engineering community such as viewing the code and the model that it implements as inseparable entities. In addition, we identified methods to potentially overcome these challenges and their limitations. Finally we describe unsolved challenges and how software engineering researchers and practitioners can help to overcome them. Scientific software presents special challenges for testing. Specifically, cultural differences between scientist developers and software engineers, along with the characteristics of the scientific software make testing more difficult. Existing techniques such as code clone detection can help to improve the testing process. Software engineers should consider special challenges posed by scientific software such as oracle problems when developing testing techniques.

Design and evaluation of a personal digital assistant- based alerting service for clinicians.

PubMed

Johnson, E Diane; Pancoast, Paul E; Mitchell, Joyce A; Shyu, Chi-Ren

2004-10-01

This study describes the system architecture and user acceptance of a suite of programs that deliver information about newly updated library resources to clinicians' personal digital assistants (PDAs). Participants received headlines delivered to their PDAs alerting them to new books, National Guideline Clearinghouse guidelines, Cochrane Reviews, and National Institutes of Health (NIH) Clinical Alerts, as well as updated content in UpToDate, Harrison's Online, Scientific American Medicine, and Clinical Evidence. Participants could request additional information for any of the headlines, and the information was delivered via e-mail during their next synchronization. Participants completed a survey at the conclusion of the study to gauge their opinions about the service. Of the 816 headlines delivered to the 16 study participants' PDAs during the project, Scientific American Medicine generated the highest proportion of headline requests at 35%. Most users of the PDA Alerts software reported that they learned about new medical developments sooner than they otherwise would have, and half reported that they learned about developments that they would not have heard about at all. While some users liked the PDA platform for receiving headlines, it seemed that a Web database that allowed tailored searches and alerts could be configured to satisfy both PDA-oriented and e-mail-oriented users.

Design and evaluation of a personal digital assistant–based alerting service for clinicians*†

PubMed Central

Johnson, E. Diane; Pancoast, Paul E.; Mitchell, Joyce A.; Shyu, Chi-Ren

2004-01-01

Purpose: This study describes the system architecture and user acceptance of a suite of programs that deliver information about newly updated library resources to clinicians' personal digital assistants (PDAs). Description: Participants received headlines delivered to their PDAs alerting them to new books, National Guideline Clearinghouse guidelines, Cochrane Reviews, and National Institutes of Health (NIH) Clinical Alerts, as well as updated content in UpToDate, Harrison's Online, Scientific American Medicine, and Clinical Evidence. Participants could request additional information for any of the headlines, and the information was delivered via email during their next synchronization. Participants completed a survey at the conclusion of the study to gauge their opinions about the service. Results/Outcome: Of the 816 headlines delivered to the 16 study participants' PDAs during the project, Scientific American Medicine generated the highest proportion of headline requests at 35%. Most users of the PDA Alerts software reported that they learned about new medical developments sooner than they otherwise would have, and half reported that they learned about developments that they would not have heard about at all. While some users liked the PDA platform for receiving headlines, it seemed that a Web database that allowed tailored searches and alerts could be configured to satisfy both PDA-oriented and email-oriented users. PMID:15494759

PYCHEM: a multivariate analysis package for python.

PubMed

Jarvis, Roger M; Broadhurst, David; Johnson, Helen; O'Boyle, Noel M; Goodacre, Royston

2006-10-15

We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. http://sourceforge.net/projects/pychem

L3 Interactive Data Language

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

Hohn, Michael; Adams, Paul

2006-09-05

The L3 system is a computational steering environment for image processing and scientific computing. It consists of an interactive graphical language and interface. Its purpose is to help advanced users in controlling their computational software and assist in the management of data accumulated during numerical experiments. L3 provides a combination of features not found in other environments; these are: - textual and graphical construction of programs - persistence of programs and associated data - direct mapping between the scripts, the parameters, and the produced data - implicit hierarchial data organization - full programmability, including conditionals and functions - incremental executionmore » of programs The software includes the l3 language and the graphical environment. The language is a single-assignment functional language; the implementation consists of lexer, parser, interpreter, storage handler, and editing support, The graphical environment is an event-driven nested list viewer/editor providing graphical elements corresponding to the language. These elements are both the represenation of a users program and active interfaces to the values computed by that program.« less

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.

1994-01-01

Envision is an interactive environment that provides researchers in the earth sciences convenient ways to manage, browse, and visualize large observed or model data sets. Its main features are support for the netCDF and HDF file formats, an easy to use X/Motif user interface, a client-server configuration, and portability to many UNIX workstations. The Envision package also provides new ways to view and change metadata in a set of data files. It permits a scientist to conveniently and efficiently manage large data sets consisting of many data files. It also provides links to popular visualization tools so that data can be quickly browsed. Envision is a public domain package, freely available to the scientific community. Envision software (binaries and source code) and documentation can be obtained from either of these servers: ftp://vista.atmos.uiuc.edu/pub/envision/ and ftp://csrp.tamu.edu/pub/envision/. Detailed descriptions of Envision capabilities and operations can be found in the User's Guide and Reference Manuals distributed with Envision software.

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.

Secure Peer-to-Peer Networks for Scientific Information Sharing

NASA Technical Reports Server (NTRS)

Karimabadi, Homa

2012-01-01

The most common means of remote scientific collaboration today includes the trio of e-mail for electronic communication, FTP for file sharing, and personalized Web sites for dissemination of papers and research results. With the growth of broadband Internet, there has been a desire to share large files (movies, files, scientific data files) over the Internet. Email has limits on the size of files that can be attached and transmitted. FTP is often used to share large files, but this requires the user to set up an FTP site for which it is hard to set group privileges, it is not straightforward for everyone, and the content is not searchable. Peer-to-peer technology (P2P), which has been overwhelmingly successful in popular content distribution, is the basis for development of a scientific collaboratory called Scientific Peer Network (SciPerNet). This technology combines social networking with P2P file sharing. SciPerNet will be a standalone application, written in Java and Swing, thus insuring portability to a number of different platforms. Some of the features include user authentication, search capability, seamless integration with a data center, the ability to create groups and social networks, and on-line chat. In contrast to P2P networks such as Gnutella, Bit Torrent, and others, SciPerNet incorporates three design elements that are critical to application of P2P for scientific purposes: User authentication, Data integrity validation, Reliable searching SciPerNet also provides a complementary solution to virtual observatories by enabling distributed collaboration and sharing of downloaded and/or processed data among scientists. This will, in turn, increase scientific returns from NASA missions. As such, SciPerNet can serve a two-fold purpose for NASA: a cost-savings software as well as a productivity tool for scientists working with data from NASA missions.

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.

Subsurface Transport Over Multiple Phases Demonstration Software

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

2016-01-05

The STOMP simulator is a suite of numerical simulators developed by Pacific Northwest National Laboratory for addressing problems involving coupled multifluid hydrologic, thermal, geochemical, and geomechanical processes in the subsurface. The simulator has been applied to problems concerning environmental remediation, environmental stewardship, carbon sequestration, conventional petroleum production, and the production of unconventional hydrocarbon fuels. The simulator is copyrighted by Battelle Memorial Institute, and is available outside of PNNL via use agreements. To promote the open exchange of scientific ideas the simulator is provided as source code. A demonstration version of the simulator has been developed, which will provide potential newmore » users with an executable (not source code) implementation of the software royalty free. Demonstration versions will be offered via the STOMP website for all currently available operational modes of the simulator. The demonstration versions of the simulator will be configured with the direct banded linear system solver and have a limit of 1,000 active grid cells. This will provide potential new users with an opportunity to apply the code to simple problems, including many of the STOMP short course problems, without having to pay a license fee. Users will be required to register on the STOMP website prior to receiving an executable.« less

The social disutility of software ownership.

PubMed

Douglas, David M

2011-09-01

Software ownership allows the owner to restrict the distribution of software and to prevent others from reading the software's source code and building upon it. However, free software is released to users under software licenses that give them the right to read the source code, modify it, reuse it, and distribute the software to others. Proponents of free software such as Richard M. Stallman and Eben Moglen argue that the social disutility of software ownership is a sufficient justification for prohibiting it. This social disutility includes the social instability of disregarding laws and agreements covering software use and distribution, inequality of software access, and the inability to help others by sharing software with them. Here I consider these and other social disutility claims against withholding specific software rights from users, in particular, the rights to read the source code, duplicate, distribute, modify, imitate, and reuse portions of the software within new programs. I find that generally while withholding these rights from software users does cause some degree of social disutility, only the rights to duplicate, modify and imitate cannot legitimately be denied to users on this basis. The social disutility of withholding the rights to distribute the software, read its source code and reuse portions of it in new programs is insufficient to prohibit software owners from denying them to users. A compromise between the software owner and user can minimise the social disutility of withholding these particular rights from users. However, the social disutility caused by software patents is sufficient for rejecting such patents as they restrict the methods of reducing social disutility possible with other forms of software ownership.

Testing Scientific Software: A Systematic Literature Review

PubMed Central

Kanewala, Upulee; Bieman, James M.

2014-01-01

Context Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to retract publications due to errors caused by software faults. Systematic testing can identify such faults in code. Objective This study aims to identify specific challenges, proposed solutions, and unsolved problems faced when testing scientific software. Method We conducted a systematic literature survey to identify and analyze relevant literature. We identified 62 studies that provided relevant information about testing scientific software. Results We found that challenges faced when testing scientific software fall into two main categories: (1) testing challenges that occur due to characteristics of scientific software such as oracle problems and (2) testing challenges that occur due to cultural differences between scientists and the software engineering community such as viewing the code and the model that it implements as inseparable entities. In addition, we identified methods to potentially overcome these challenges and their limitations. Finally we describe unsolved challenges and how software engineering researchers and practitioners can help to overcome them. Conclusions Scientific software presents special challenges for testing. Specifically, cultural differences between scientist developers and software engineers, along with the characteristics of the scientific software make testing more difficult. Existing techniques such as code clone detection can help to improve the testing process. Software engineers should consider special challenges posed by scientific software such as oracle problems when developing testing techniques. PMID:25125798

Paramedir: A Tool for Programmable Performance Analysis

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

Performance analysis of parallel scientific applications is time consuming and requires great expertise in areas such as programming paradigms, system software, and computer hardware architectures. In this paper we describe a tool that facilitates the programmability of performance metric calculations thereby allowing the automation of the analysis and reducing the application development time. We demonstrate how the system can be used to capture knowledge and intuition acquired by advanced parallel programmers in order to be transferred to novice users.

SNS programming environment user's guide

NASA Technical Reports Server (NTRS)

Tennille, Geoffrey M.; Howser, Lona M.; Humes, D. Creig; Cronin, Catherine K.; Bowen, John T.; Drozdowski, Joseph M.; Utley, Judith A.; Flynn, Theresa M.; Austin, Brenda A.

1992-01-01

The computing environment is briefly described for the Supercomputing Network Subsystem (SNS) of the Central Scientific Computing Complex of NASA Langley. The major SNS computers are a CRAY-2, a CRAY Y-MP, a CONVEX C-210, and a CONVEX C-220. The software is described that is common to all of these computers, including: the UNIX operating system, computer graphics, networking utilities, mass storage, and mathematical libraries. Also described is file management, validation, SNS configuration, documentation, and customer services.

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

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.

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.

Electronic journals: Their use by teachers/researchers of engineering and social sciences

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

Martins, Fernanda, E-mail: mmartins@letras.up.pt; Machado, Diana, E-mail: mmartins@letras.up.pt; Fernandes, Alberto, E-mail: mmartins@letras.up.pt

Libraries must attend the needs of their different users. Academics are usually a particular kind of users with specific needs. Universities are environments where scientific communication is essential and where electronic format of journals is becoming more and more frequently used. This way it becomes increasingly important to understand how academics from different scientific areas use the available electronic resources. The aim of this study is to better understand the existing differences among the users of electronic journals in Engineering and Social Sciences. The research undertaken was mainly focused on the study of the use of electronic journals by teachers/researchersmore » from the Faculties of Engineering and of Arts from the University of Porto, Portugal. In this study an international survey was used in order to characterize the levels of use and access of electronic journals by these communities. The ways of seeking and using scientific information, namely in terms frequency of access, the number of articles consulted, the use of databases and the preference of publishing in electronic journals were analyzed. A set of comparisons were established and results indicate an extensive use of the electronic format, regardless the faculty. However, some differences emerge when it comes to details. Such is the case of the usage rate of reference management software which is considerably more used by Engineering academics than Social Science ones. Generally, electronic journals meeting the information needs of its users and are increasingly used as a preferred means of research. Though, some particular differences in the use of them have emerged, when comparing academics from these two faculties.« less

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

Negotiation and Decision Making with Collaborative Software: How MarineMap 'Changed the Game' in California's Marine Life Protected Act Initiative.

PubMed

Cravens, Amanda E

2016-02-01

Environmental managers and planners have become increasingly enthusiastic about the potential of decision support tools (DSTs) to improve environmental decision-making processes as information technology transforms many aspects of daily life. Discussions about DSTs, however, rarely recognize the range of ways software can influence users' negotiation, problem-solving, or decision-making strategies and incentives, in part because there are few empirical studies of completed processes that used technology. This mixed-methods study-which draws on data from approximately 60 semi-structured interviews and an online survey--examines how one geospatial DST influenced participants' experiences during a multi-year marine planning process in California. Results suggest that DSTs can facilitate communication by creating a common language, help users understand the geography and scientific criteria in play during the process, aid stakeholders in identifying shared or diverging interests, and facilitate joint problem solving. The same design features that enabled the tool to aid in decision making, however, also presented surprising challenges in certain circumstances by, for example, making it difficult for participants to discuss information that was not spatially represented on the map-based interface. The study also highlights the importance of the social context in which software is developed and implemented, suggesting that the relationship between the software development team and other participants may be as important as technical software design in shaping how DSTs add value. The paper concludes with considerations to inform the future use of DSTs in environmental decision-making processes.

Negotiation and Decision Making with Collaborative Software: How MarineMap `Changed the Game' in California's Marine Life Protected Act Initiative

NASA Astrophysics Data System (ADS)

Cravens, Amanda E.

2016-02-01

Environmental managers and planners have become increasingly enthusiastic about the potential of decision support tools (DSTs) to improve environmental decision-making processes as information technology transforms many aspects of daily life. Discussions about DSTs, however, rarely recognize the range of ways software can influence users' negotiation, problem-solving, or decision-making strategies and incentives, in part because there are few empirical studies of completed processes that used technology. This mixed-methods study—which draws on data from approximately 60 semi-structured interviews and an online survey—examines how one geospatial DST influenced participants' experiences during a multi-year marine planning process in California. Results suggest that DSTs can facilitate communication by creating a common language, help users understand the geography and scientific criteria in play during the process, aid stakeholders in identifying shared or diverging interests, and facilitate joint problem solving. The same design features that enabled the tool to aid in decision making, however, also presented surprising challenges in certain circumstances by, for example, making it difficult for participants to discuss information that was not spatially represented on the map-based interface. The study also highlights the importance of the social context in which software is developed and implemented, suggesting that the relationship between the software development team and other participants may be as important as technical software design in shaping how DSTs add value. The paper concludes with considerations to inform the future use of DSTs in environmental decision-making processes.

Argonne Leadership Computing Facility 2011 annual report : Shaping future supercomputing.

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

Papka, M.; Messina, P.; Coffey, R.

The ALCF's Early Science Program aims to prepare key applications for the architecture and scale of Mira and to solidify libraries and infrastructure that will pave the way for other future production applications. Two billion core-hours have been allocated to 16 Early Science projects on Mira. The projects, in addition to promising delivery of exciting new science, are all based on state-of-the-art, petascale, parallel applications. The project teams, in collaboration with ALCF staff and IBM, have undertaken intensive efforts to adapt their software to take advantage of Mira's Blue Gene/Q architecture, which, in a number of ways, is a precursormore » to future high-performance-computing architecture. The Argonne Leadership Computing Facility (ALCF) enables transformative science that solves some of the most difficult challenges in biology, chemistry, energy, climate, materials, physics, and other scientific realms. Users partnering with ALCF staff have reached research milestones previously unattainable, due to the ALCF's world-class supercomputing resources and expertise in computation science. In 2011, the ALCF's commitment to providing outstanding science and leadership-class resources was honored with several prestigious awards. Research on multiscale brain blood flow simulations was named a Gordon Bell Prize finalist. Intrepid, the ALCF's BG/P system, ranked No. 1 on the Graph 500 list for the second consecutive year. The next-generation BG/Q prototype again topped the Green500 list. Skilled experts at the ALCF enable researchers to conduct breakthrough science on the Blue Gene system in key ways. The Catalyst Team matches project PIs with experienced computational scientists to maximize and accelerate research in their specific scientific domains. The Performance Engineering Team facilitates the effective use of applications on the Blue Gene system by assessing and improving the algorithms used by applications and the techniques used to implement those algorithms. The Data Analytics and Visualization Team lends expertise in tools and methods for high-performance, post-processing of large datasets, interactive data exploration, batch visualization, and production visualization. The Operations Team ensures that system hardware and software work reliably and optimally; system tools are matched to the unique system architectures and scale of ALCF resources; the entire system software stack works smoothly together; and I/O performance issues, bug fixes, and requests for system software are addressed. The User Services and Outreach Team offers frontline services and support to existing and potential ALCF users. The team also provides marketing and outreach to users, DOE, and the broader community.« less

Machine learning for micro-tomography

NASA Astrophysics Data System (ADS)

Parkinson, Dilworth Y.; Pelt, Daniël. M.; Perciano, Talita; Ushizima, Daniela; Krishnan, Harinarayan; Barnard, Harold S.; MacDowell, Alastair A.; Sethian, James

2017-09-01

Machine learning has revolutionized a number of fields, but many micro-tomography users have never used it for their work. The micro-tomography beamline at the Advanced Light Source (ALS), in collaboration with the Center for Applied Mathematics for Energy Research Applications (CAMERA) at Lawrence Berkeley National Laboratory, has now deployed a series of tools to automate data processing for ALS users using machine learning. This includes new reconstruction algorithms, feature extraction tools, and image classification and recommen- dation systems for scientific image. Some of these tools are either in automated pipelines that operate on data as it is collected or as stand-alone software. Others are deployed on computing resources at Berkeley Lab-from workstations to supercomputers-and made accessible to users through either scripting or easy-to-use graphical interfaces. This paper presents a progress report on this work.

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.

Whole earth modeling: developing and disseminating scientific software for computational geophysics.

NASA Astrophysics Data System (ADS)

Kellogg, L. H.

2016-12-01

Historically, a great deal of specialized scientific software for modeling and data analysis has been developed by individual researchers or small groups of scientists working on their own specific research problems. As the magnitude of available data and computer power has increased, so has the complexity of scientific problems addressed by computational methods, creating both a need to sustain existing scientific software, and expand its development to take advantage of new algorithms, new software approaches, and new computational hardware. To that end, communities like the Computational Infrastructure for Geodynamics (CIG) have been established to support the use of best practices in scientific computing for solid earth geophysics research and teaching. Working as a scientific community enables computational geophysicists to take advantage of technological developments, improve the accuracy and performance of software, build on prior software development, and collaborate more readily. The CIG community, and others, have adopted an open-source development model, in which code is developed and disseminated by the community in an open fashion, using version control and software repositories like Git. One emerging issue is how to adequately identify and credit the intellectual contributions involved in creating open source scientific software. The traditional method of disseminating scientific ideas, peer reviewed publication, was not designed for review or crediting scientific software, although emerging publication strategies such software journals are attempting to address the need. We are piloting an integrated approach in which authors are identified and credited as scientific software is developed and run. Successful software citation requires integration with the scholarly publication and indexing mechanisms as well, to assign credit, ensure discoverability, and provide provenance for software.

EVEREST: a virtual research environment for the Earth Sciences

NASA Astrophysics Data System (ADS)

Glaves, H. M.; Marelli, F.; Albani, M.

2015-12-01

There is an increasing requirement for researchers to work collaboratively using common resources whilst being geographically dispersed. By creating a virtual research environment (VRE) using a service oriented architecture (SOA) tailored to the needs of Earth Science (ES) communities, the EVEREST project will provide a range of both generic and domain specific data management services to support a dynamic approach to collaborative research. EVER-EST will provide the means to overcome existing barriers to sharing of Earth Science data and information allowing research teams to discover, access, share and process heterogeneous data, algorithms, results and experiences within and across their communities, including those domains beyond Earth Science. Data providers will be also able to monitor user experiences and collect feedback through the VRE, improving their capacity to adapt to the changing requirements of their end-users. The EVER-EST e-infrastructure will be validated by four virtual research communities (VRC) covering different multidisciplinary ES domains: including ocean monitoring, selected natural hazards (flooding, ground instability and extreme weather events), land monitoring and risk management (volcanoes and seismicity). Each of the VRC represents a different collaborative use case for the VRE according to its own specific requirements for data, software, best practice and community engagement. The diverse use cases will demonstrate how the VRE can be used for a range of activities from straight forward data/software sharing to investigating ways to improve cooperative working. Development of the EVEREST VRE will leverage on the results of several previous projects which have produced state-of-the-art technologies for scientific data management and curation as well those initiatives which have developed models, techniques and tools for the preservation of scientific methods and their implementation in computational forms such as scientific workflows.

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.

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

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

The StratusLab cloud distribution: Use-cases and support for scientific applications

NASA Astrophysics Data System (ADS)

Floros, E.

2012-04-01

The StratusLab project is integrating an open cloud software distribution that enables organizations to setup and provide their own private or public IaaS (Infrastructure as a Service) computing clouds. StratusLab distribution capitalizes on popular infrastructure virtualization solutions like KVM, the OpenNebula virtual machine manager, Claudia service manager and SlipStream deployment platform, which are further enhanced and expanded with additional components developed within the project. The StratusLab distribution covers the core aspects of a cloud IaaS architecture, namely Computing (life-cycle management of virtual machines), Storage, Appliance management and Networking. The resulting software stack provides a packaged turn-key solution for deploying cloud computing services. The cloud computing infrastructures deployed using StratusLab can support a wide range of scientific and business use cases. Grid computing has been the primary use case pursued by the project and for this reason the initial priority has been the support for the deployment and operation of fully virtualized production-level grid sites; a goal that has already been achieved by operating such a site as part of EGI's (European Grid Initiative) pan-european grid infrastructure. In this area the project is currently working to provide non-trivial capabilities like elastic and autonomic management of grid site resources. Although grid computing has been the motivating paradigm, StratusLab's cloud distribution can support a wider range of use cases. Towards this direction, we have developed and currently provide support for setting up general purpose computing solutions like Hadoop, MPI and Torque clusters. For what concerns scientific applications the project is collaborating closely with the Bioinformatics community in order to prepare VM appliances and deploy optimized services for bioinformatics applications. In a similar manner additional scientific disciplines like Earth Science can take advantage of StratusLab cloud solutions. Interested users are welcomed to join StratusLab's user community by getting access to the reference cloud services deployed by the project and offered to the public.

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

Vang, Leng; Prescott, Steven R; Smith, Curtis

In collaborating scientific research arena it is important to have an environment where analysts have access to a shared of information documents, software tools and be able to accurately maintain and track historical changes in models. A new cloud-based environment would be accessible remotely from anywhere regardless of computing platforms given that the platform has available of Internet access and proper browser capabilities. Information stored at this environment would be restricted based on user assigned credentials. This report reviews development of a Cloud-based Architecture Capabilities (CAC) as a web portal for PRA tools.

The fast azimuthal integration Python library: pyFAI.

PubMed

Ashiotis, Giannis; Deschildre, Aurore; Nawaz, Zubair; Wright, Jonathan P; Karkoulis, Dimitrios; Picca, Frédéric Emmanuel; Kieffer, Jérôme

2015-04-01

pyFAI is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.

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.

After an Earthquake: Accessing Near Real-Time Data in the Classroom

NASA Astrophysics Data System (ADS)

Bravo, T. K.; Coleman, B.; Hubenthal, M.; Owens, T. J.; Taber, J.; Welti, R.; Weertman, B. R.

2010-12-01

One of the best ways to engage students in scientific content is to give them opportunities to work with real scientific instruments and data and enable them to experience the discovery of scientific information. In addition, newsworthy earthquakes can capture the attention and imagination of students. IRIS and collaborating partners provide a range of options to leverage that attention through access to near-real-time earthquake location and waveform data stored in the IRIS Data Management System and elsewhere via a number of web-based tools and a new Java-based application. The broadest audience is reached by the Seismic Monitor, a simple Web-based tool for observing near-real-time seismicity. The IRIS Earthquake Browser (IEB) allows users to explore recent and cataloged earthquakes and aftershock patterns online with more flexibility, and K-12 classroom activities for understanding plate tectonics and estimating seismic hazards have been designed around its use. Waveforms are easily viewed and explored on the web using the Rapid Earthquake Viewer (REV), developed by the University of South Carolina in collaboration with IRIS E&O. Data from recent well-known earthquakes available via REV are used in exercises to determine Earth’s internal structure and to locate earthquakes. Three component data is presented to the students, allowing a much more realistic analysis of the data than is presented in most textbooks. The Seismographs in Schools program uses real-time data in the classroom to interest and engage students about recent earthquakes. Through the IRIS website, schools can share event data and 24-hr images. Additionally, data is available in real-time via the API. This API allows anyone to extract data, re-purpose it, and display it however they need to, as is being done by the British Geological Survey Seismographs in Schools program. Over 350 schools throughout the US and internationally are currently registered with the IRIS Seismographs in Schools database. IRIS E&O is collaborating with Moravian College on a Java-based software application to replace the current educational seismometer software. This software facilitates the study of seismological concepts in middle school through introductory undergraduate classrooms. Users can view a graphical representation of seismic data in real time and can process this data to determine characteristics of seismograms such as time of occurrence, distance from the epicenter to the station, magnitude, and location (via triangulation). The software interface makes these tasks easy to accomplish and also provides interactive assistance to users. Data can be collected and viewed from a suite of instruments as well as streaming data in true real time. This allows multiple classrooms within a school to display data from their seismograph and for schools without an instrument to display data from another school.

Mfold web server for nucleic acid folding and hybridization prediction.

PubMed

Zuker, Michael

2003-07-01

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.

Hydrology for Engineers, Geologists, and Environmental Professionals

NASA Astrophysics Data System (ADS)

Ince, Simon

For people who are involved in the applied aspects of hydrology, it is refreshing to find a textbook that begins with a meaningful disclaimer, albeit in fine print on the back side of the frontispiece:“The present book and the accompanying software have been written according to the latest techniques in scientific hydrology. However, hydrology is at best an inexact science. A good book and a good computer software by themselves do not guarantee accurate or even realistic predictions. Acceptable results in the applications of hydrologic methods to engineering and environmental problems depend to a greater extend (sic) on the skills, logical assumptions, and practical experience of the user, and on the quantity and quality of long-term hydrologic data available. Neither the author nor the publisher assumes any responsibility or any liability, explicitly or implicitly, on the results or the consequences of using the information contained in this book or its accompanying software.”

Open source software and low cost sensors for teaching UAV science

NASA Astrophysics Data System (ADS)

Kefauver, S. C.; Sanchez-Bragado, R.; El-Haddad, G.; Araus, J. L.

2016-12-01

Drones, also known as UASs (unmanned aerial systems), UAVs (Unmanned Aerial Vehicles) or RPAS (Remotely piloted aircraft systems), are both useful advanced scientific platforms and recreational toys that are appealing to younger generations. As such, they can make for excellent education tools as well as low-cost scientific research project alternatives. However, the process of taking pretty pictures to remote sensing science can be daunting if one is presented with only expensive software and sensor options. There are a number of open-source tools and low cost platform and sensor options available that can provide excellent scientific research results, and, by often requiring more user-involvement than commercial software and sensors, provide even greater educational benefits. Scale-invariant feature transform (SIFT) algorithm implementations, such as the Microsoft Image Composite Editor (ICE), which can create quality 2D image mosaics with some motion and terrain adjustments and VisualSFM (Structure from Motion), which can provide full image mosaicking with movement and orthorectification capacities. RGB image quantification using alternate color space transforms, such as the BreedPix indices, can be calculated via plugins in the open-source software Fiji (http://fiji.sc/Fiji; http://github.com/george-haddad/CIMMYT). Recent analyses of aerial images from UAVs over different vegetation types and environments have shown RGB metrics can outperform more costly commercial sensors. Specifically, Hue-based pixel counts, the Triangle Greenness Index (TGI), and the Normalized Green Red Difference Index (NGRDI) consistently outperformed NDVI in estimating abiotic and biotic stress impacts on crop health. Also, simple kits are available for NDVI camera conversions. Furthermore, suggestions for multivariate analyses of the different RGB indices in the "R program for statistical computing", such as classification and regression trees can allow for a more approachable interpretation of results in the classroom.

InSAR Scientific Computing Environment - The Home Stretch

NASA Astrophysics Data System (ADS)

Rosen, P. A.; Gurrola, E. M.; Sacco, G.; Zebker, H. A.

2011-12-01

The Interferometric Synthetic Aperture Radar (InSAR) Scientific Computing Environment (ISCE) is a software development effort in its third and final year within the NASA Advanced Information Systems and Technology program. The ISCE is a new computing environment for geodetic image processing for InSAR sensors enabling scientists to reduce measurements directly from radar satellites to new geophysical products with relative ease. The environment can serve as the core of a centralized processing center to bring Level-0 raw radar data up to Level-3 data products, but is adaptable to alternative processing approaches for science users interested in new and different ways to exploit mission data. Upcoming international SAR missions will deliver data of unprecedented quantity and quality, making possible global-scale studies in climate research, natural hazards, and Earth's ecosystem. The InSAR Scientific Computing Environment has the functionality to become a key element in processing data from NASA's proposed DESDynI mission into higher level data products, supporting a new class of analyses that take advantage of the long time and large spatial scales of these new data. At the core of ISCE is a new set of efficient and accurate InSAR algorithms. These algorithms are placed into an object-oriented, flexible, extensible software package that is informed by modern programming methods, including rigorous componentization of processing codes, abstraction and generalization of data models. The environment is designed to easily allow user contributions, enabling an open source community to extend the framework into the indefinite future. ISCE supports data from nearly all of the available satellite platforms, including ERS, EnviSAT, Radarsat-1, Radarsat-2, ALOS, TerraSAR-X, and Cosmo-SkyMed. The code applies a number of parallelization techniques and sensible approximations for speed. It is configured to work on modern linux-based computers with gcc compilers and python. ISCE is now a complete, functional package, under configuration management, and with extensive documentation and tested use cases appropriate to geodetic imaging applications. The software has been tested with canonical simulated radar data ("point targets") as well as with a variety of existing satellite data, cross-compared with other software packages. Its extensibility has already been proven by the straightforward addition of polarimetric processing and calibration, and derived filtering and estimation routines associated with polarimetry that supplement the original InSAR geodetic functionality. As of October 2011, the software is available for non-commercial use through UNAVCO's WinSAR consortium.

Introduction to the scientific application system of DAMPE (On behalf of DAMPE collaboration)

NASA Astrophysics Data System (ADS)

Zang, Jingjing

2016-07-01

The Dark Matter Particle Explorer (DAMPE) is a high energy particle physics experiment satellite, launched on 17 Dec 2015. The science data processing and payload operation maintenance for DAMPE will be provided by the DAMPE Scientific Application System (SAS) at the Purple Mountain Observatory (PMO) of Chinese Academy of Sciences. SAS is consisted of three subsystems - scientific operation subsystem, science data and user management subsystem and science data processing subsystem. In cooperation with the Ground Support System (Beijing), the scientific operation subsystem is responsible for proposing observation plans, monitoring the health of satellite, generating payload control commands and participating in all activities related to payload operation. Several databases developed by the science data and user management subsystem of DAMPE methodically manage all collected and reconstructed science data, down linked housekeeping data, payload configuration and calibration data. Under the leadership of DAMPE Scientific Committee, this subsystem is also responsible for publication of high level science data and supporting all science activities of the DAMPE collaboration. The science data processing subsystem of DAMPE has already developed a series of physics analysis software to reconstruct basic information about detected cosmic ray particle. This subsystem also maintains the high performance computing system of SAS to processing all down linked science data and automatically monitors the qualities of all produced data. In this talk, we will describe all functionalities of whole DAMPE SAS system and show you main performances of data processing ability.

Component Technology for High-Performance Scientific Simulation Software

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

Epperly, T; Kohn, S; Kumfert, G

2000-11-09

We are developing scientific software component technology to manage the complexity of modem, parallel simulation software and increase the interoperability and re-use of scientific software packages. In this paper, we describe a language interoperability tool named Babel that enables the creation and distribution of language-independent software libraries using interface definition language (IDL) techniques. We have created a scientific IDL that focuses on the unique interface description needs of scientific codes, such as complex numbers, dense multidimensional arrays, complicated data types, and parallelism. Preliminary results indicate that in addition to language interoperability, this approach provides useful tools for thinking about themore » design of modem object-oriented scientific software libraries. Finally, we also describe a web-based component repository called Alexandria that facilitates the distribution, documentation, and re-use of scientific components and libraries.« less

Variational Trajectory Optimization Tool Set: Technical description and user's manual

NASA Technical Reports Server (NTRS)

Bless, Robert R.; Queen, Eric M.; Cavanaugh, Michael D.; Wetzel, Todd A.; Moerder, Daniel D.

1993-01-01

The algorithms that comprise the Variational Trajectory Optimization Tool Set (VTOTS) package are briefly described. The VTOTS is a software package for solving nonlinear constrained optimal control problems from a wide range of engineering and scientific disciplines. The VTOTS package was specifically designed to minimize the amount of user programming; in fact, for problems that may be expressed in terms of analytical functions, the user needs only to define the problem in terms of symbolic variables. This version of the VTOTS does not support tabular data; thus, problems must be expressed in terms of analytical functions. The VTOTS package consists of two methods for solving nonlinear optimal control problems: a time-domain finite-element algorithm and a multiple shooting algorithm. These two algorithms, under the VTOTS package, may be run independently or jointly. The finite-element algorithm generates approximate solutions, whereas the shooting algorithm provides a more accurate solution to the optimization problem. A user's manual, some examples with results, and a brief description of the individual subroutines are included.

Software for Remote Monitoring of Space-Station Payloads

NASA Technical Reports Server (NTRS)

Schneider, Michelle; Lippincott, Jeff; Chubb, Steve; Whitaker, Jimmy; Gillis, Robert; Sellers, Donna; Sims, Chris; Rice, James

2003-01-01

Telescience Resource Kit (TReK) is a suite of application programs that enable geographically dispersed users to monitor scientific payloads aboard the International Space Station (ISS). TReK provides local ground support services that can simultaneously receive, process, record, playback, and display data from multiple sources. TReK also provides interfaces to use the remote services provided by the Payload Operations Integration Center which manages all ISS payloads. An application programming interface (API) allows for payload users to gain access to all data processed by TReK and allows payload-specific tools and programs to be built or integrated with TReK. Used in conjunction with other ISS-provided tools, TReK provides the ability to integrate payloads with the operational ground system early in the lifecycle. This reduces the potential for operational problems and provides "cradle-to-grave" end-to-end operations. TReK contains user guides and self-paced tutorials along with training applications to allow the user to become familiar with the system.

Using component technology to facilitate external software reuse in ground-based planning systems

NASA Technical Reports Server (NTRS)

Chase, A.

2003-01-01

APGEN (Activity Plan GENerator - 314), a multi-mission planning tool, must interface with external software to vest serve its users. AP-GEN's original method for incorporating external software, the User-Defined library mechanism, has been very successful in allowing APGEN users access to external software functionality.

Grids: The Top Ten Questions

DOE PAGES

Schopf, Jennifer M.; Nitzberg, Bill

2002-01-01

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

Giovanni - The Bridge Between Data and Science

NASA Technical Reports Server (NTRS)

Liu, Zhong; Acker, James

2017-01-01

This article describes new features in the Geospatial Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni), a user-friendly online tool that enables visualization, analysis, and assessment of NASA Earth science data sets without downloading data and software. Since the satellite era began, data collected from Earth-observing satellites have been widely used in research and applications; however, using satellite-based data sets can still be a challenge to many. To facilitate data access and evaluation, as well as scientific exploration and discovery, the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC) has developed Giovanni for a wide range of users around the world. This article describes the latest capabilities of Giovanni with examples, and discusses future plans for this innovative system.

A new dataset validation system for the Planetary Science Archive

NASA Astrophysics Data System (ADS)

Manaud, N.; Zender, J.; Heather, D.; Martinez, S.

2007-08-01

The Planetary Science Archive is the official archive for the Mars Express mission. It has received its first data by the end of 2004. These data are delivered by the PI teams to the PSA team as datasets, which are formatted conform to the Planetary Data System (PDS). The PI teams are responsible for analyzing and calibrating the instrument data as well as the production of reduced and calibrated data. They are also responsible of the scientific validation of these data. ESA is responsible of the long-term data archiving and distribution to the scientific community and must ensure, in this regard, that all archived products meet quality. To do so, an archive peer-review is used to control the quality of the Mars Express science data archiving process. However a full validation of its content is missing. An independent review board recently recommended that the completeness of the archive as well as the consistency of the delivered data should be validated following well-defined procedures. A new validation software tool is being developed to complete the overall data quality control system functionality. This new tool aims to improve the quality of data and services provided to the scientific community through the PSA, and shall allow to track anomalies in and to control the completeness of datasets. It shall ensure that the PSA end-users: (1) can rely on the result of their queries, (2) will get data products that are suitable for scientific analysis, (3) can find all science data acquired during a mission. We defined dataset validation as the verification and assessment process to check the dataset content against pre-defined top-level criteria, which represent the general characteristics of good quality datasets. The dataset content that is checked includes the data and all types of information that are essential in the process of deriving scientific results and those interfacing with the PSA database. The validation software tool is a multi-mission tool that has been designed to provide the user with the flexibility of defining and implementing various types of validation criteria, to iteratively and incrementally validate datasets, and to generate validation reports.

Hyperspectral Soil Mapper (HYSOMA) software interface: Review and future plans

NASA Astrophysics Data System (ADS)

Chabrillat, Sabine; Guillaso, Stephane; Eisele, Andreas; Rogass, Christian

2014-05-01

With the upcoming launch of the next generation of hyperspectral satellites that will routinely deliver high spectral resolution images for the entire globe (e.g. EnMAP, HISUI, HyspIRI, HypXIM, PRISMA), an increasing demand for the availability/accessibility of hyperspectral soil products is coming from the geoscience community. Indeed, many robust methods for the prediction of soil properties based on imaging spectroscopy already exist and have been successfully used for a wide range of soil mapping airborne applications. Nevertheless, these methods require expert know-how and fine-tuning, which makes them used sparingly. More developments are needed toward easy-to-access soil toolboxes as a major step toward the operational use of hyperspectral soil products for Earth's surface processes monitoring and modelling, to allow non-experienced users to obtain new information based on non-expensive software packages where repeatability of the results is an important prerequisite. In this frame, based on the EU-FP7 EUFAR (European Facility for Airborne Research) project and EnMAP satellite science program, higher performing soil algorithms were developed at the GFZ German Research Center for Geosciences as demonstrators for end-to-end processing chains with harmonized quality measures. The algorithms were built-in into the HYSOMA (Hyperspectral SOil MApper) software interface, providing an experimental platform for soil mapping applications of hyperspectral imagery that gives the choice of multiple algorithms for each soil parameter. The software interface focuses on fully automatic generation of semi-quantitative soil maps such as soil moisture, soil organic matter, iron oxide, clay content, and carbonate content. Additionally, a field calibration option calculates fully quantitative soil maps provided ground truth soil data are available. Implemented soil algorithms have been tested and validated using extensive in-situ ground truth data sets. The source of the HYSOMA code was developed as standalone IDL software to allow easy implementation in the hyperspectral and non-hyperspectral communities. Indeed, within the hyperspectral community, IDL language is very widely used, and for non-expert users that do not have an ENVI license, such software can be executed as a binary version using the free IDL virtual machine under various operating systems. Based on the growing interest of users in the software interface, the experimental software was adapted for public release version in 2012, and since then ~80 users of hyperspectral soil products downloaded the soil algorithms at www.gfz-potsdam.de/hysoma. The software interface was distributed for free as IDL plug-ins under the IDL-virtual machine. Up-to-now distribution of HYSOMA was based on a close source license model, for non-commercial and educational purposes. Currently, the HYSOMA is being under further development in the context of the EnMAP satellite mission, for extension and implementation in the EnMAP Box as EnSoMAP (EnMAP SOil MAPper). The EnMAP Box is a freely available, platform-independent software distributed under an open source license. In the presentation we will focus on an update of the HYSOMA software interface status and upcoming implementation in the EnMAP Box. Scientific software validation, associated publication record and users responses as well as software management and transition to open source will be discussed.

Concurrent Image Processing Executive (CIPE). Volume 1: Design overview

NASA Technical Reports Server (NTRS)

Lee, Meemong; Groom, Steven L.; Mazer, Alan S.; Williams, Winifred I.

1990-01-01

The design and implementation of a Concurrent Image Processing Executive (CIPE), which is intended to become the support system software for a prototype high performance science analysis workstation are described. The target machine for this software is a JPL/Caltech Mark 3fp Hypercube hosted by either a MASSCOMP 5600 or a Sun-3, Sun-4 workstation; however, the design will accommodate other concurrent machines of similar architecture, i.e., local memory, multiple-instruction-multiple-data (MIMD) machines. The CIPE system provides both a multimode user interface and an applications programmer interface, and has been designed around four loosely coupled modules: user interface, host-resident executive, hypercube-resident executive, and application functions. The loose coupling between modules allows modification of a particular module without significantly affecting the other modules in the system. In order to enhance hypercube memory utilization and to allow expansion of image processing capabilities, a specialized program management method, incremental loading, was devised. To minimize data transfer between host and hypercube, a data management method which distributes, redistributes, and tracks data set information was implemented. The data management also allows data sharing among application programs. The CIPE software architecture provides a flexible environment for scientific analysis of complex remote sensing image data, such as planetary data and imaging spectrometry, utilizing state-of-the-art concurrent computation capabilities.

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.

Internet-Based Software Tools for Analysis and Processing of LIDAR Point Cloud Data via the OpenTopography Portal

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C. J.; Baru, C.; Arrowsmith, R.

2009-12-01

LIDAR is an excellent example of the new generation of powerful remote sensing data now available to Earth science researchers. Capable of producing digital elevation models (DEMs) more than an order of magnitude higher resolution than those currently available, LIDAR data allows earth scientists to study the processes that contribute to landscape evolution at resolutions not previously possible, yet essential for their appropriate representation. Along with these high-resolution datasets comes an increase in the volume and complexity of data that the user must efficiently manage and process in order for it to be scientifically useful. Although there are expensive commercial LIDAR software applications available, processing and analysis of these datasets are typically computationally inefficient on the conventional hardware and software that is currently available to most of the Earth science community. We have designed and implemented an Internet-based system, the OpenTopography Portal, that provides integrated access to high-resolution LIDAR data as well as web-based tools for processing of these datasets. By using remote data storage and high performance compute resources, the OpenTopography Portal attempts to simplify data access and standard LIDAR processing tasks for the Earth Science community. The OpenTopography Portal allows users to access massive amounts of raw point cloud LIDAR data as well as a suite of DEM generation tools to enable users to generate custom digital elevation models to best fit their science applications. The Cyberinfrastructure software tools for processing the data are freely available via the portal and conveniently integrated with the data selection in a single user-friendly interface. The ability to run these tools on powerful Cyberinfrastructure resources instead of their own labs provides a huge advantage in terms of performance and compute power. The system also encourages users to explore data processing methods and the variations in algorithm parameters since all of the processing is done remotely and numerous jobs can be submitted in sequence. The web-based software also eliminates the need for users to deal with the hassles and costs associated with software installation and licensing while providing adequate disk space for storage and personal job archival capability. Although currently limited to data access and DEM generation tasks, the OpenTopography system is modular in design and can be modified to accommodate new processing tools as they become available. We are currently exploring implementation of higher-level DEM analysis tasks in OpenTopography, since such processing is often computationally intensive and thus lends itself to utilization of cyberinfrastructure. Products derived from OpenTopography processing are available in a variety of formats ranging from simple Google Earth visualizations of LIDAR-derived hillshades to various GIS-compatible grid formats. To serve community users less interested in data processing, OpenTopography also hosts 1 km^2 digital elevation model tiles as well as Google Earth image overlays for a synoptic view of the data.

Idea Paper: The Lifecycle of Software for Scientific Simulations

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

Dubey, Anshu; McInnes, Lois C.

The software lifecycle is a well researched topic that has produced many models to meet the needs of different types of software projects. However, one class of projects, software development for scientific computing, has received relatively little attention from lifecycle researchers. In particular, software for end-to-end computations for obtaining scientific results has received few lifecycle proposals and no formalization of a development model. An examination of development approaches employed by the teams implementing large multicomponent codes reveals a great deal of similarity in their strategies. This idea paper formalizes these related approaches into a lifecycle model for end-to-end scientific applicationmore » software, featuring loose coupling between submodels for development of infrastructure and scientific capability. We also invite input from stakeholders to converge on a model that captures the complexity of this development processes and provides needed lifecycle guidance to the scientific software community.« less

AtomPy: an open atomic-data curation environment

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores.

PubMed

Chikkagoudar, Satish; Wang, Kai; Li, Mingyao

2011-05-26

Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/.

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

PubMed Central

2011-01-01

Background Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Findings Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. Conclusions GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/. PMID:21615923

High-performance scientific computing in the cloud

NASA Astrophysics Data System (ADS)

Jorissen, Kevin; Vila, Fernando; Rehr, John

2011-03-01

Cloud computing has the potential to open up high-performance computational science to a much broader class of researchers, owing to its ability to provide on-demand, virtualized computational resources. However, before such approaches can become commonplace, user-friendly tools must be developed that hide the unfamiliar cloud environment and streamline the management of cloud resources for many scientific applications. We have recently shown that high-performance cloud computing is feasible for parallelized x-ray spectroscopy calculations. We now present benchmark results for a wider selection of scientific applications focusing on electronic structure and spectroscopic simulation software in condensed matter physics. These applications are driven by an improved portable interface that can manage virtual clusters and run various applications in the cloud. We also describe a next generation of cluster tools, aimed at improved performance and a more robust cluster deployment. Supported by NSF grant OCI-1048052.

The crustal dynamics intelligent user interface anthology

NASA Technical Reports Server (NTRS)

Short, Nicholas M., Jr.; Campbell, William J.; Roelofs, Larry H.; Wattawa, Scott L.

1987-01-01

The National Space Science Data Center (NSSDC) has initiated an Intelligent Data Management (IDM) research effort which has, as one of its components, the development of an Intelligent User Interface (IUI). The intent of the IUI is to develop a friendly and intelligent user interface service based on expert systems and natural language processing technologies. The purpose of such a service is to support the large number of potential scientific and engineering users that have need of space and land-related research and technical data, but have little or no experience in query languages or understanding of the information content or architecture of the databases of interest. This document presents the design concepts, development approach and evaluation of the performance of a prototype IUI system for the Crustal Dynamics Project Database, which was developed using a microcomputer-based expert system tool (M. 1), the natural language query processor THEMIS, and the graphics software system GSS. The IUI design is based on a multiple view representation of a database from both the user and database perspective, with intelligent processes to translate between the views.

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.

Harnessing Scientific Literature Reports for Pharmacovigilance

PubMed Central

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

2017-01-01

Summary Objectives 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. Methods 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. Results 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. Conclusions 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. PMID:28326432

Challenges in Managing Trustworthy Large-scale Digital Science

NASA Astrophysics Data System (ADS)

Evans, B. J. K.

2017-12-01

The increased use of large-scale international digital science has opened a number of challenges for managing, handling, using and preserving scientific information. The large volumes of information are driven by three main categories - model outputs including coupled models and ensembles, data products that have been processing to a level of usability, and increasingly heuristically driven data analysis. These data products are increasingly the ones that are usable by the broad communities, and far in excess of the raw instruments data outputs. The data, software and workflows are then shared and replicated to allow broad use at an international scale, which places further demands of infrastructure to support how the information is managed reliably across distributed resources. Users necessarily rely on these underlying "black boxes" so that they are productive to produce new scientific outcomes. The software for these systems depend on computational infrastructure, software interconnected systems, and information capture systems. This ranges from the fundamentals of the reliability of the compute hardware, system software stacks and libraries, and the model software. Due to these complexities and capacity of the infrastructure, there is an increased emphasis of transparency of the approach and robustness of the methods over the full reproducibility. Furthermore, with large volume data management, it is increasingly difficult to store the historical versions of all model and derived data. Instead, the emphasis is on the ability to access the updated products and the reliability by which both previous outcomes are still relevant and can be updated for the new information. We will discuss these challenges and some of the approaches underway that are being used to address these issues.

ReGaTE: Registration of Galaxy Tools in Elixir

PubMed Central

Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; van den Beek, Marius; Grüning, Björn; Ison, Jon; Ménager, Hervé

2017-01-01

Abstract Background: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. Findings: We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusions: ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE. PMID:28402416

Reducing Time to Science: Unidata and JupyterHub Technology Using the Jetstream Cloud

NASA Astrophysics Data System (ADS)

Chastang, J.; Signell, R. P.; Fischer, J. L.

2017-12-01

Cloud computing can accelerate scientific workflows, discovery, and collaborations by reducing research and data friction. We describe the deployment of Unidata and JupyterHub technologies on the NSF-funded XSEDE Jetstream cloud. With the aid of virtual machines and Docker technology, we deploy a Unidata JupyterHub server co-located with a Local Data Manager (LDM), THREDDS data server (TDS), and RAMADDA geoscience content management system. We provide Jupyter Notebooks and the pre-built Python environments needed to run them. The notebooks can be used for instruction and as templates for scientific experimentation and discovery. We also supply a large quantity of NCEP forecast model results to allow data-proximate analysis and visualization. In addition, users can transfer data using Globus command line tools, and perform their own data-proximate analysis and visualization with Notebook technology. These data can be shared with others via a dedicated TDS server for scientific distribution and collaboration. There are many benefits of this approach. Not only is the cloud computing environment fast, reliable and scalable, but scientists can analyze, visualize, and share data using only their web browser. No local specialized desktop software or a fast internet connection is required. This environment will enable scientists to spend less time managing their software and more time doing science.

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.

Sustainable access to data, products, services and software from the European seismological Research Infrastructures: the EPOS TCS Seismology

NASA Astrophysics Data System (ADS)

Haslinger, Florian; Dupont, Aurelien; Michelini, Alberto; Rietbrock, Andreas; Sleeman, Reinoud; Wiemer, Stefan; Basili, Roberto; Bossu, Rémy; Cakti, Eser; Cotton, Fabrice; Crawford, Wayne; Diaz, Jordi; Garth, Tom; Locati, Mario; Luzi, Lucia; Pinho, Rui; Pitilakis, Kyriazis; Strollo, Angelo

2016-04-01

Easy, efficient and comprehensive access to data, data products, scientific services and scientific software is a key ingredient in enabling research at the frontiers of science. Organizing this access across the European Research Infrastructures in the field of seismology, so that it best serves user needs, takes advantage of state-of-the-art ICT solutions, provides cross-domain interoperability, and is organizationally and financially sustainable in the long term, is the core challenge of the implementation phase of the Thematic Core Service (TCS) Seismology within the EPOS-IP project. Building upon the existing European-level infrastructures ORFEUS for seismological waveforms, EMSC for seismological products, and EFEHR for seismological hazard and risk information, and implementing a pilot Computational Earth Science service starting from the results of the VERCE project, the work within the EPOS-IP project focuses on improving and extending the existing services, aligning them with global developments, to at the end produce a well coordinated framework that is technically, organizationally, and financially integrated with the EPOS architecture. This framework needs to respect the roles and responsibilities of the underlying national research infrastructures that are the data owners and main providers of data and products, and allow for active input and feedback from the (scientific) user community. At the same time, it needs to remain flexible enough to cope with unavoidable challenges in the availability of resources and dynamics of contributors. The technical work during the next years is organized in four areas: - constructing the next generation software architecture for the European Integrated (waveform) Data Archive EIDA, developing advanced metadata and station information services, fully integrate strong motion waveforms and derived parametric engineering-domain data, and advancing the integration of mobile (temporary) networks and OBS deployments in EIDA; - further development and expansion of services to access seismological products of scientific interest as provided by the community by implementing a common collection and development (IT) platform, improvements in the earthquake information services e.g. by introducing more robust quality indicators and diversifying collection and dissemination mechanisms, as well as improving historical earthquake data services; - development of a comprehensive suite of earthquake hazard products, tools, and services harmonized on the European level and available through a common access platform, encompassing information on seismic sources, seismogenic faults, ground-motion prediction equations, geotechnical information, and strong-motion recordings in buildings, together with an interface to earthquake risk; - a portal implementation of computational seismology tools and services, specifically for seismic waveform propagation in complex 3D media following the results of the VERCE project, and initiating the inclusion of further suitable codes on that portal in discussion with the community, forming the basis of EPOS computational earth science infrastructure. This will be accompanied by development and implementation of integrated and interoperable metadata structures, adequate and referencable persistent identifiers, and appropriate user access and authorization mechanisms. Here we present further detail on the work plan with the attempt to foster interaction with the target user community on the spectrum of services as well as on feedback mechanisms and governance.

Design and implementation of Skype USB user gateway software

NASA Astrophysics Data System (ADS)

Qi, Yang

2017-08-01

With the widespread application of VoIP, the client with private protocol becomes more and more popular. Skype is one of the representatives. How to connect Skype with PSTN just by Skype client has gradually become hot. This paper design and implement the software based on a kind of USB User Gateway. With the software Skype user can freely communicate with PSTN phone. FSM is designed as the core of the software, and Skype control is separated by the USB Gateway control. In this way, the communication becomes more flexible and efficient. In the actual user testing, the software obtains good results.

The Spectral Image Processing System (SIPS) - Interactive visualization and analysis of imaging spectrometer data

NASA Technical Reports Server (NTRS)

Kruse, F. A.; Lefkoff, A. B.; Boardman, J. W.; Heidebrecht, K. B.; Shapiro, A. T.; Barloon, P. J.; Goetz, A. F. H.

1993-01-01

The Center for the Study of Earth from Space (CSES) at the University of Colorado, Boulder, has developed a prototype interactive software system called the Spectral Image Processing System (SIPS) using IDL (the Interactive Data Language) on UNIX-based workstations. SIPS is designed to take advantage of the combination of high spectral resolution and spatial data presentation unique to imaging spectrometers. It streamlines analysis of these data by allowing scientists to rapidly interact with entire datasets. SIPS provides visualization tools for rapid exploratory analysis and numerical tools for quantitative modeling. The user interface is X-Windows-based, user friendly, and provides 'point and click' operation. SIPS is being used for multidisciplinary research concentrating on use of physically based analysis methods to enhance scientific results from imaging spectrometer data. The objective of this continuing effort is to develop operational techniques for quantitative analysis of imaging spectrometer data and to make them available to the scientific community prior to the launch of imaging spectrometer satellite systems such as the Earth Observing System (EOS) High Resolution Imaging Spectrometer (HIRIS).

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

Web-GIS platform for monitoring and forecasting of regional climate and ecological changes

NASA Astrophysics Data System (ADS)

Gordov, E. P.; Krupchatnikov, V. N.; Lykosov, V. N.; Okladnikov, I.; Titov, A. G.; Shulgina, T. M.

2012-12-01

Growing volume of environmental data from sensors and model outputs makes development of based on modern information-telecommunication technologies software infrastructure for information support of integrated scientific researches in the field of Earth sciences urgent and important task (Gordov et al, 2012, van der Wel, 2005). It should be considered that original heterogeneity of datasets obtained from different sources and institutions not only hampers interchange of data and analysis results but also complicates their intercomparison leading to a decrease in reliability of analysis results. However, modern geophysical data processing techniques allow combining of different technological solutions for organizing such information resources. Nowadays it becomes a generally accepted opinion that information-computational infrastructure should rely on a potential of combined usage of web- and GIS-technologies for creating applied information-computational web-systems (Titov et al, 2009, Gordov et al. 2010, Gordov, Okladnikov and Titov, 2011). Using these approaches for development of internet-accessible thematic information-computational systems, and arranging of data and knowledge interchange between them is a very promising way of creation of distributed information-computation environment for supporting of multidiscipline regional and global research in the field of Earth sciences including analysis of climate changes and their impact on spatial-temporal vegetation distribution and state. Experimental software and hardware platform providing operation of a web-oriented production and research center for regional climate change investigations which combines modern web 2.0 approach, GIS-functionality and capabilities of running climate and meteorological models, large geophysical datasets processing, visualization, joint software development by distributed research groups, scientific analysis and organization of students and post-graduate students education is presented. Platform software developed (Shulgina et al, 2012, Okladnikov et al, 2012) includes dedicated modules for numerical processing of regional and global modeling results for consequent analysis and visualization. Also data preprocessing, run and visualization of modeling results of models WRF and «Planet Simulator» integrated into the platform is provided. All functions of the center are accessible by a user through a web-portal using common graphical web-browser in the form of an interactive graphical user interface which provides, particularly, capabilities of visualization of processing results, selection of geographical region of interest (pan and zoom) and data layers manipulation (order, enable/disable, features extraction). Platform developed provides users with capabilities of heterogeneous geophysical data analysis, including high-resolution data, and discovering of tendencies in climatic and ecosystem changes in the framework of different multidisciplinary researches (Shulgina et al, 2011). Using it even unskilled user without specific knowledge can perform computational processing and visualization of large meteorological, climatological and satellite monitoring datasets through unified graphical web-interface.

JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age (Invited)

NASA Astrophysics Data System (ADS)

Mueller, D.; Dimitoglou, G.; Langenberg, M.; Pagel, S.; Dau, A.; Nuhn, M.; Garcia Ortiz, J. P.; Dietert, H.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

2010-12-01

The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is bound to be accessible only from a few repositories and users will have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community.

PiCO QL: A software library for runtime interactive queries on program data

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

PiCO QL is an open source C/C++ software whose scientific scope is real-time interactive analysis of in-memory data through SQL queries. It exposes a relational view of a system's or application's data structures, which is queryable through SQL. While the application or system is executing, users can input queries through a web-based interface or issue web service requests. Queries execute on the live data structures through the respective relational views. PiCO QL makes a good candidate for ad-hoc data analysis in applications and for diagnostics in systems settings. Applications of PiCO QL include the Linux kernel, the Valgrind instrumentation framework, a GIS application, a virtual real-time observatory of stellar objects, and a source code analyser.

Data management integration for biomedical core facilities

NASA Astrophysics Data System (ADS)

Zhang, Guo-Qiang; Szymanski, Jacek; Wilson, David

2007-03-01

We present the design, development, and pilot-deployment experiences of MIMI, a web-based, Multi-modality Multi-Resource Information Integration environment for biomedical core facilities. This is an easily customizable, web-based software tool that integrates scientific and administrative support for a biomedical core facility involving a common set of entities: researchers; projects; equipments and devices; support staff; services; samples and materials; experimental workflow; large and complex data. With this software, one can: register users; manage projects; schedule resources; bill services; perform site-wide search; archive, back-up, and share data. With its customizable, expandable, and scalable characteristics, MIMI not only provides a cost-effective solution to the overarching data management problem of biomedical core facilities unavailable in the market place, but also lays a foundation for data federation to facilitate and support discovery-driven research.

Geometric registration of remotely sensed data with SAMIR

NASA Astrophysics Data System (ADS)

Gianinetto, Marco; Barazzetti, Luigi; Dini, Luigi; Fusiello, Andrea; Toldo, Roberto

2015-06-01

The commercial market offers several software packages for the registration of remotely sensed data through standard one-to-one image matching. Although very rapid and simple, this strategy does not take into consideration all the interconnections among the images of a multi-temporal data set. This paper presents a new scientific software, called Satellite Automatic Multi-Image Registration (SAMIR), able to extend the traditional registration approach towards multi-image global processing. Tests carried out with high-resolution optical (IKONOS) and high-resolution radar (COSMO-SkyMed) data showed that SAMIR can improve the registration phase with a more rigorous and robust workflow without initial approximations, user's interaction or limitation in spatial/spectral data size. The validation highlighted a sub-pixel accuracy in image co-registration for the considered imaging technologies, including optical and radar imagery.

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.

Programming Makes Software; Support Makes Users

NASA Astrophysics Data System (ADS)

Batcheller, A. L.

2010-12-01

Skilled software engineers may build fantastic software for climate modeling, yet fail to achieve their project’s objectives. Software support and related activities are just as critical as writing software. This study followed three different software projects in the climate sciences, using interviews, observation, and document analysis to examine the value added by support work. Supporting the project and interacting with users was a key task for software developers, who often spent 50% of their time on it. Such support work most often involved replying to questions on an email list, but also included talking to users on teleconference calls and in person. Software support increased adoption by building the software’s reputation and showing individuals how the software can meet their needs. In the process of providing support, developers often learned new of requirements as users reported features they desire and bugs they found. As software matures and gains widespread use, support work often increases. In fact, such increases can be one signal that the software has achieved broad acceptance. Maturing projects also find demand for instructional classes, online tutorials and detailed examples of how to use the software. The importance of support highlights the fact that building software systems involves both social and technical aspects. Yes, we need to build the software, but we also need to “build” the users and practices that can take advantage of it.

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.

A method for interactive specification of multiple-block topologies

NASA Technical Reports Server (NTRS)

Sorenson, Reese L.; Mccann, Karen M.

1991-01-01

A method is presented for dealing with the vast amount of topological and other data which must be specified to generate a multiple-block computational grid. Specific uses of the graphical capabilities of a powerful scientific workstation are described which reduce the burden on the user of collecting and formatting such large amounts of data. A program to implement this method, 3DPREP, is described. A plotting transformation algorithm, some useful software tools, notes on programming, and a database organization are also presented. Example grids developed using the method are shown.

Framework Development Supporting the Safety Portal

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

Prescott, Steven Ralph; Kvarfordt, Kellie Jean; Vang, Leng

2015-07-01

In a collaborating scientific research arena it is important to have an environment where analysts have access to a shared repository of information, documents, and software tools, and be able to accurately maintain and track historical changes in models. The new Safety Portal cloud-based environment will be accessible remotely from anywhere regardless of computing platforms given that the platform has available Internet access and proper browser capabilities. Information stored at this environment would be restricted based on user assigned credentials. This report discusses current development of a cloud-based web portal for PRA tools.

Tutorial examples for uncertainty quantification methods.

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

De Bord, Sarah

2015-08-01

This report details the work accomplished during my 2015 SULI summer internship at Sandia National Laboratories in Livermore, CA. During this internship, I worked on multiple tasks with the common goal of making uncertainty quantification (UQ) methods more accessible to the general scientific community. As part of my work, I created a comprehensive numerical integration example to incorporate into the user manual of a UQ software package. Further, I developed examples involving heat transfer through a window to incorporate into tutorial lectures that serve as an introduction to UQ methods.

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)

Distributed observing facility for remote access to multiple telescopes

NASA Astrophysics Data System (ADS)

Callegari, Massimo; Panciatici, Antonio; Pasian, Fabio; Pucillo, Mauro; Santin, Paolo; Aro, Simo; Linde, Peter; Duran, Maria A.; Rodriguez, Jose A.; Genova, Francoise; Ochsenbein, Francois; Ponz, J. D.; Talavera, Antonio

2000-06-01

The REMOT (Remote Experiment Monitoring and conTrol) project was financed by 1996 by the European Community in order to investigate the possibility of generalizing the remote access to scientific instruments. After the feasibility of this idea was demonstrated, the DYNACORE (DYNAmically, COnfigurable Remote Experiment monitoring and control) project was initiated as a REMOT follow-up. Its purpose is to develop software technology to support scientists in two different domains, astronomy and plasma physics. The resulting system allows (1) simultaneous multiple user access to different experimental facilities, (2) dynamic adaptability to different kinds of real instruments, (3) exploitation of the communication infrastructures features, (4) ease of use through intuitive graphical interfaces, and (5) additional inter-user communication using off-the-shelf projects such as video-conference tools, chat programs and shared blackboards.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

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 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.

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.

Software Repository

NASA Technical Reports Server (NTRS)

Merwarth, P., D.

1983-01-01

The Common Software Module Repository (CSMR) is computerized library system with high product and service visibility to potential users. Online capabilities of system allow both librarian and user to interact with library. Librarian is responsible for maintaining information in CSMR library. User searches library to locate software modules that meet his or her current needs.

The EOSDIS software challenge

NASA Astrophysics Data System (ADS)

Jaworski, Allan

1993-08-01

The Earth Observing System (EOS) Data and Information System (EOSDIS) will serve as a major resource for the earth science community, supporting both command and control of complex instruments onboard the EOS spacecraft and the archiving, distribution, and analysis of data. The scale of EOSDIS and the volume of multidisciplinary research to be conducted using EOSDIS resources will produce unparalleled needs for technology transparency, data integration, and system interoperability. The scale of this effort far outscopes any previous scientific data system in its breadth or operational and performance needs. Modern hardware technology can meet the EOSDIS technical challenge. Multiprocessing speeds of many giga-flops are being realized by modern computers. Online storage disk, optical disk, and videocassette libraries with storage capacities of many terabytes are now commercially available. Radio frequency and fiber optics communications networks with gigabit rates are demonstrable today. It remains, of course, to perform the system engineering to establish the requirements, architectures, and designs that will implement the EOSDIS systems. Software technology, however, has not enjoyed the price/performance advances of hardware. Although we have learned to engineer hardware systems which have several orders of magnitude greater complexity and performance than those built in the 1960's, we have not made comparable progress in dramatically reducing the cost of software development. This lack of progress may significantly reduce our capabilities to achieve economically the types of highly interoperable, responsive, integraded, and productive environments which are needed by the earth science community. This paper describes some of the EOSDIS software requirements and current activities in the software community which are applicable to meeting the EOSDIS challenge. Some of these areas include intelligent user interfaces, software reuse libraries, and domain engineering. Also included are discussions of applicable standards in the areas of operating systems interfaces, user interfaces, communications interfaces, data transport, and science algorithm support, and their role in supporting the software development process.

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.

Software Piracy, Ethics, and the Academician.

ERIC Educational Resources Information Center

Bassler, Richard A.

The numerous software programs available for easy, low-cost copying raise ethical questions. The problem can be examined from the viewpoints of software users, teachers, authors, vendors, and distributors. Software users might hesitate to purchase or use software which prevents the making of back-up copies for program protection. Teachers in…

Software Engineering Laboratory (SEL) data base reporting software user's guide and system description. Volume 1: Introduction and user's guide

NASA Technical Reports Server (NTRS)

1983-01-01

Reporting software programs provide formatted listings and summary reports of the Software Engineering Laboratory (SEL) data base contents. The operating procedures and system information for 18 different reporting software programs are described. Sample output reports from each program are provided.

NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data

PubMed Central

Rothman, Jason S.; Silver, R. Angus

2018-01-01

Acquisition, analysis and simulation of electrophysiological properties of the nervous system require multiple software packages. This makes it difficult to conserve experimental metadata and track the analysis performed. It also complicates certain experimental approaches such as online analysis. To address this, we developed NeuroMatic, an open-source software toolkit that performs data acquisition (episodic, continuous and triggered recordings), data analysis (spike rasters, spontaneous event detection, curve fitting, stationarity) and simulations (stochastic synaptic transmission, synaptic short-term plasticity, integrate-and-fire and Hodgkin-Huxley-like single-compartment models). The merging of a wide range of tools into a single package facilitates a more integrated style of research, from the development of online analysis functions during data acquisition, to the simulation of synaptic conductance trains during dynamic-clamp experiments. Moreover, NeuroMatic has the advantage of working within Igor Pro, a platform-independent environment that includes an extensive library of built-in functions, a history window for reviewing the user's workflow and the ability to produce publication-quality graphics. Since its original release, NeuroMatic has been used in a wide range of scientific studies and its user base has grown considerably. NeuroMatic version 3.0 can be found at http://www.neuromatic.thinkrandom.com and https://github.com/SilverLabUCL/NeuroMatic. PMID:29670519

Automating NEURON Simulation Deployment in Cloud Resources.

PubMed

Stockton, David B; Santamaria, Fidel

2017-01-01

Simulations in neuroscience are performed on local servers or High Performance Computing (HPC) facilities. Recently, cloud computing has emerged as a potential computational platform for neuroscience simulation. In this paper we compare and contrast HPC and cloud resources for scientific computation, then report how we deployed NEURON, a widely used simulator of neuronal activity, in three clouds: Chameleon Cloud, a hybrid private academic cloud for cloud technology research based on the OpenStack software; Rackspace, a public commercial cloud, also based on OpenStack; and Amazon Elastic Cloud Computing, based on Amazon's proprietary software. We describe the manual procedures and how to automate cloud operations. We describe extending our simulation automation software called NeuroManager (Stockton and Santamaria, Frontiers in Neuroinformatics, 2015), so that the user is capable of recruiting private cloud, public cloud, HPC, and local servers simultaneously with a simple common interface. We conclude by performing several studies in which we examine speedup, efficiency, total session time, and cost for sets of simulations of a published NEURON model.

Automating NEURON Simulation Deployment in Cloud Resources

PubMed Central

Santamaria, Fidel

2016-01-01

Simulations in neuroscience are performed on local servers or High Performance Computing (HPC) facilities. Recently, cloud computing has emerged as a potential computational platform for neuroscience simulation. In this paper we compare and contrast HPC and cloud resources for scientific computation, then report how we deployed NEURON, a widely used simulator of neuronal activity, in three clouds: Chameleon Cloud, a hybrid private academic cloud for cloud technology research based on the Open-Stack software; Rackspace, a public commercial cloud, also based on OpenStack; and Amazon Elastic Cloud Computing, based on Amazon’s proprietary software. We describe the manual procedures and how to automate cloud operations. We describe extending our simulation automation software called NeuroManager (Stockton and Santamaria, Frontiers in Neuroinformatics, 2015), so that the user is capable of recruiting private cloud, public cloud, HPC, and local servers simultaneously with a simple common interface. We conclude by performing several studies in which we examine speedup, efficiency, total session time, and cost for sets of simulations of a published NEURON model. PMID:27655341

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.

Mfold web server for nucleic acid folding and hybridization prediction

PubMed Central

Zuker, Michael

2003-01-01

The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’. PMID:12824337

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 .

ReGaTE: Registration of Galaxy Tools in Elixir.

PubMed

Doppelt-Azeroual, Olivia; Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; van den Beek, Marius; Grüning, Björn; Ison, Jon; Ménager, Hervé

2017-06-01

Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE . © The Author 2017. Published by Oxford University Press.

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.

Introduction of A New Toolbox for Processing Digital Images From Multiple Camera Networks: FMIPROT

NASA Astrophysics Data System (ADS)

Melih Tanis, Cemal; Nadir Arslan, Ali

2017-04-01

Webcam networks intended for scientific monitoring of ecosystems is providing digital images and other environmental data for various studies. Also, other types of camera networks can also be used for scientific purposes, e.g. usage of traffic webcams for phenological studies, camera networks for ski tracks and avalanche monitoring over mountains for hydrological studies. To efficiently harness the potential of these camera networks, easy to use software which can obtain and handle images from different networks having different protocols and standards is necessary. For the analyses of the images from webcam networks, numerous software packages are freely available. These software packages have different strong features not only for analyzing but also post processing digital images. But specifically for the ease of use, applicability and scalability, a different set of features could be added. Thus, a more customized approach would be of high value, not only for analyzing images of comprehensive camera networks, but also considering the possibility to create operational data extraction and processing with an easy to use toolbox. At this paper, we introduce a new toolbox, entitled; Finnish Meteorological Institute Image PROcessing Tool (FMIPROT) which a customized approach is followed. FMIPROT has currently following features: • straightforward installation, • no software dependencies that require as extra installations, • communication with multiple camera networks, • automatic downloading and handling images, • user friendly and simple user interface, • data filtering, • visualizing results on customizable plots, • plugins; allows users to add their own algorithms. Current image analyses in FMIPROT include "Color Fraction Extraction" and "Vegetation Indices". The analysis of color fraction extraction is calculating the fractions of the colors in a region of interest, for red, green and blue colors along with brightness and luminance parameters. The analysis of vegetation indices is a collection of indices used in vegetation phenology and includes "Green Fraction" (green chromatic coordinate), "Green-Red Vegetation Index" and "Green Excess Index". "Snow cover fraction" analysis which detects snow covered pixels in the images and georeference them on a geospatial plane to calculate the snow cover fraction is being implemented at the moment. FMIPROT is being developed during the EU Life+ MONIMET project. Altogether we mounted 28 cameras at 14 different sites in Finland as MONIMET camera network. In this paper, we will present details of FMIPROT and analysis results from MONIMET camera network. We will also discuss on future planned developments of FMIPROT.

An Intelligent Tutoring System (ITS) for Operating Training of ROCSAT TT&C Groung Station

NASA Astrophysics Data System (ADS)

Shr, Arthur M. D.; Miau, Jiun Jih

2000-07-01

ROCS AT-1 is the first small satellite developed by the Republic of China and is a lowearth orbit experimental satellite. The goal of ROCSAT-1 is to carry out scientific research missions. To successfully accomplish ROCSAT missions, the ROCSAT Mission Operations Team (RMOT) is formed to handle the daily operation and maintenance activities. These activities are onerous and complex. Hence, RMOT is concerned with future personnel training. In this paper, we propose an Intelligent Tutoring System (ITS) which is capable of integrating the training courses into a software program. ITS uses a great amount of information to present a subject for a user to learn. In the process of teaching, an ITS is capable of presenting the course materials in a structured format to the user and to judge if the user has mastered the subject or not. ITS is the tool to integrate the RMOT training courses and to develop a multi-function computer-assisted instruction (CAI) system. It can not only provide a practical method for users recurrently, but also make self-teaching easily.

Towards Model-Driven End-User Development in CALL

ERIC Educational Resources Information Center

Farmer, Rod; Gruba, Paul

2006-01-01

The purpose of this article is to introduce end-user development (EUD) processes to the CALL software development community. EUD refers to the active participation of end-users, as non-professional developers, in the software development life cycle. Unlike formal software engineering approaches, the focus in EUD on means/ends development is…

Freva - Freie Univ Evaluation System Framework for Scientific Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Schartner, Thomas; Kirchner, Ingo; Rust, Henning W.; Cubasch, Ulrich; Ulbrich, Uwe

2016-04-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science. Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitation of the provision and usage of tools and climate data automatically increases the number of scientists working with the data sets and identifying discrepancies. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Therefore, plugged-in tools benefit from transparency and reproducibility. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Freva - Freie Univ Evaluation System Framework for Scientific HPC Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Schartner, T.; Grieger, J.; Kirchner, I.; Rust, H.; Cubasch, U.; Ulbrich, U.

2017-12-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science (e.g. www-miklip.dkrz.de, cmip-eval.dkrz.de). Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Agile data management for curation of genomes to watershed datasets

NASA Astrophysics Data System (ADS)

Varadharajan, C.; Agarwal, D.; Faybishenko, B.; Versteeg, R.

2015-12-01

A software platform is being developed for data management and assimilation [DMA] as part of the U.S. Department of Energy's Genomes to Watershed Sustainable Systems Science Focus Area 2.0. The DMA components and capabilities are driven by the project science priorities and the development is based on agile development techniques. The goal of the DMA software platform is to enable users to integrate and synthesize diverse and disparate field, laboratory, and simulation datasets, including geological, geochemical, geophysical, microbiological, hydrological, and meteorological data across a range of spatial and temporal scales. The DMA objectives are (a) developing an integrated interface to the datasets, (b) storing field monitoring data, laboratory analytical results of water and sediments samples collected into a database, (c) providing automated QA/QC analysis of data and (d) working with data providers to modify high-priority field and laboratory data collection and reporting procedures as needed. The first three objectives are driven by user needs, while the last objective is driven by data management needs. The project needs and priorities are reassessed regularly with the users. After each user session we identify development priorities to match the identified user priorities. For instance, data QA/QC and collection activities have focused on the data and products needed for on-going scientific analyses (e.g. water level and geochemistry). We have also developed, tested and released a broker and portal that integrates diverse datasets from two different databases used for curation of project data. The development of the user interface was based on a user-centered design process involving several user interviews and constant interaction with data providers. The initial version focuses on the most requested feature - i.e. finding the data needed for analyses through an intuitive interface. Once the data is found, the user can immediately plot and download data through the portal. The resulting product has an interface that is more intuitive and presents the highest priority datasets that are needed by the users. Our agile approach has enabled us to build a system that is keeping pace with the science needs while utilizing limited resources.

Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case.

PubMed

Russ, Thomas A; Ramakrishnan, Cartic; Hovy, Eduard H; Bota, Mihail; Burns, Gully A P C

2011-08-22

We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to supply the supporting evidence. We present web-application software as part of the 'BioScholar' project (R01-GM083871) that fully instantiates this process for a well-defined domain: using tract-tracing experiments to study the neural connectivity of the rat brain. The main contribution of this work is to provide the first instantiation of a knowledge representation for experimental observations called 'Knowledge Engineering from Experimental Design' (KEfED) based on experimental variables and their interdependencies. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a 'neural connection matrix' interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. BioScholar is built in Flex 3.5. It uses Persevere (a noSQL database) as a flexible data store and PowerLoom® (a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology. We first introduce the KEfED approach as a general approach and describe its possible role as a way of introducing structured reasoning into models of argumentation within new models of scientific publication. We then describe the design and implementation of our example application: the BioScholar software. This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS).

Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case

PubMed Central

2011-01-01

Background We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to supply the supporting evidence. We present web-application software as part of the 'BioScholar' project (R01-GM083871) that fully instantiates this process for a well-defined domain: using tract-tracing experiments to study the neural connectivity of the rat brain. Results The main contribution of this work is to provide the first instantiation of a knowledge representation for experimental observations called 'Knowledge Engineering from Experimental Design' (KEfED) based on experimental variables and their interdependencies. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a 'neural connection matrix' interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. BioScholar is built in Flex 3.5. It uses Persevere (a noSQL database) as a flexible data store and PowerLoom® (a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology. Conclusions We first introduce the KEfED approach as a general approach and describe its possible role as a way of introducing structured reasoning into models of argumentation within new models of scientific publication. We then describe the design and implementation of our example application: the BioScholar software. This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS). PMID:21859449

JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age

NASA Astrophysics Data System (ADS)

Mueller, D.; Dimitoglou, G.; Garcia Ortiz, J.; Langenberg, M.; Nuhn, M.; Dau, A.; Pagel, S.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

2011-12-01

The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is accessible only from a few repositories and users have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the ESA/NASA Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community. In addition, the easy-to-use graphical user interface enables the general public and educators to access, enjoy and reuse data from space missions without barriers.

Software Prototyping: Designing Systems for Users.

ERIC Educational Resources Information Center

Spies, Phyllis Bova

1983-01-01

Reports on major change in computer software development process--the prototype model, i.e., implementation of skeletal system that is enhanced during interaction with users. Expensive and unreliable software, software design errors, traditional development approach, resources required for prototyping, success stories, and systems designer's role…

Software agents for the dissemination of remote terrestrial sensing data

NASA Technical Reports Server (NTRS)

Toomey, Christopher N.; Simoudis, Evangelos; Johnson, Raymond W.; Mark, William S.

1994-01-01

Remote terrestrial sensing (RTS) data is constantly being collected from a variety of space-based and earth-based sensors. The collected data, and especially 'value-added' analyses of the data, are finding growing application for commercial, government, and scientific purposes. The scale of this data collection and analysis is truly enormous; e.g., by 1995, the amount of data available in just one sector, NASA space science, will reach 5 petabytes. Moreover, the amount of data, and the value of analyzing the data, are expected to increase dramatically as new satellites and sensors become available (e.g., NASA's Earth Observing System satellites). Lockheed and other companies are beginning to provide data and analysis commercially. A critical issue for the exploitation of collected data is the dissemination of data and value-added analyses to a diverse and widely distributed customer base. Customers must be able to use their computational environment (eventually the National Information Infrastructure) to obtain timely and complete information, without having to know the details of where the relevant data resides and how it is accessed. Customers must be able to routinely use standard, widely available (and, therefore, low cost) analyses, while also being able to readily create on demand highly customized analyses to make crucial decisions. The diversity of user needs creates a difficult software problem: how can users easily state their needs, while the computational environment assumes the responsibility of finding (or creating) relevant information, and then delivering the results in a form that users understand? A software agent is a self-contained, active software module that contains an explicit representation of its operational knowledge. This explicit representation allows agents to examine their own capabilities in order to modify their goals to meet changing needs and to take advantage of dynamic opportunities. In addition, the explicit representation allows agents to advertize their capabilities and results to other agents, thereby allowing the collection of agents to reuse each others work.

Scalable Adaptive Graphics Environment (SAGE) Software for the Visualization of Large Data Sets on a Video Wall

NASA Technical Reports Server (NTRS)

Jedlovec, Gary; Srikishen, Jayanthi; Edwards, Rita; Cross, David; Welch, Jon; Smith, Matt

2013-01-01

The use of collaborative scientific visualization systems for the analysis, visualization, and sharing of "big data" available from new high resolution remote sensing satellite sensors or four-dimensional numerical model simulations is propelling the wider adoption of ultra-resolution tiled display walls interconnected by high speed networks. These systems require a globally connected and well-integrated operating environment that provides persistent visualization and collaboration services. This abstract and subsequent presentation describes a new collaborative visualization system installed for NASA's Shortterm Prediction Research and Transition (SPoRT) program at Marshall Space Flight Center and its use for Earth science applications. The system consists of a 3 x 4 array of 1920 x 1080 pixel thin bezel video monitors mounted on a wall in a scientific collaboration lab. The monitors are physically and virtually integrated into a 14' x 7' for video display. The display of scientific data on the video wall is controlled by a single Alienware Aurora PC with a 2nd Generation Intel Core 4.1 GHz processor, 32 GB memory, and an AMD Fire Pro W600 video card with 6 mini display port connections. Six mini display-to-dual DVI cables are used to connect the 12 individual video monitors. The open source Scalable Adaptive Graphics Environment (SAGE) windowing and media control framework, running on top of the Ubuntu 12 Linux operating system, allows several users to simultaneously control the display and storage of high resolution still and moving graphics in a variety of formats, on tiled display walls of any size. The Ubuntu operating system supports the open source Scalable Adaptive Graphics Environment (SAGE) software which provides a common environment, or framework, enabling its users to access, display and share a variety of data-intensive information. This information can be digital-cinema animations, high-resolution images, high-definition video-teleconferences, presentation slides, documents, spreadsheets or laptop screens. SAGE is cross-platform, community-driven, open-source visualization and collaboration middleware that utilizes shared national and international cyberinfrastructure for the advancement of scientific research and education.

Scalable Adaptive Graphics Environment (SAGE) Software for the Visualization of Large Data Sets on a Video Wall

NASA Astrophysics Data System (ADS)

Jedlovec, G.; Srikishen, J.; Edwards, R.; Cross, D.; Welch, J. D.; Smith, M. R.

2013-12-01

The use of collaborative scientific visualization systems for the analysis, visualization, and sharing of 'big data' available from new high resolution remote sensing satellite sensors or four-dimensional numerical model simulations is propelling the wider adoption of ultra-resolution tiled display walls interconnected by high speed networks. These systems require a globally connected and well-integrated operating environment that provides persistent visualization and collaboration services. This abstract and subsequent presentation describes a new collaborative visualization system installed for NASA's Short-term Prediction Research and Transition (SPoRT) program at Marshall Space Flight Center and its use for Earth science applications. The system consists of a 3 x 4 array of 1920 x 1080 pixel thin bezel video monitors mounted on a wall in a scientific collaboration lab. The monitors are physically and virtually integrated into a 14' x 7' for video display. The display of scientific data on the video wall is controlled by a single Alienware Aurora PC with a 2nd Generation Intel Core 4.1 GHz processor, 32 GB memory, and an AMD Fire Pro W600 video card with 6 mini display port connections. Six mini display-to-dual DVI cables are used to connect the 12 individual video monitors. The open source Scalable Adaptive Graphics Environment (SAGE) windowing and media control framework, running on top of the Ubuntu 12 Linux operating system, allows several users to simultaneously control the display and storage of high resolution still and moving graphics in a variety of formats, on tiled display walls of any size. The Ubuntu operating system supports the open source Scalable Adaptive Graphics Environment (SAGE) software which provides a common environment, or framework, enabling its users to access, display and share a variety of data-intensive information. This information can be digital-cinema animations, high-resolution images, high-definition video-teleconferences, presentation slides, documents, spreadsheets or laptop screens. SAGE is cross-platform, community-driven, open-source visualization and collaboration middleware that utilizes shared national and international cyberinfrastructure for the advancement of scientific research and education.

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…

Facing the Challenges of Accessing, Managing, and Integrating Large Observational Datasets in Ecology: Enabling and Enriching the Use of NEON's Observational Data

NASA Astrophysics Data System (ADS)

Thibault, K. M.

2013-12-01

As the construction of NEON and its transition to operations progresses, more and more data will become available to the scientific community, both from NEON directly and from the concomitant growth of existing data repositories. Many of these datasets include ecological observations of a diversity of taxa in both aquatic and terrestrial environments. Although observational data have been collected and used throughout the history of organismal biology, the field has not yet fully developed a culture of data management, documentation, standardization, sharing and discoverability to facilitate the integration and synthesis of datasets. Moreover, the tools required to accomplish these goals, namely database design, implementation, and management, and automation and parallelization of analytical tasks through computational techniques, have not historically been included in biology curricula, at either the undergraduate or graduate levels. To ensure the success of data-generating projects like NEON in advancing organismal ecology and to increase transparency and reproducibility of scientific analyses, an acceleration of the cultural shift to open science practices, the development and adoption of data standards, such as the DarwinCore standard for taxonomic data, and increased training in computational approaches for biologists need to be realized. Here I highlight several initiatives that are intended to increase access to and discoverability of publicly available datasets and equip biologists and other scientists with the skills that are need to manage, integrate, and analyze data from multiple large-scale projects. The EcoData Retriever (ecodataretriever.org) is a tool that downloads publicly available datasets, re-formats the data into an efficient relational database structure, and then automatically imports the data tables onto a user's local drive into the database tool of the user's choice. The automation of these tasks results in nearly instantaneous execution of tasks that previously required hours to days of each data user's time, with decreased error rates and increased useability of the data. The Ecological Data wiki (ecologicaldata.org) provides a forum for users of ecological datasets to share relevant metadata and tips and tricks for using the data, in order to flatten learning curves, as well as minimize redundancy of efforts among users of the same datasets. Finally, Software Carpentry (software-carpentry.org) has developed curricula for scientific computing and provides both online training and low cost, short courses that can be tailored to the specific needs of the students. Demand for these courses has been increasing exponentially in recent years, and represent a significant educational resource for biologists. I will conclude by linking these initiatives to the challenges facing ecologists related to the effective and efficient exploitation of NEON's diverse data streams.

Remote Internet access to advanced analytical facilities: a new approach with Web-based services.

PubMed

Sherry, N; Qin, J; Fuller, M Suominen; Xie, Y; Mola, O; Bauer, M; McIntyre, N S; Maxwell, D; Liu, D; Matias, E; Armstrong, C

2012-09-04

Over the past decade, the increasing availability of the World Wide Web has held out the possibility that the efficiency of scientific measurements could be enhanced in cases where experiments were being conducted at distant facilities. Examples of early successes have included X-ray diffraction (XRD) experimental measurements of protein crystal structures at synchrotrons and access to scanning electron microscopy (SEM) and NMR facilities by users from institutions that do not possess such advanced capabilities. Experimental control, visual contact, and receipt of results has used some form of X forwarding and/or VNC (virtual network computing) software that transfers the screen image of a server at the experimental site to that of the users' home site. A more recent development is a web services platform called Science Studio that provides teams of scientists with secure links to experiments at one or more advanced research facilities. The software provides a widely distributed team with a set of controls and screens to operate, observe, and record essential parts of the experiment. As well, Science Studio provides high speed network access to computing resources to process the large data sets that are often involved in complex experiments. The simple web browser and the rapid transfer of experimental data to a processing site allow efficient use of the facility and assist decision making during the acquisition of the experimental results. The software provides users with a comprehensive overview and record of all parts of the experimental process. A prototype network is described involving X-ray beamlines at two different synchrotrons and an SEM facility. An online parallel processing facility has been developed that analyzes the data in near-real time using stream processing. Science Studio and can be expanded to include many other analytical applications, providing teams of users with rapid access to processed results along with the means for detailed discussion of their significance.

The InSAR Scientific Computing Environment (ISCE): An Earth Science SAR Processing Framework, Toolbox, and Foundry

NASA Astrophysics Data System (ADS)

Agram, P. S.; Gurrola, E. M.; Lavalle, M.; Sacco, G. F.; Rosen, P. A.

2016-12-01

The InSAR Scientific Computing Environment (ISCE) provides both a modular, flexible, and extensible framework for building software components and applications that work together seamlessly as well as a toolbox for processing InSAR data into higher level geodetic image products from a diverse array of radar satellites and aircraft. ISCE easily scales to serve as the SAR processing engine at the core of the NASA JPL Advanced Rapid Imaging and Analysis (ARIA) Center for Natural Hazards as well as a software toolbox for individual scientists working with SAR data. ISCE is planned as the foundational element in processing NISAR data, enabling a new class of analyses that take greater advantage of the long time and large spatial scales of these data. ISCE in ARIA is also a SAR Foundry for development of new processing components and workflows to meet the needs of both large processing centers and individual users. The ISCE framework contains object-oriented Python components layered to construct Python InSAR components that manage legacy Fortran/C InSAR programs. The Python user interface enables both command-line deployment of workflows as well as an interactive "sand box" (the Python interpreter) where scientists can "play" with the data. Recent developments in ISCE include the addition of components to ingest Sentinel-1A SAR data (both stripmap and TOPS-mode) and a new workflow for processing the TOPS-mode data. New components are being developed to exploit polarimetric-SAR data to provide the ecosystem and land-cover/land-use change communities with rigorous and efficient tools to perform multi-temporal, polarimetric and tomographic analyses in order to generate calibrated, geocoded and mosaicked Level-2 and Level-3 products (e.g., maps of above-ground biomass or forest disturbance). ISCE has been downloaded by over 200 users by a license for WinSAR members through the Unavco.org website. Others may apply directly to JPL for a license at download.jpl.nasa.gov.

Encyclopedia of software components

NASA Technical Reports Server (NTRS)

Vanwarren, Lloyd (Inventor); Beckman, Brian C. (Inventor)

1991-01-01

Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component.

Encyclopedia of Software Components

NASA Technical Reports Server (NTRS)

Warren, Lloyd V. (Inventor); Beckman, Brian C. (Inventor)

1997-01-01

Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component.

Evaluating non-relational storage technology for HEP metadata and meta-data catalog

NASA Astrophysics Data System (ADS)

Grigorieva, M. A.; Golosova, M. V.; Gubin, M. Y.; Klimentov, A. A.; Osipova, V. V.; Ryabinkin, E. A.

2016-10-01

Large-scale scientific experiments produce vast volumes of data. These data are stored, processed and analyzed in a distributed computing environment. The life cycle of experiment is managed by specialized software like Distributed Data Management and Workload Management Systems. In order to be interpreted and mined, experimental data must be accompanied by auxiliary metadata, which are recorded at each data processing step. Metadata describes scientific data and represent scientific objects or results of scientific experiments, allowing them to be shared by various applications, to be recorded in databases or published via Web. Processing and analysis of constantly growing volume of auxiliary metadata is a challenging task, not simpler than the management and processing of experimental data itself. Furthermore, metadata sources are often loosely coupled and potentially may lead to an end-user inconsistency in combined information queries. To aggregate and synthesize a range of primary metadata sources, and enhance them with flexible schema-less addition of aggregated data, we are developing the Data Knowledge Base architecture serving as the intelligence behind GUIs and APIs.

adwTools Developed: New Bulk Alloy and Surface Analysis Software for the Alloy Design Workbench

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Morse, Jeffrey A.; Noebe, Ronald D.; Abel, Phillip B.

2004-01-01

A suite of atomistic modeling software, called the Alloy Design Workbench, has been developed by the Computational Materials Group at the NASA Glenn Research Center and the Ohio Aerospace Institute (OAI). The main goal of this software is to guide and augment experimental materials research and development efforts by creating powerful, yet intuitive, software that combines a graphical user interface with an operating code suitable for real-time atomistic simulations of multicomponent alloy systems. Targeted for experimentalists, the interface is straightforward and requires minimum knowledge of the underlying theory, allowing researchers to focus on the scientific aspects of the work. The centerpiece of the Alloy Design Workbench suite is the adwTools module, which concentrates on the atomistic analysis of surfaces and bulk alloys containing an arbitrary number of elements. An additional module, adwParams, handles ab initio input for the parameterization used in adwTools. Future modules planned for the suite include adwSeg, which will provide numerical predictions for segregation profiles to alloy surfaces and interfaces, and adwReport, which will serve as a window into the database, providing public access to the parameterization data and a repository where users can submit their own findings from the rest of the suite. The entire suite is designed to run on desktop-scale computers. The adwTools module incorporates a custom OAI/Glenn-developed Fortran code based on the BFS (Bozzolo- Ferrante-Smith) method for alloys, ref. 1). The heart of the suite, this code is used to calculate the energetics of different compositions and configurations of atoms.

A Freeware Path to Neutron Computed Tomography

NASA Astrophysics Data System (ADS)

Schillinger, Burkhard; Craft, Aaron E.

Neutron computed tomography has become a routine method at many neutron sources due to the availability of digital detection systems, powerful computers and advanced software. The commercial packages Octopus by Inside Matters and VGStudio by Volume Graphics have been established as a quasi-standard for high-end computed tomography. However, these packages require a stiff investment and are available to the users only on-site at the imaging facility to do their data processing. There is a demand from users to have image processing software at home to do further data processing; in addition, neutron computed tomography is now being introduced even at smaller and older reactors. Operators need to show a first working tomography setup before they can obtain a budget to build an advanced tomography system. Several packages are available on the web for free; however, these have been developed for X-rays or synchrotron radiation and are not immediately useable for neutron computed tomography. Three reconstruction packages and three 3D-viewers have been identified and used even for Gigabyte datasets. This paper is not a scientific publication in the classic sense, but is intended as a review to provide searchable help to make the described packages usable for the tomography community. It presents the necessary additional preprocessing in ImageJ, some workarounds for bugs in the software, and undocumented or badly documented parameters that need to be adapted for neutron computed tomography. The result is a slightly complicated, but surprisingly high-quality path to neutron computed tomography images in 3D, but not a replacement for the even more powerful commercial software mentioned above.

Software framework for automatic learning of telescope operation

NASA Astrophysics Data System (ADS)

Rodríguez, Jose A.; Molgó, Jordi; Guerra, Dailos

2016-07-01

The "Gran Telescopio de Canarias" (GTC) is an optical-infrared 10-meter segmented mirror telescope at the ORM observatory in Canary Islands (Spain). The GTC Control System (GCS) is a distributed object and component oriented system based on RT-CORBA and it is responsible for the operation of the telescope, including its instrumentation. The current development state of GCS is mature and fully operational. On the one hand telescope users as PI's implement the sequences of observing modes of future scientific instruments that will be installed in the telescope and operators, in turn, design their own sequences for maintenance. On the other hand engineers develop new components that provide new functionality required by the system. This great work effort is possible to minimize so that costs are reduced, especially if one considers that software maintenance is the most expensive phase of the software life cycle. Could we design a system that allows the progressive assimilation of sequences of operation and maintenance of the telescope, through an automatic self-programming system, so that it can evolve from one Component oriented organization to a Service oriented organization? One possible way to achieve this is to use mechanisms of learning and knowledge consolidation to reduce to the minimum expression the effort to transform the specifications of the different telescope users to the operational deployments. This article proposes a framework for solving this problem based on the combination of the following tools: data mining, self-Adaptive software, code generation, refactoring based on metrics, Hierarchical Agglomerative Clustering and Service Oriented Architectures.

PLUME-FEATHER, Referencing and Finding Software for Research and Education

NASA Astrophysics Data System (ADS)

Bénassy, O.; Caron, C.; Ferret-Canape, C.; Cheylus, A.; Courcelle, E.; Dantec, C.; Dayre, P.; Dostes, T.; Durand, A.; Facq, A.; Gambini, G.; Geahchan, E.; Helft, C.; Hoffmann, D.; Ingarao, M.; Joly, P.; Kieffer, J.; Larré, J.-M.; Libes, M.; Morris, F.; Parmentier, H.; Pérochon, L.; Porte, O.; Romier, G.; Rousse, D.; Tournoy, R.; Valeins, H.

2014-06-01

PLUME-FEATHER is a non-profit project created to Promote economicaL, Useful and Maintained softwarEFor theHigher Education And THE Research communities. The site references software, mainly Free/Libre Open Source Software (FLOSS) from French universities and national research organisations, (CNRS, INRA...), laboratories or departments as well as other FLOSS software used and evaluated by users within these institutions. Each software is represented by a reference card, which describes origin, aim, installation, cost (if applicable) and user experience from the point of view of an academic user for academic users. Presently over 1000 programs are referenced on PLUME by more than 900 contributors. Although the server is maintained by a French institution, it is open to international contributions in the academic domain. All contained and validated contents are visible to anonymous public, whereas (presently more than 2000) registered users can contribute, starting with comments on single software reference cards up to help with the organisation and presentation of the referenced software products. The project has been presented to the HEP community in 2012 for the first time [1]. This is an update of the status and a call for (further) contributions.

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.

JINR cloud infrastructure evolution

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

A Space and Atmospheric Visualization Science System

NASA Technical Reports Server (NTRS)

Szuszczewicz, E. P.; Blanchard, P.; Mankofsky, A.; Goodrich, C.; Kamins, D.; Kulkarni, R.; Mcnabb, D.; Moroh, M.

1994-01-01

SAVS (a Space and Atmospheric Visualization Science system) is an integrated system with user-friendly functionality that employs a 'push-button' software environment that mimics the logical scientific processes in data acquisition, reduction, analysis, and visualization. All of this is accomplished without requiring a detailed understanding of the methods, networks, and modules that link the tools and effectively execute the functions. This report describes SAVS and its components, followed by several applications based on generic research interests in interplanetary and magnetospheric physics (IMP/ISTP), active experiments in space (CRRES), and mission planning focused on the earth's thermospheric, ionospheric, and mesospheric domains (TIMED). The final chapters provide a user-oriented description of interface functionalities, hands-on operations, and customized modules, with details of the primary modules presented in the appendices. The overall intent of the report is to reflect the accomplishments of the three-year development effort and to introduce potential users to the power and utility of the integrated data acquisition, analysis, and visualization system.

Software-defined Quantum Networking Ecosystem

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

Humble, Travis S.; Sadlier, Ronald

The software enables a user to perform modeling and simulation of software-defined quantum networks. The software addresses the problem of how to synchronize transmission of quantum and classical signals through multi-node networks and to demonstrate quantum information protocols such as quantum teleportation. The software approaches this problem by generating a graphical model of the underlying network and attributing properties to each node and link in the graph. The graphical model is then simulated using a combination of discrete-event simulators to calculate the expected state of each node and link in the graph at a future time. A user interacts withmore » the software by providing an initial network model and instantiating methods for the nodes to transmit information with each other. This includes writing application scripts in python that make use of the software library interfaces. A user then initiates the application scripts, which invokes the software simulation. The user then uses the built-in diagnostic tools to query the state of the simulation and to collect statistics on synchronization.« less

SHARP pre-release v1.0 - Current Status and Documentation

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

Mahadevan, Vijay S.; Rahaman, Ronald O.

The NEAMS Reactor Product Line effort aims to develop an integrated multiphysics simulation capability for the design and analysis of future generations of nuclear power plants. The Reactor Product Line code suite’s multi-resolution hierarchy is being designed to ultimately span the full range of length and time scales present in relevant reactor design and safety analyses, as well as scale from desktop to petaflop computing platforms. In this report, building on a several previous report issued in September 2014, we describe our continued efforts to integrate thermal/hydraulics, neutronics, and structural mechanics modeling codes to perform coupled analysis of a representativemore » fast sodium-cooled reactor core in preparation for a unified release of the toolkit. The work reported in the current document covers the software engineering aspects of managing the entire stack of components in the SHARP toolkit and the continuous integration efforts ongoing to prepare a release candidate for interested reactor analysis users. Here we report on the continued integration effort of PROTEUS/Nek5000 and Diablo into the NEAMS framework and the software processes that enable users to utilize the capabilities without losing scientific productivity. Due to the complexity of the individual modules and their necessary/optional dependency library chain, we focus on the configuration and build aspects for the SHARP toolkit, which includes capability to autodownload dependencies and configure/install with optimal flags in an architecture-aware fashion. Such complexity is untenable without strong software engineering processes such as source management, source control, change reviews, unit tests, integration tests and continuous test suites. Details on these processes are provided in the report as a building step for a SHARP user guide that will accompany the first release, expected by Mar 2016.« less

Computational Simulations and the Scientific Method

NASA Technical Reports Server (NTRS)

Kleb, Bil; Wood, Bill

2005-01-01

As scientific simulation software becomes more complicated, the scientific-software implementor's need for component tests from new model developers becomes more crucial. The community's ability to follow the basic premise of the Scientific Method requires independently repeatable experiments, and model innovators are in the best position to create these test fixtures. Scientific software developers also need to quickly judge the value of the new model, i.e., its cost-to-benefit ratio in terms of gains provided by the new model and implementation risks such as cost, time, and quality. This paper asks two questions. The first is whether other scientific software developers would find published component tests useful, and the second is whether model innovators think publishing test fixtures is a feasible approach.

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.

Cloud Computing for the Grid: GridControl: A Software Platform to Support the Smart Grid

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

None

GENI Project: Cornell University is creating a new software platform for grid operators called GridControl that will utilize cloud computing to more efficiently control the grid. In a cloud computing system, there are minimal hardware and software demands on users. The user can tap into a network of computers that is housed elsewhere (the cloud) and the network runs computer applications for the user. The user only needs interface software to access all of the cloud’s data resources, which can be as simple as a web browser. Cloud computing can reduce costs, facilitate innovation through sharing, empower users, and improvemore » the overall reliability of a dispersed system. Cornell’s GridControl will focus on 4 elements: delivering the state of the grid to users quickly and reliably; building networked, scalable grid-control software; tailoring services to emerging smart grid uses; and simulating smart grid behavior under various conditions.« less

Advanced software development workstation project ACCESS user's guide

NASA Technical Reports Server (NTRS)

1990-01-01

ACCESS is a knowledge based software information system designed to assist the user in modifying retrieved software to satisfy user specifications. A user's guide is presented for the knowledge engineer who wishes to create for ACCESS a knowledge base consisting of representations of objects in some software system. This knowledge is accessible to an end user who wishes to use the catalogued software objects to create a new application program or an input stream for an existing system. The application specific portion of an ACCESS knowledge base consists of a taxonomy of object classes, as well as instances of these classes. All objects in the knowledge base are stored in an associative memory. ACCESS provides a standard interface for the end user to browse and modify objects. In addition, the interface can be customized by the addition of application specific data entry forms and by specification of display order for the taxonomy and object attributes. These customization options are described.

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.

MUST - An integrated system of support tools for research flight software engineering. [Multipurpose User-oriented Software Technology

NASA Technical Reports Server (NTRS)

Straeter, T. A.; Foudriat, E. C.; Will, R. W.

1977-01-01

The objectives of NASA's MUST (Multipurpose User-oriented Software Technology) program at Langley Research Center are to cut the cost of producing software which effectively utilizes digital systems for flight research. These objectives will be accomplished by providing an integrated system of support software tools for use throughout the research flight software development process. A description of the overall MUST program and its progress toward the release of a first MUST system will be presented. This release includes: a special interactive user interface, a library of subroutines, assemblers, a compiler, automatic documentation tools, and a test and simulation system.

A service-based framework for pharmacogenomics data integration

NASA Astrophysics Data System (ADS)

Wang, Kun; Bai, Xiaoying; Li, Jing; Ding, Cong

2010-08-01

Data are central to scientific research and practices. The advance of experiment methods and information retrieval technologies leads to explosive growth of scientific data and databases. However, due to the heterogeneous problems in data formats, structures and semantics, it is hard to integrate the diversified data that grow explosively and analyse them comprehensively. As more and more public databases are accessible through standard protocols like programmable interfaces and Web portals, Web-based data integration becomes a major trend to manage and synthesise data that are stored in distributed locations. Mashup, a Web 2.0 technique, presents a new way to compose content and software from multiple resources. The paper proposes a layered framework for integrating pharmacogenomics data in a service-oriented approach using the mashup technology. The framework separates the integration concerns from three perspectives including data, process and Web-based user interface. Each layer encapsulates the heterogeneous issues of one aspect. To facilitate the mapping and convergence of data, the ontology mechanism is introduced to provide consistent conceptual models across different databases and experiment platforms. To support user-interactive and iterative service orchestration, a context model is defined to capture information of users, tasks and services, which can be used for service selection and recommendation during a dynamic service composition process. A prototype system is implemented and cases studies are presented to illustrate the promising capabilities of the proposed approach.

Open source integrated modeling environment Delta Shell

NASA Astrophysics Data System (ADS)

Donchyts, G.; Baart, F.; Jagers, B.; van Putten, H.

2012-04-01

In the last decade, integrated modelling has become a very popular topic in environmental modelling since it helps solving problems, which is difficult to model using a single model. However, managing complexity of integrated models and minimizing time required for their setup remains a challenging task. The integrated modelling environment Delta Shell simplifies this task. The software components of Delta Shell are easy to reuse separately from each other as well as a part of integrated environment that can run in a command-line or a graphical user interface mode. The most components of the Delta Shell are developed using C# programming language and include libraries used to define, save and visualize various scientific data structures as well as coupled model configurations. Here we present two examples showing how Delta Shell simplifies process of setting up integrated models from the end user and developer perspectives. The first example shows coupling of a rainfall-runoff, a river flow and a run-time control models. The second example shows how coastal morphological database integrates with the coastal morphological model (XBeach) and a custom nourishment designer. Delta Shell is also available as open-source software released under LGPL license and accessible via http://oss.deltares.nl.

Code Parallelization with CAPO: A User Manual

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2001-01-01

A software tool has been developed to assist the parallelization of scientific codes. This tool, CAPO, extends an existing parallelization toolkit, CAPTools developed at the University of Greenwich, to generate OpenMP parallel codes for shared memory architectures. This is an interactive toolkit to transform a serial Fortran application code to an equivalent parallel version of the software - in a small fraction of the time normally required for a manual parallelization. We first discuss the way in which loop types are categorized and how efficient OpenMP directives can be defined and inserted into the existing code using the in-depth interprocedural analysis. The use of the toolkit on a number of application codes ranging from benchmark to real-world application codes is presented. This will demonstrate the great potential of using the toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of processors. The second part of the document gives references to the parameters and the graphic user interface implemented in the toolkit. Finally a set of tutorials is included for hands-on experiences with this toolkit.

The in-plant evaluation of a uranium NDA system

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

Sprinkle, J.K. Jr.; Baxman, H.R.; Langner, D.G.

1979-12-31

The Los Alamos Scientific Laboratory has an unirradiated enriched uranium reprocessing facility. Various types of solutions are generated in this facility, including distillates and raffinates containing ppm of uranium and concentrated solutions with up to 400 grams U/t. In addition to uranyl nitrate and HNO{sub 3}, the solutions may also contain zirconium, niobium, fluoride, and small amounts of many metals. A uranium solution assay system (USAS) has been installed to allow accurate and more timely process control, accountability, and criticality data to be obtained. The USAS assays are made by a variety of techniques that depend upon state-of-the-art high-resolution Ge(Li)more » gamma-ray spectroscopy integrated with an interactive, user-oriented computer software package. Tight control of the system`s performance is maintained by constantly monitoring the USAS status. Daily measurement control sequences are required, and the user is forced by the software to perform these sequences. Routine assays require 400 or 1000 seconds for a precision of 0.5% over the concentration range of 5--400 g/t. A comparison of the USAS precision and accuracy with that obtained by traditional destructive analytical chemistry techniques (colorimetric and volumetric) is presented.« less

The in-plant evaluation of a uranium NDA system

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

Sprinkle, J.K. Jr.; Baxman, H.R.; Langner, D.G.

1979-01-01

The Los Alamos Scientific Laboratory has an unirradiated enriched uranium reprocessing facility. Various types of solutions are generated in this facility, including distillates and raffinates containing ppm of uranium and concentrated solutions with up to 400 grams U/t. In addition to uranyl nitrate and HNO{sub 3}, the solutions may also contain zirconium, niobium, fluoride, and small amounts of many metals. A uranium solution assay system (USAS) has been installed to allow accurate and more timely process control, accountability, and criticality data to be obtained. The USAS assays are made by a variety of techniques that depend upon state-of-the-art high-resolution Ge(Li)more » gamma-ray spectroscopy integrated with an interactive, user-oriented computer software package. Tight control of the system's performance is maintained by constantly monitoring the USAS status. Daily measurement control sequences are required, and the user is forced by the software to perform these sequences. Routine assays require 400 or 1000 seconds for a precision of 0.5% over the concentration range of 5--400 g/t. A comparison of the USAS precision and accuracy with that obtained by traditional destructive analytical chemistry techniques (colorimetric and volumetric) is presented.« less

Data from selected U.S. Geological Survey National Stream Water Quality Monitoring Networks

USGS Publications Warehouse

Alexander, Richard B.; Slack, James R.; Ludtke, Amy S.; Fitzgerald, Kathleen K.; Schertz, Terry L.

1998-01-01

A nationally consistent and well-documented collection of water quality and quantity data compiled during the past 30 years for streams and rivers in the United States is now available on CD-ROM and accessible over the World Wide Web. The data include measurements from two U.S. Geological Survey (USGS) national networks for 122 physical, chemical, and biological properties of water collected at 680 monitoring stations from 1962 to 1995, quality assurance information that describes the sample collection agencies, laboratories, analytical methods, and estimates of laboratory measurement error (bias and variance), and information on selected cultural and natural characteristics of the station watersheds. The data are easily accessed via user-supplied software including Web browser, spreadsheet, and word processor, or may be queried and printed according to user-specified criteria using the supplied retrieval software on CD-ROM. The water quality data serve a variety of scientific uses including research and educational applications related to trend detection, flux estimation, investigations of the effects of the natural environment and cultural sources on water quality, and the development of statistical methods for designing efficient monitoring networks and interpreting water resources data.

GLOBE Program's Data and Information System

NASA Astrophysics Data System (ADS)

Memarsadeghi, N.; Overoye, D.; Lewis, C.; Butler, D. M.; Ramapriyan, H.

2016-12-01

"The Global Learning and Observations to Benefit the Environment (GLOBE) Program is an international science and education program that provides students and the public worldwide with the opportunity to participate in data collection and the scientific process, and contribute meaningfully to our understanding of the Earth system and global environment" (www.globe.gov ). GLOBE Program has a rich community of students, teachers, scientists, trainers, country coordinators, and alumni across the world, technologically spanning both high- and low-end users. There are 117 GLOBE participating countries from around the world. GLOBE's Science data protocols and educational material span atmosphere, biosphere, hydrosphere, soil (pedosphere), and Earth as a System scientific areas (http://www.globe.gov/do-globe/globe-teachers-guide). GLOBE's Data and Information System (DIS), when first introduced in 1995, was a cutting edge system that was well-received and innovative for its time. However, internet-based technologies have changed dramatically since then. Projects to modernize and evolve the GLOBE DIS started in 2010, resulting in today's GLOBE DIS. The current GLOBE DIS is now built upon the latest information technologies and is engaging and supporting the user community with advanced tools and services to further the goals of the GLOBE Program. GLOBE DIS consists of over 20 years of observation and training data, a rich set of software systems and applications for data entry, visualization, and analysis, as well as tools for training users in various science data protocols and enabling collaborations among members of the international user community. We present the existing GLOBE DIS, application technologies, and lessons learned for their operations, development, sustaining engineering, and data management practices. Examples of GLOBE DIS technologies include Liferay System for integrated user and content management, a Postgress/PostGIS database, Ruby on Rails for Data Entry systems, and OpenGeo for Visualization system.

Advancements in Large-Scale Data/Metadata Management for Scientific Data.

NASA Astrophysics Data System (ADS)

Guntupally, K.; Devarakonda, R.; Palanisamy, G.; Frame, M. T.

2017-12-01

Scientific data often comes with complex and diverse metadata which are critical for data discovery and users. The Online Metadata Editor (OME) tool, which was developed by an Oak Ridge National Laboratory team, effectively manages diverse scientific datasets across several federal data centers, such as DOE's Atmospheric Radiation Measurement (ARM) Data Center and USGS's Core Science Analytics, Synthesis, and Libraries (CSAS&L) project. This presentation will focus mainly on recent developments and future strategies for refining OME tool within these centers. The ARM OME is a standard based tool (https://www.archive.arm.gov/armome) that allows scientists to create and maintain metadata about their data products. The tool has been improved with new workflows that help metadata coordinators and submitting investigators to submit and review their data more efficiently. The ARM Data Center's newly upgraded Data Discovery Tool (http://www.archive.arm.gov/discovery) uses rich metadata generated by the OME to enable search and discovery of thousands of datasets, while also providing a citation generator and modern order-delivery techniques like Globus (using GridFTP), Dropbox and THREDDS. The Data Discovery Tool also supports incremental indexing, which allows users to find new data as and when they are added. The USGS CSAS&L search catalog employs a custom version of the OME (https://www1.usgs.gov/csas/ome), which has been upgraded with high-level Federal Geographic Data Committee (FGDC) validations and the ability to reserve and mint Digital Object Identifiers (DOIs). The USGS's Science Data Catalog (SDC) (https://data.usgs.gov/datacatalog) allows users to discover a myriad of science data holdings through a web portal. Recent major upgrades to the SDC and ARM Data Discovery Tool include improved harvesting performance and migration using new search software, such as Apache Solr 6.0 for serving up data/metadata to scientific communities. Our presentation will highlight the future enhancements of these tools which enable users to retrieve fast search results, along with parallelizing the retrieval process from online and High Performance Storage Systems. In addition, these improvements to the tools will support additional metadata formats like the Large-Eddy Simulation (LES) ARM Symbiotic and Observation (LASSO) bundle data.

What Comes First, the OWL or the Bean? Creating Reusable Scientific Software with OWL/RDF Vocabularies.

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

Stephan, Eric G.; Elsethagen, Todd O.; Kleese van Dam, Kerstin

In the spring of 2013 the U.S. White House by executive order mandated: “Government information shall be managed as an asset throughout its life cycle to promote interoperability and openness, and, wherever possible and legally permissible, to ensure that data are released to the public in ways that make the data easy to find, accessible, and usable.” Key for the reusability of any scientific data is hereby the availability of metadata describing the published data in a vocabulary that is familiar to its potential users. The objective of this paper is to help scientific application developers who want to adoptmore » the continuous stream of new community vocabularies to help make their data sharable, self-describable, and easily understood. To achieve this we suggest semantic vocabulary and application integration best practices and discuss the tradeoffs of encoding vocabularies through code versus deriving code from vocabularies.« less

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.

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.

PubMed

Fähnrich, Anke; Krebbel, Moritz; Decker, Normann; Leucker, Martin; Lange, Felix D; Kalies, Kathrin; Möller, Steffen

2017-03-11

Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background. To facilitate the analysis of T and B cell repertoires by less experienced users, software is needed that combines the most common tools for repertoire analysis. We introduce a graphical user interface (GUI) providing a complete analysis pipeline for processing raw NGS data for human and animal TCR and BCR clonotype determination and advanced differential repertoire studies. It provides two applications. ClonoCalc prepares the raw data for downstream analyses. It combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal TCR/BCR sequences. ClonoPlot wraps the R package tcR and further contributes self-developed plots for the descriptive comparative investigation of immune repertoires. This workflow reduces the amount of programming required to perform the respective analyses and supports both communication and training between scientists and technicians, and across scientific disciplines. The Open Source development in Java and R is modular and invites advanced users to extend its functionality. Software and documentation are freely available at https://bitbucket.org/ClonoSuite/clonocalc-plot .

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

Navarro, Carmen; Martínez, Victor; Blanco, Armando; Cano, Carlos

2017-12-01

Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest or they lack the flexibility to analyze user-defined data. We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk with Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform cross-validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long noncoding RNAs (lncRNAs) to disease prioritization. ProphTools is robust prioritization software that provides the flexibility not present in other state-of-the-art network analysis approaches, enabling researchers to perform prioritization tasks on any user-defined heterogeneous network. Furthermore, the application to lncRNA-disease prioritization shows that ProphTools can reach the performance levels of ad hoc prioritization tools without losing its generality. © The Authors 2017. Published by Oxford University Press.

An interactive, multi-touch videowall for scientific data exploration

NASA Astrophysics Data System (ADS)

Blower, Jon; Griffiths, Guy; van Meersbergen, Maarten; Lusher, Scott; Styles, Jon

2014-05-01

The use of videowalls for scientific data exploration is rising as hardware becomes cheaper and the availability of software and multimedia content grows. Most videowalls are used primarily for outreach and communication purposes, but there is increasing interest in using large display screens to support exploratory visualization as an integral part of scientific research. In this PICO presentation we will present a brief overview of a new videowall system at the University of Reading, which is designed specifically to support interactive, exploratory visualization activities in climate science and Earth Observation. The videowall consists of eight 42-inch full-HD screens (in 4x2 formation), giving a total resolution of about 16 megapixels. The display is managed by a videowall controller, which can direct video to the screen from up to four external laptops, a purpose-built graphics workstation, or any combination thereof. A multi-touch overlay provides the capability for the user to interact directly with the data. There are many ways to use the videowall, and a key technical challenge is to make the most of the touch capabilities - touch has the potential to greatly reduce the learning curve in interactive data exploration, but most software is not yet designed for this purpose. In the PICO we will present an overview of some ways in which the wall can be employed in science, seeking feedback and discussion from the community. The system was inspired by an existing and highly-successful system (known as the "Collaboratorium") at the Netherlands e-Science Center (NLeSC). We will demonstrate how we have adapted NLeSC's visualization software to our system for touch-enabled multi-screen climate data exploration.

Globus: Service and Platform for Research Data Lifecycle Management

NASA Astrophysics Data System (ADS)

Ananthakrishnan, R.; Foster, I.

2017-12-01

Globus offers a range of data management capabilities to the community as hosted services, encompassing data transfer and sharing, user identity and authorization, and data publication. Globus capabilities are accessible via both a web browser and REST APIs. Web access allows researchers to use Globus capabilities through a software-as-a-service model; and the REST APIs address the needs of developers of research services, who can now use Globus as a platform, outsourcing complex user and data management tasks to Globus services. In this presentation, we review Globus capabilities and outline how it is being applied as a platform for scientific services, and highlight work done to link computational analysis flows to the underlying data through an interactive Jupyter notebook environment to promote immediate data usability, reusability of these flows by other researchers, and future analysis extensibility.

New developments in the McStas neutron instrument simulation package

NASA Astrophysics Data System (ADS)

Willendrup, P. K.; Knudsen, E. B.; Klinkby, E.; Nielsen, T.; Farhi, E.; Filges, U.; Lefmann, K.

2014-07-01

The McStas neutron ray-tracing software package is a versatile tool for building accurate simulators of neutron scattering instruments at reactors, short- and long-pulsed spallation sources such as the European Spallation Source. McStas is extensively used for design and optimization of instruments, virtual experiments, data analysis and user training. McStas was founded as a scientific, open-source collaborative code in 1997. This contribution presents the project at its current state and gives an overview of the main new developments in McStas 2.0 (December 2012) and McStas 2.1 (expected fall 2013), including many new components, component parameter uniformisation, partial loss of backward compatibility, updated source brilliance descriptions, developments toward new tools and user interfaces, web interfaces and a new method for estimating beam losses and background from neutron optics.

Requirements UML Tool (RUT) Expanded for Extreme Programming (CI02)

NASA Technical Reports Server (NTRS)

McCoy, James R.

2003-01-01

A procedure for capturing and managing system requirements that incorporates XP user stories. Because costs associated with identifying problems in requirements increase dramatically over the lifecycle of a project, a method for identifying sources of software risks in user stories is urgently needed. This initiative aims to determine a set of guide-lines for user stories that will result in high-quality requirement. To further this initiative, a tool is needed to analyze user stories that can assess the quality of individual user stories, detect sources cf software risk's, produce software metrics, and identify areas in user stories that can be improved.

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

Real-Time Multimission Event Notification System for Mars Relay

NASA Technical Reports Server (NTRS)

Wallick, Michael N.; Allard, Daniel A.; Gladden, Roy E.; Wang, Paul; Hy, Franklin H.

2013-01-01

As the Mars Relay Network is in constant flux (missions and teams going through their daily workflow), it is imperative that users are aware of such state changes. For example, a change by an orbiter team can affect operations on a lander team. This software provides an ambient view of the real-time status of the Mars network. The Mars Relay Operations Service (MaROS) comprises a number of tools to coordinate, plan, and visualize various aspects of the Mars Relay Network. As part of MaROS, a feature set was developed that operates on several levels of the software architecture. These levels include a Web-based user interface, a back-end "ReSTlet" built in Java, and databases that store the data as it is received from the network. The result is a real-time event notification and management system, so mission teams can track and act upon events on a moment-by-moment basis. This software retrieves events from MaROS and displays them to the end user. Updates happen in real time, i.e., messages are pushed to the user while logged into the system, and queued when the user is not online for later viewing. The software does not do away with the email notifications, but augments them with in-line notifications. Further, this software expands the events that can generate a notification, and allows user-generated notifications. Existing software sends a smaller subset of mission-generated notifications via email. A common complaint of users was that the system-generated e-mails often "get lost" with other e-mail that comes in. This software allows for an expanded set (including user-generated) of notifications displayed in-line of the program. By separating notifications, this can improve a user's workflow.

The new Planetary Science Archive: A tool for exploration and discovery of scientific datasets from ESA's planetary missions

NASA Astrophysics Data System (ADS)

Heather, David

2016-07-01

Introduction: The Planetary Science Archive (PSA) is the European Space Agency's (ESA) repository of science data from all planetary science and exploration missions. The PSA provides access to scientific datasets through various interfaces (e.g. FTP browser, Map based, Advanced search, and Machine interface): http://archives.esac.esa.int/psa All datasets are scientifically peer-reviewed by independent scientists, and are compliant with the Planetary Data System (PDS) standards. Updating the PSA: The PSA is currently implementing a number of significant changes, both to its web-based interface to the scientific community, and to its database structure. The new PSA will be up-to-date with versions 3 and 4 of the PDS standards, as PDS4 will be used for ESA's upcoming ExoMars and BepiColombo missions. The newly designed PSA homepage will provide direct access to scientific datasets via a text search for targets or missions. This will significantly reduce the complexity for users to find their data and will promote one-click access to the datasets. Additionally, the homepage will provide direct access to advanced views and searches of the datasets. Users will have direct access to documentation, information and tools that are relevant to the scientific use of the dataset, including ancillary datasets, Software Interface Specification (SIS) documents, and any tools/help that the PSA team can provide. A login mechanism will provide additional functionalities to the users to aid / ease their searches (e.g. saving queries, managing default views). Queries to the PSA database will be possible either via the homepage (for simple searches of missions or targets), or through a filter menu for more tailored queries. The filter menu will offer multiple options to search for a particular dataset or product, and will manage queries for both in-situ and remote sensing instruments. Parameters such as start-time, phase angle, and heliocentric distance will be emphasized. A further advanced search function will allow users to query all the metadata present in the PSA database. Results will be displayed in 3 different ways: 1) A table listing all the corresponding data matching the criteria in the filter menu, 2) a projection of the products onto the surface of the object when applicable (i.e. planets, small bodies), and 3) a list of images for the relevant instruments to enjoy the beauty of our Solar System. These different ways of viewing the datasets will ensure that scientists and non-professionals alike will have access to the specific data they are looking for, regardless of their background. Conclusions: The new PSA will maintain the various interfaces and services it had in the past, and will include significant improvements designed to allow easier and more effective access to the scientific data and supporting materials. The new PSA is expected to be released by mid-2016. It will support the past, present and future missions, ancillary datasets, and will enhance the scientific output of ESA's missions. As such, the PSA will become a unique archive ensuring the long-term preservation and usage of scientific datasets together with user-friendly access.

The new Planetary Science Archive: A tool for exploration and discovery of scientific datasets from ESA's planetary missions.

NASA Astrophysics Data System (ADS)

Heather, David; Besse, Sebastien; Barbarisi, Isa; Arviset, Christophe; de Marchi, Guido; Barthelemy, Maud; Docasal, Ruben; Fraga, Diego; Grotheer, Emmanuel; Lim, Tanya; Macfarlane, Alan; Martinez, Santa; Rios, Carlos

2016-04-01

Introduction: The Planetary Science Archive (PSA) is the European Space Agency's (ESA) repository of science data from all planetary science and exploration missions. The PSA provides access to scientific datasets through various interfaces (e.g. FTP browser, Map based, Advanced search, and Machine interface): http://archives.esac.esa.int/psa All datasets are scientifically peer-reviewed by independent scientists, and are compliant with the Planetary Data System (PDS) standards. Updating the PSA: The PSA is currently implementing a number of significant changes, both to its web-based interface to the scientific community, and to its database structure. The new PSA will be up-to-date with versions 3 and 4 of the PDS standards, as PDS4 will be used for ESA's upcoming ExoMars and BepiColombo missions. The newly designed PSA homepage will provide direct access to scientific datasets via a text search for targets or missions. This will significantly reduce the complexity for users to find their data and will promote one-click access to the datasets. Additionally, the homepage will provide direct access to advanced views and searches of the datasets. Users will have direct access to documentation, information and tools that are relevant to the scientific use of the dataset, including ancillary datasets, Software Interface Specification (SIS) documents, and any tools/help that the PSA team can provide. A login mechanism will provide additional functionalities to the users to aid / ease their searches (e.g. saving queries, managing default views). Queries to the PSA database will be possible either via the homepage (for simple searches of missions or targets), or through a filter menu for more tailored queries. The filter menu will offer multiple options to search for a particular dataset or product, and will manage queries for both in-situ and remote sensing instruments. Parameters such as start-time, phase angle, and heliocentric distance will be emphasized. A further advanced search function will allow users to query all the metadata present in the PSA database. Results will be displayed in 3 different ways: 1) A table listing all the corresponding data matching the criteria in the filter menu, 2) a projection of the products onto the surface of the object when applicable (i.e. planets, small bodies), and 3) a list of images for the relevant instruments to enjoy the beauty of our Solar System. These different ways of viewing the datasets will ensure that scientists and non-professionals alike will have access to the specific data they are looking for, regardless of their background. Conclusions: The new PSA will maintain the various interfaces and services it had in the past, and will include significant improvements designed to allow easier and more effective access to the scientific data and supporting materials. The new PSA is expected to be released by mid-2016. It will support the past, present and future missions, ancillary datasets, and will enhance the scientific output of ESA's missions. As such, the PSA will become a unique archive ensuring the long-term preservation and usage of scientific datasets together with user-friendly access.

A Cloud-Based Infrastructure for Near-Real-Time Processing and Dissemination of NPP Data

NASA Astrophysics Data System (ADS)

Evans, J. D.; Valente, E. G.; Chettri, S. S.

2011-12-01

We are building a scalable cloud-based infrastructure for generating and disseminating near-real-time data products from a variety of geospatial and meteorological data sources, including the new National Polar-Orbiting Environmental Satellite System (NPOESS) Preparatory Project (NPP). Our approach relies on linking Direct Broadcast and other data streams to a suite of scientific algorithms coordinated by NASA's International Polar-Orbiter Processing Package (IPOPP). The resulting data products are directly accessible to a wide variety of end-user applications, via industry-standard protocols such as OGC Web Services, Unidata Local Data Manager, or OPeNDAP, using open source software components. The processing chain employs on-demand computing resources from Amazon.com's Elastic Compute Cloud and NASA's Nebula cloud services. Our current prototype targets short-term weather forecasting, in collaboration with NASA's Short-term Prediction Research and Transition (SPoRT) program and the National Weather Service. Direct Broadcast is especially crucial for NPP, whose current ground segment is unlikely to deliver data quickly enough for short-term weather forecasters and other near-real-time users. Direct Broadcast also allows full local control over data handling, from the receiving antenna to end-user applications: this provides opportunities to streamline processes for data ingest, processing, and dissemination, and thus to make interpreted data products (Environmental Data Records) available to practitioners within minutes of data capture at the sensor. Cloud computing lets us grow and shrink computing resources to meet large and rapid fluctuations in data availability (twice daily for polar orbiters) - and similarly large fluctuations in demand from our target (near-real-time) users. This offers a compelling business case for cloud computing: the processing or dissemination systems can grow arbitrarily large to sustain near-real time data access despite surges in data volumes or user demand, but that computing capacity (and hourly costs) can be dropped almost instantly once the surge passes. Cloud computing also allows low-risk experimentation with a variety of machine architectures (processor types; bandwidth, memory, and storage capacities, etc.) and of system configurations (including massively parallel computing patterns). Finally, our service-based approach (in which user applications invoke software processes on a Web-accessible server) facilitates access into datasets of arbitrary size and resolution, and allows users to request and receive tailored products on demand. To maximize the usefulness and impact of our technology, we have emphasized open, industry-standard software interfaces. We are also using and developing open source software to facilitate the widespread adoption of similar, derived, or interoperable systems for processing and serving near-real-time data from NPP and other sources.

User systems guidelines for software projects

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

Abrahamson, L.

1986-04-01

This manual presents guidelines for software standards which were developed so that software project-development teams and management involved in approving the software could have a generalized view of all phases in the software production procedure and the steps involved in completing each phase. Guidelines are presented for six phases of software development: project definition, building a user interface, designing software, writing code, testing code, and preparing software documentation. The discussions for each phase include examples illustrating the recommended guidelines. 45 refs. (DWL)

The 1 MV multi-element AMS system for biomedical applications at the Netherlands Organization for Applied Scientific Research (TNO)

NASA Astrophysics Data System (ADS)

Klein, Matthias; Vaes, W. H. J.; Fabriek, B.; Sandman, H.; Mous, D. J. W.; Gottdang, A.

2013-01-01

The Netherlands Organization for Applied Scientific Research (TNO) has installed a compact 1 MV multi-element AMS system manufactured by High Voltage Engineering Europa B.V., The Netherlands. TNO performs clinical research programs for pharmaceutical and innovative foods industry to obtain early pharmacokinetic data and to provide anti-osteoporotic efficacy data of new treatments. The AMS system will analyze carbon, iodine and calcium samples for this purpose. The first measurements on blank samples indicate background levels in the low 10-12 for calcium and iodine, making the system well suited for these biomedical applications. Carbon blanks have been measured at low 10-16. For unattended, around-the-clock analysis, the system features the 200 sample version of the SO110 hybrid ion source and user friendly control software.

DESI-Detection of early-season invasives (software-installation manual and user's guide version 1.0)

USGS Publications Warehouse

Kokaly, Raymond F.

2011-01-01

This report describes a software system for detecting early-season invasive plant species, such as cheatgrass. The report includes instructions for installing the software and serves as a user's guide in processing Landsat satellite remote sensing data to map the distributions of cheatgrass and other early-season invasive plants. The software was developed for application to the semi-arid regions of southern Utah; however, the detection parameters can be altered by the user for application to other areas.

Working Notes from the 1992 AAAI Workshop on Automating Software Design. Theme: Domain Specific Software Design

NASA Technical Reports Server (NTRS)

Keller, Richard M. (Editor); Barstow, David; Lowry, Michael R.; Tong, Christopher H.

1992-01-01

The goal of this workshop is to identify different architectural approaches to building domain-specific software design systems and to explore issues unique to domain-specific (vs. general-purpose) software design. Some general issues that cut across the particular software design domain include: (1) knowledge representation, acquisition, and maintenance; (2) specialized software design techniques; and (3) user interaction and user interface.

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.

SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

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

Jiang, S; Dolly, S; Cai, B

Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deepmore » modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.« less

SBOL Visual: A Graphical Language for Genetic Designs.

PubMed

Quinn, Jacqueline Y; Cox, Robert Sidney; Adler, Aaron; Beal, Jacob; Bhatia, Swapnil; Cai, Yizhi; Chen, Joanna; Clancy, Kevin; Galdzicki, Michal; Hillson, Nathan J; Le Novère, Nicolas; Maheshwari, Akshay J; McLaughlin, James Alastair; Myers, Chris J; P, Umesh; Pocock, Matthew; Rodriguez, Cesar; Soldatova, Larisa; Stan, Guy-Bart V; Swainston, Neil; Wipat, Anil; Sauro, Herbert M

2015-12-01

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.

BATSE Solar Flare Spectroscopy

NASA Technical Reports Server (NTRS)

Schwartz, R. A.

1998-01-01

This final report describes the progress originally proposed: (1) the continued improvement of a software and database environment capable of supporting all users of BATSE solar data as well as providing scientific expertise and effort to the BATSE solar community; (2) the continued participation with the PI team and other guest investigators in the detailed analysis of the BATSE detectors' response at low energies; (3) using spectroscopic techniques to fully exploit the potential of electron time-of-flight studies; and, (4) a full search for flare gamma-ray line emission at 2.2 MeV from all GOES X-class flares observed with BATSE.

The use of Graphic User Interface for development of a user-friendly CRS-Stack software

NASA Astrophysics Data System (ADS)

Sule, Rachmat; Prayudhatama, Dythia; Perkasa, Muhammad D.; Hendriyana, Andri; Fatkhan; Sardjito; Adriansyah

2017-04-01

The development of a user-friendly Common Reflection Surface (CRS) Stack software that has been built by implementing Graphical User Interface (GUI) is described in this paper. The original CRS-Stack software developed by WIT Consortium is compiled in the unix/linux environment, which is not a user-friendly software, so that a user must write the commands and parameters manually in a script file. Due to this limitation, the CRS-Stack become a non popular method, although applying this method is actually a promising way in order to obtain better seismic sections, which have better reflector continuity and S/N ratio. After obtaining successful results that have been tested by using several seismic data belong to oil companies in Indonesia, it comes to an idea to develop a user-friendly software in our own laboratory. Graphical User Interface (GUI) is a type of user interface that allows people to interact with computer programs in a better way. Rather than typing commands and module parameters, GUI allows the users to use computer programs in much simple and easy. Thus, GUI can transform the text-based interface into graphical icons and visual indicators. The use of complicated seismic unix shell script can be avoided. The Java Swing GUI library is used to develop this CRS-Stack GUI. Every shell script that represents each seismic process is invoked from Java environment. Besides developing interactive GUI to perform CRS-Stack processing, this CRS-Stack GUI is design to help geophysicists to manage a project with complex seismic processing procedures. The CRS-Stack GUI software is composed by input directory, operators, and output directory, which are defined as a seismic data processing workflow. The CRS-Stack processing workflow involves four steps; i.e. automatic CMP stack, initial CRS-Stack, optimized CRS-Stack, and CRS-Stack Supergather. Those operations are visualized in an informative flowchart with self explanatory system to guide the user inputting the parameter values for each operation. The knowledge of CRS-Stack processing procedure is still preserved in the software, which is easy and efficient to be learned. The software will still be developed in the future. Any new innovative seismic processing workflow will also be added into this GUI software.

Ionosphere Waves Service - A demonstration

NASA Astrophysics Data System (ADS)

Crespon, François

2013-04-01

In the frame of the FP7 POPDAT project the Ionosphere Waves Service was developed by ionosphere experts to answer several questions: How make the old ionosphere missions more valuable? How provide scientific community with a new insight on wave processes that take place in the ionosphere? The answer is a unique data mining service accessing a collection of topical catalogues that characterize a huge number of Atmospheric Gravity Waves, Travelling Ionosphere Disturbances and Whistlers events. The Ionosphere Waves Service regroups databases of specific events extracted by experts from a ten of ionosphere missions which end users can access by applying specific searches and by using statistical analysis modules for their domain of interest. The scientific applications covered by the IWS are relative to earthquake precursors, ionosphere climatology, geomagnetic storms, troposphere-ionosphere energy transfer, and trans-ionosphere link perturbations. In this presentation we propose to detail the service design, the hardware and software architecture, and the service functions. The service interface and capabilities will be the focus of a demonstration in order to help potential end-users for their first access to the Ionosphere Waves Service portal. This work is made with the support of FP7 grant # 263240.

Open semantic annotation of scientific publications using DOMEO.

PubMed

Ciccarese, Paolo; Ocana, Marco; Clark, Tim

2012-04-24

Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies.Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF's next full release.Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.

Open semantic annotation of scientific publications using DOMEO

PubMed Central

2012-01-01

Background Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Methods The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies. Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. Results We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF’s next full release. Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework. PMID:22541592

A Unified Framework for Periodic, On-Demand, and User-Specified Software Information

NASA Technical Reports Server (NTRS)

Kolano, Paul Z.

2004-01-01

Although grid computing can increase the number of resources available to a user; not all resources on the grid may have a software environment suitable for running a given application. To provide users with the necessary assistance for selecting resources with compatible software environments and/or for automatically establishing such environments, it is necessary to have an accurate source of information about the software installed across the grid. This paper presents a new OGSI-compliant software information service that has been implemented as part of NASA's Information Power Grid project. This service is built on top of a general framework for reconciling information from periodic, on-demand, and user-specified sources. Information is retrieved using standard XPath queries over a single unified namespace independent of the information's source. Two consumers of the provided software information, the IPG Resource Broker and the IPG Neutralization Service, are briefly described.

Adaptable Computing Environment/Self-Assembling Software

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

Osbourn, Gordon C.; Bouchard, Ann M.; Bartholomew, John W.

Complex software applications are difficult to learn to use and to remember how to use. Further, the user has no control over the functionality available in a given application. The software we use can be created and modified only by a relatively small group of elite, highly skilled artisans known as programmers. "Normal users" are powerless to create and modify software themselves, because the tools for software development, designed by and for programmers, are a barrier to entry. This software, when completed, will be a user-adaptable computing environment in which the user is really in control of his/her own software,more » able to adapt the system, make new parts of the system interactive, and even modify the behavior of the system itself. Som key features of the basic environment that have been implemented are (a) books in bookcases, where all data is stored, (b) context-sensitive compass menus (compass, because the buttons are located in compass directions relative to the mouose cursor position), (c) importing tabular data and displaying it in a book, (d) light-weight table querying/sorting, (e) a Reach&Get capability (sort of a "smart" copy/paste that prevents the user from copying invalid data), and (f) a LogBook that automatically logs all user actions that change data or the system itself. To bootstrap toward full end-user adaptability, we implemented a set of development tools. With the development tools, compass menus can be made and customized.« less

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.

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

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

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

DOE PAGES

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina; ...

2017-03-01

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

Software-Reconfigurable Processors for Spacecraft

NASA Technical Reports Server (NTRS)

Farrington, Allen; Gray, Andrew; Bell, Bryan; Stanton, Valerie; Chong, Yong; Peters, Kenneth; Lee, Clement; Srinivasan, Jeffrey

2005-01-01

A report presents an overview of an architecture for a software-reconfigurable network data processor for a spacecraft engaged in scientific exploration. When executed on suitable electronic hardware, the software performs the functions of a physical layer (in effect, acts as a software radio in that it performs modulation, demodulation, pulse-shaping, error correction, coding, and decoding), a data-link layer, a network layer, a transport layer, and application-layer processing of scientific data. The software-reconfigurable network processor is undergoing development to enable rapid prototyping and rapid implementation of communication, navigation, and scientific signal-processing functions; to provide a long-lived communication infrastructure; and to provide greatly improved scientific-instrumentation and scientific-data-processing functions by enabling science-driven in-flight reconfiguration of computing resources devoted to these functions. This development is an extension of terrestrial radio and network developments (e.g., in the cellular-telephone industry) implemented in software running on such hardware as field-programmable gate arrays, digital signal processors, traditional digital circuits, and mixed-signal application-specific integrated circuits (ASICs).

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization.

PubMed

Jung, Sang-Kyu; McDonald, Karen

2011-08-16

Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

PubMed Central

2011-01-01

Background Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. Results The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Conclusion Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net. PMID:21846353

Designing for User Cognition and Affect in Software Instructions

ERIC Educational Resources Information Center

van der Meij, Hans

2008-01-01

In this paper we examine how to design software instructions for user cognition and affect. A basic and co-user manual are compared. The first provides fundamental support for both; the latter includes a buddy to further optimize support for user affect. The basic manual was faster and judged as easier to process than the co-user manual. In…

NEDLite user's manual: forest inventory for Palm OS handheld computers

Treesearch

Peter D. Knopp; Mark J. Twery

2006-01-01

A user's manual for NEDLite, software that enables collection of forest inventory data on Palm OS handheld computers, with the option of transferring data into NED software for analysis and subsequent prescription development. NEDLite software is included. Download the NEDLite software at: http://www.fs.fed.us/ne/burlington/ned

DATALINK: Records inventory data collection software. User`s guide

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

Cole, B.A.

1995-03-01

DATALINK was created to provide an easy to use data collection program for records management software products. It provides several useful tools for capturing and validating record index data in the field. It also allows users to easily create a comma delimited, ASCII text file for data export into most records management software products. It runs on virtually any computer us MS-DOS.

User Driven Image Stacking for ODI Data and Beyond via a Highly Customizable Web Interface

NASA Astrophysics Data System (ADS)

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

2015-09-01

While some astronomical archives have begun serving standard calibrated data products, the process of producing stacked images remains a challenge left to the end-user. The benefits of astronomical image stacking are well established, and dither patterns are recommended for almost all observing targets. Some archives automatically produce stacks of limited scientific usefulness without any fine-grained user or operator configurability. In this paper, we present PPA Stack, a web based stacking framework within the ODI - Portal, Pipeline, and Archive system. PPA Stack offers a web user interface with built-in heuristics (based on pointing, filter, and other metadata information) to pre-sort images into a set of likely stacks while still allowing the user or operator complete control over the images and parameters for each of the stacks they wish to produce. The user interface, designed using AngularJS, provides multiple views of the input dataset and parameters, all of which are synchronized in real time. A backend consisting of a Python application optimized for ODI data, wrapped around the SWarp software, handles the execution of stacking workflow jobs on Indiana University's Big Red II supercomputer, and the subsequent ingestion of the combined images back into the PPA archive. PPA Stack is designed to enable seamless integration of other stacking applications in the future, so users can select the most appropriate option for their science.

Users Do the Darndest Things: True Stories from the CyLab Usable Privacy and Security Laboratory

NASA Astrophysics Data System (ADS)

Cranor, Lorrie Faith

How can we make security and privacy software more usable? The first step is to study our users. Ideally, we would watch them interacting with security or privacy software in situations where they face actual risk. But everyday computer users don't sit around fiddling with security software, and subjecting users to actual security attacks raises ethical and legal concerns. Thus, it can be difficult to observe users interacting with security and privacy software in their natural habitat. At the CyLab Usable Privacy and Security Laboratory, we've conducted a wide variety of studies aimed at understanding how users think about security and privacy and how they interact with security and privacy software. In this talk I'll give a behind the scenes tour of some of the techniques we've used to study users both in the laboratory and in the wild. I'll discuss the trials and tribulations of designing and carrying out security and privacy user studies, and highlight some of our surprising observations. Find out what privacy-sensitive items you can actually get study participants to purchase, how you can observe users' responses to a man-in-the-middle attack without actually conducting such an attack, why it's hard to get people to use high tech cell phones even when you give them away, and what's actually in that box behind the couch in my office.

Implications of the Social Web Environment for User Story Education

ERIC Educational Resources Information Center

Fancott, Terrill; Kamthan, Pankaj; Shahmir, Nazlie

2012-01-01

In recent years, user stories have emerged in academia, as well as industry, as a notable approach for expressing user requirements of interactive software systems that are developed using agile methodologies. There are social aspects inherent to software development, in general, and user stories, in particular. This paper presents directions and…

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research

PubMed Central

Campagnola, Luke; Kratz, Megan B.; Manis, Paul B.

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org. PMID:24523692

cit: hypothesis testing software for mediation analysis in genomic applications.

PubMed

Millstein, Joshua; Chen, Gary K; Breton, Carrie V

2016-08-01

The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated by the software and (iii) low power of common multiple testing approaches. The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation. Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies. The cit open-source R package is freely available from the CRAN website (https://cran.r-project.org/web/packages/cit/index.html) with embedded C ++ code that utilizes the GNU Scientific Library, also freely available (http://www.gnu.org/software/gsl/). joshua.millstein@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

ConcreteWorks v3 training/user manual (P1) : ConcreteWorks software (P2).

DOT National Transportation Integrated Search

2017-04-01

ConcreteWorks is designed to be a user-friendly software package that can help concrete : professionals optimize concrete mixture proportioning, perform a concrete thermal analysis, and : increase the chloride diffusion service life. The software pac...

Design Optimization Toolkit: Users' Manual

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

Aguilo Valentin, Miguel Alejandro

The Design Optimization Toolkit (DOTk) is a stand-alone C++ software package intended to solve complex design optimization problems. DOTk software package provides a range of solution methods that are suited for gradient/nongradient-based optimization, large scale constrained optimization, and topology optimization. DOTk was design to have a flexible user interface to allow easy access to DOTk solution methods from external engineering software packages. This inherent flexibility makes DOTk barely intrusive to other engineering software packages. As part of this inherent flexibility, DOTk software package provides an easy-to-use MATLAB interface that enables users to call DOTk solution methods directly from the MATLABmore » command window.« less

SoftLab: A Soft-Computing Software for Experimental Research with Commercialization Aspects

NASA Technical Reports Server (NTRS)

Akbarzadeh-T, M.-R.; Shaikh, T. S.; Ren, J.; Hubbell, Rob; Kumbla, K. K.; Jamshidi, M

1998-01-01

SoftLab is a software environment for research and development in intelligent modeling/control using soft-computing paradigms such as fuzzy logic, neural networks, genetic algorithms, and genetic programs. SoftLab addresses the inadequacies of the existing soft-computing software by supporting comprehensive multidisciplinary functionalities from management tools to engineering systems. Furthermore, the built-in features help the user process/analyze information more efficiently by a friendly yet powerful interface, and will allow the user to specify user-specific processing modules, hence adding to the standard configuration of the software environment.

General-Purpose Electronic System Tests Aircraft

NASA Technical Reports Server (NTRS)

Glover, Richard D.

1989-01-01

Versatile digital equipment supports research, development, and maintenance. Extended aircraft interrogation and display system is general-purpose assembly of digital electronic equipment on ground for testing of digital electronic systems on advanced aircraft. Many advanced features, including multiple 16-bit microprocessors, pipeline data-flow architecture, advanced operating system, and resident software-development tools. Basic collection of software includes program for handling many types of data and for displays in various formats. User easily extends basic software library. Hardware and software interfaces to subsystems provided by user designed for flexibility in configuration to meet user's requirements.

Cloud Computing with iPlant Atmosphere.

PubMed

McKay, Sheldon J; Skidmore, Edwin J; LaRose, Christopher J; Mercer, Andre W; Noutsos, Christos

2013-10-15

Cloud Computing refers to distributed computing platforms that use virtualization software to provide easy access to physical computing infrastructure and data storage, typically administered through a Web interface. Cloud-based computing provides access to powerful servers, with specific software and virtual hardware configurations, while eliminating the initial capital cost of expensive computers and reducing the ongoing operating costs of system administration, maintenance contracts, power consumption, and cooling. This eliminates a significant barrier to entry into bioinformatics and high-performance computing for many researchers. This is especially true of free or modestly priced cloud computing services. The iPlant Collaborative offers a free cloud computing service, Atmosphere, which allows users to easily create and use instances on virtual servers preconfigured for their analytical needs. Atmosphere is a self-service, on-demand platform for scientific computing. This unit demonstrates how to set up, access and use cloud computing in Atmosphere. Copyright © 2013 John Wiley & Sons, Inc.

ePMV embeds molecular modeling into professional animation software environments.

PubMed

Johnson, Graham T; Autin, Ludovic; Goodsell, David S; Sanner, Michel F; Olson, Arthur J

2011-03-09

Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties, and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

ePMV Embeds Molecular Modeling into Professional Animation Software Environments

PubMed Central

Johnson, Graham T.; Autin, Ludovic; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

2011-01-01

SUMMARY Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers, we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology. PMID:21397181

WebGL-enabled 3D visualization of a Solar Flare Simulation

NASA Astrophysics Data System (ADS)

Chen, A.; Cheung, C. M. M.; Chintzoglou, G.

2016-12-01

The visualization of magnetohydrodynamic (MHD) simulations of astrophysical systems such as solar flares often requires specialized software packages (e.g. Paraview and VAPOR). A shortcoming of using such software packages is the inability to share our findings with the public and scientific community in an interactive and engaging manner. By using the javascript-based WebGL application programming interface (API) and the three.js javascript package, we create an online in-browser experience for rendering solar flare simulations that will be interactive and accessible to the general public. The WebGL renderer displays objects such as vector flow fields, streamlines and textured isosurfaces. This allows the user to explore the spatial relation between the solar coronal magnetic field and the thermodynamic structure of the plasma in which the magnetic field is embedded. Plans for extending the features of the renderer will also be presented.

The pilot climate data system

NASA Technical Reports Server (NTRS)

Reph, M. G.; Treinish, L. A.; Smith, P. H.

1984-01-01

The Pilot Climate Data System (PCDS) is an interactive scientific information management system for locating, obtaining, manipulating, and displaying climate-research data. The PCDS was developed to manage a large collection of data of interest to the National Aeronautics and Space Administration's (NASA) research community and currently provides such support for approximately twenty data sets. In order to provide the PCDS capabilities, NASA's Goddard Space Flight Center (NASA/GSFC) has integrated the capabilities of several general-purpose software packages with specialized software for reading and reformatting the supported data sets. These capabilities were integrated in a manner which allows the PCDS to be easily expanded, either to provide support for additional data sets or to provide additional functional capabilities. This also allows the PCDS to take advantage of new technology as it becomes available, since parts of the system can be replaced with more powerful components without significantly affecting the user interface.

Free/Libre Open Source Software Implementation in Schools: Evidence from the Field and Implications for the Future

ERIC Educational Resources Information Center

Lin, Yu-Wei; Zini, Enrico

2008-01-01

This empirical paper shows how free/libre open source software (FLOSS) contributes to mutual and collaborative learning in an educational environment. Unlike proprietary software, FLOSS allows extensive customisation of software to support the needs of local users better. This also allows users to participate more proactively in the development…

NCEP BUFRLIB Software User Guide

Science.gov Websites

Integration Branch > Decoders > BUFRLIB BUFRLIB Software User Guide This document set describes how to use the NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on background knowledge of the basic concepts of BUFR and will focus solely on how to use the BUFRLIB software

Front-End/Gateway Software: Availability and Usefulness.

ERIC Educational Resources Information Center

Kesselman, Martin

1985-01-01

Reviews features of front-end software packages (interface between user and online system)--database selection, search strategy development, saving and downloading, hardware and software requirements, training and documentation, online systems and database accession, and costs--and discusses gateway services (user searches through intermediary…

DAS: A Data Management System for Instrument Tests and Operations

NASA Astrophysics Data System (ADS)

Frailis, M.; Sartor, S.; Zacchei, A.; Lodi, M.; Cirami, R.; Pasian, F.; Trifoglio, M.; Bulgarelli, A.; Gianotti, F.; Franceschi, E.; Nicastro, L.; Conforti, V.; Zoli, A.; Smart, R.; Morbidelli, R.; Dadina, M.

2014-05-01

The Data Access System (DAS) is a and data management software system, providing a reusable solution for the storage of data acquired both from telescopes and auxiliary data sources during the instrument development phases and operations. It is part of the Customizable Instrument WorkStation system (CIWS-FW), a framework for the storage, processing and quick-look at the data acquired from scientific instruments. The DAS provides a data access layer mainly targeted to software applications: quick-look displays, pre-processing pipelines and scientific workflows. It is logically organized in three main components: an intuitive and compact Data Definition Language (DAS DDL) in XML format, aimed for user-defined data types; an Application Programming Interface (DAS API), automatically adding classes and methods supporting the DDL data types, and providing an object-oriented query language; a data management component, which maps the metadata of the DDL data types in a relational Data Base Management System (DBMS), and stores the data in a shared (network) file system. With the DAS DDL, developers define the data model for a particular project, specifying for each data type the metadata attributes, the data format and layout (if applicable), and named references to related or aggregated data types. Together with the DDL user-defined data types, the DAS API acts as the only interface to store, query and retrieve the metadata and data in the DAS system, providing both an abstract interface and a data model specific one in C, C++ and Python. The mapping of metadata in the back-end database is automatic and supports several relational DBMSs, including MySQL, Oracle and PostgreSQL.

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

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

Hasenkamp, Daren; Sim, Alexander; Wehner, Michael

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

Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7

NASA Astrophysics Data System (ADS)

Petras, Vaclav; Petrasova, Anna; Chemin, Yann; Zambelli, Pietro; Landa, Martin; Gebbert, Sören; Neteler, Markus; Löwe, Peter

2015-04-01

GRASS GIS 7 is a free and open source GIS software developed and used by many scientists (Neteler et al., 2012). While some users of GRASS GIS prefer its graphical user interface, significant part of the scientific community takes advantage of various scripting and programing interfaces offered by GRASS GIS to develop new models and algorithms. Here we will present different interfaces added to GRASS GIS 7 and available in Python, a popular programming language and environment in geosciences. These Python interfaces are designed to satisfy the needs of scientists and programmers under various circumstances. PyGRASS (Zambelli et al., 2013) is a new object-oriented interface to GRASS GIS modules and libraries. The GRASS GIS libraries are implemented in C to ensure maximum performance and the PyGRASS interface provides an intuitive, pythonic access to their functionality. GRASS GIS Python scripting library is another way of accessing GRASS GIS modules. It combines the simplicity of Bash and the efficiency of the Python syntax. When full access to all low-level and advanced functions and structures from GRASS GIS library is required, Python programmers can use an interface based on the Python ctypes package. Ctypes interface provides complete, direct access to all functionality as it would be available to C programmers. GRASS GIS provides specialized Python library for managing and analyzing spatio-temporal data (Gebbert and Pebesma, 2014). The temporal library introduces space time datasets representing time series of raster, 3D raster or vector maps and allows users to combine various spatio-temporal operations including queries, aggregation, sampling or the analysis of spatio-temporal topology. We will also discuss the advantages of implementing scientific algorithm as a GRASS GIS module and we will show how to write such module in Python. To facilitate the development of the module, GRASS GIS provides a Python library for testing (Petras and Gebbert, 2014) which helps researchers to ensure the robustness of the algorithm, correctness of the results in edge cases as well as the detection of changes in results due to new development. For all modules GRASS GIS automatically creates standardized command line and graphical user interfaces and documentation. Finally, we will show how GRASS GIS can be used together with powerful Python tools such as the NumPy package and the IPython Notebook. References: Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environmental Modelling & Software 53, 1-12. Neteler, M., Bowman, M.H., Landa, M. and Metz, M., 2012. GRASS GIS: a multi-purpose Open Source GIS. Environmental Modelling & Software 31: 124-130. Petras, V., Gebbert, S., 2014. Testing framework for GRASS GIS: ensuring reproducibility of scientific geospatial computing. Poster presented at: AGU Fall Meeting, December 15-19, 2014, San Francisco, USA. Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS International Journal of Geo-Information 2, 201-219.

User Interface Design for Dynamic Geometry Software

ERIC Educational Resources Information Center

Kortenkamp, Ulrich; Dohrmann, Christian

2010-01-01

In this article we describe long-standing user interface issues with Dynamic Geometry Software and common approaches to address them. We describe first prototypes of multi-touch-capable DGS. We also give some hints on the educational benefits of proper user interface design.

Near-Earth Object Survey Simulation Software

NASA Astrophysics Data System (ADS)

Naidu, Shantanu P.; Chesley, Steven R.; Farnocchia, Davide

2017-10-01

There is a significant interest in Near-Earth objects (NEOs) because they pose an impact threat to Earth, offer valuable scientific information, and are potential targets for robotic and human exploration. The number of NEO discoveries has been rising rapidly over the last two decades with over 1800 being discovered last year, making the total number of known NEOs >16000. Pan-STARRS and the Catalina Sky Survey are currently the most prolific NEO surveys, having discovered >1600 NEOs between them in 2016. As next generation surveys such as Large Synoptic Survey Telescope (LSST) and the proposed Near-Earth Object Camera (NEOCam) become operational in the next decade, the discovery rate is expected to increase tremendously. Coordination between various survey telescopes will be necessary in order to optimize NEO discoveries and create a unified global NEO discovery network. We are collaborating on a community-based, open-source software project to simulate asteroid surveys to facilitate such coordination and develop strategies for improving discovery efficiency. Our effort so far has focused on development of a fast and efficient tool capable of accepting user-defined asteroid population models and telescope parameters such as a list of pointing angles and camera field-of-view, and generating an output list of detectable asteroids. The software takes advantage of the widely used and tested SPICE library and architecture developed by NASA’s Navigation and Ancillary Information Facility (Acton, 1996) for saving and retrieving asteroid trajectories and camera pointing. Orbit propagation is done using OpenOrb (Granvik et al. 2009) but future versions will allow the user to plug in a propagator of their choice. The software allows the simulation of both ground-based and space-based surveys. Performance is being tested using the Grav et al. (2011) asteroid population model and the LSST simulated survey “enigma_1189”.

Software design and code generation for the engineering graphical user interface of the ASTRI SST-2M prototype for the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Tanci, Claudio; Tosti, Gino; Antolini, Elisa; Gambini, Giorgio F.; Bruno, Pietro; Canestrari, Rodolfo; Conforti, Vito; Lombardi, Saverio; Russo, Federico; Sangiorgi, Pierluca; Scuderi, Salvatore

2016-08-01

ASTRI is an on-going project developed in the framework of the Cherenkov Telescope Array (CTA). An end- to-end prototype of a dual-mirror small-size telescope (SST-2M) has been installed at the INAF observing station on Mt. Etna, Italy. The next step is the development of the ASTRI mini-array composed of nine ASTRI SST-2M telescopes proposed to be installed at the CTA southern site. The ASTRI mini-array is a collaborative and international effort carried on by Italy, Brazil and South-Africa and led by the Italian National Institute of Astrophysics, INAF. To control the ASTRI telescopes, a specific ASTRI Mini-Array Software System (MASS) was designed using a scalable and distributed architecture to monitor all the hardware devices for the telescopes. Using code generation we built automatically from the ASTRI Interface Control Documents a set of communication libraries and extensive Graphical User Interfaces that provide full access to the capabilities offered by the telescope hardware subsystems for testing and maintenance. Leveraging these generated libraries and components we then implemented a human designed, integrated, Engineering GUI for MASS to perform the verification of the whole prototype and test shared services such as the alarms, configurations, control systems, and scientific on-line outcomes. In our experience the use of code generation dramatically reduced the amount of effort in development, integration and testing of the more basic software components and resulted in a fast software release life cycle. This approach could be valuable for the whole CTA project, characterized by a large diversity of hardware components.

BYMUR software: a free and open source tool for quantifying and visualizing multi-risk analyses

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Selva, Jacopo

2013-04-01

The BYMUR software aims to provide an easy-to-use open source tool for both computing multi-risk and managing/visualizing/comparing all the inputs (e.g. hazard, fragilities and exposure) as well as the corresponding results (e.g. risk curves, risk indexes). For all inputs, a complete management of inter-model epistemic uncertainty is considered. The BYMUR software will be one of the final products provided by the homonymous ByMuR project (http://bymur.bo.ingv.it/) funded by Italian Ministry of Education, Universities and Research (MIUR), focused to (i) provide a quantitative and objective general method for a comprehensive long-term multi-risk analysis in a given area, accounting for inter-model epistemic uncertainty through Bayesian methodologies, and (ii) apply the methodology to seismic, volcanic and tsunami risks in Naples (Italy). More specifically, the BYMUR software will be able to separately account for the probabilistic hazard assessment of different kind of hazardous phenomena, the relative (time-dependent/independent) vulnerabilities and exposure data, and their possible (predefined) interactions: the software will analyze these inputs and will use them to estimate both single- and multi- risk associated to a specific target area. In addition, it will be possible to connect the software to further tools (e.g., a full hazard analysis), allowing a dynamic I/O of results. The use of Python programming language guarantees that the final software will be open source and platform independent. Moreover, thanks to the integration of some most popular and rich-featured Python scientific modules (Numpy, Matplotlib, Scipy) with the wxPython graphical user toolkit, the final tool will be equipped with a comprehensive Graphical User Interface (GUI) able to control and visualize (in the form of tables, maps and/or plots) any stage of the multi-risk analysis. The additional features of importing/exporting data in MySQL databases and/or standard XML formats (for instance, the global standards defined in the frame of GEM project for seismic hazard and risk) will grant the interoperability with other FOSS software and tools and, at the same time, to be on hand of the geo-scientific community. An already available example of connection is represented by the BET_VH(**) tool, which probabilistic volcanic hazard outputs will be used as input for BYMUR. Finally, the prototype version of BYMUR will be used for the case study of the municipality of Naples, by considering three different natural hazards (volcanic eruptions, earthquakes and tsunamis) and by assessing the consequent long-term risk evaluation. (**)BET_VH (Bayesian Event Tree for Volcanic Hazard) is probabilistic tool for long-term volcanic hazard assessment, recently re-designed and adjusted to be run on the Vhub cyber-infrastructure, a free web-based collaborative tool in volcanology research (see http://vhub.org/resources/betvh).

A Python-based interface to examine motions in time series of solar images

NASA Astrophysics Data System (ADS)

Campos-Rozo, J. I.; Vargas Domínguez, S.

2017-10-01

Python is considered to be a mature programming language, besides of being widely accepted as an engaging option for scientific analysis in multiple areas, as will be presented in this work for the particular case of solar physics research. SunPy is an open-source library based on Python that has been recently developed to furnish software tools to solar data analysis and visualization. In this work we present a graphical user interface (GUI) based on Python and Qt to effectively compute proper motions for the analysis of time series of solar data. This user-friendly computing interface, that is intended to be incorporated to the Sunpy library, uses a local correlation tracking technique and some extra tools that allows the selection of different parameters to calculate, vizualize and analyze vector velocity fields of solar data, i.e. time series of solar filtergrams and magnetograms.

Upon the Shoulders of Giants: Open-Source Hardware and Software in Analytical Chemistry.

PubMed

Dryden, Michael D M; Fobel, Ryan; Fobel, Christian; Wheeler, Aaron R

2017-04-18

Isaac Newton famously observed that "if I have seen further it is by standing on the shoulders of giants." We propose that this sentiment is a powerful motivation for the "open-source" movement in scientific research, in which creators provide everything needed to replicate a given project online, as well as providing explicit permission for users to use, improve, and share it with others. Here, we write to introduce analytical chemists who are new to the open-source movement to best practices and concepts in this area and to survey the state of open-source research in analytical chemistry. We conclude by considering two examples of open-source projects from our own research group, with the hope that a description of the process, motivations, and results will provide a convincing argument about the benefits that this movement brings to both creators and users.

Analog-to-digital clinical data collection on networked workstations with graphic user interface.

PubMed

Lunt, D

1991-02-01

An innovative respiratory examination system has been developed that combines physiological response measurement, real-time graphic displays, user-driven operating sequences, and networked file archiving and review into a scientific research and clinical diagnosis tool. This newly constructed computer network is being used to enhance the research center's ability to perform patient pulmonary function examinations. Respiratory data are simultaneously acquired and graphically presented during patient breathing maneuvers and rapidly transformed into graphic and numeric reports, suitable for statistical analysis or database access. The environment consists of the hardware (Macintosh computer, MacADIOS converters, analog amplifiers), the software (HyperCard v2.0, HyperTalk, XCMDs), and the network (AppleTalk, fileservers, printers) as building blocks for data acquisition, analysis, editing, and storage. System operation modules include: Calibration, Examination, Reports, On-line Help Library, Graphic/Data Editing, and Network Storage.

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.

Database Access Manager for the Software Engineering Laboratory (DAMSEL) user's guide

NASA Technical Reports Server (NTRS)

1990-01-01

Operating instructions for the Database Access Manager for the Software Engineering Laboratory (DAMSEL) system are presented. Step-by-step instructions for performing various data entry and report generation activities are included. Sample sessions showing the user interface display screens are also included. Instructions for generating reports are accompanied by sample outputs for each of the reports. The document groups the available software functions by the classes of users that may access them.

Web Time-Management Tool

NASA Technical Reports Server (NTRS)

2000-01-01

Oak Grove Reactor, developed by Oak Grove Systems, is a new software program that allows users to integrate workflow processes. It can be used with portable communication devices. The software can join e-mail, calendar/scheduling and legacy applications into one interactive system via the web. Priority tasks and due dates are organized and highlighted to keep the user up to date with developments. Reactor works with existing software and few new skills are needed to use it. Using a web browser, a user can can work on something while other users can work on the same procedure or view its status while it is being worked on at another site. The software was developed by the Jet Propulsion Lab and originally put to use at Johnson Space Center.

Open release of the DCA++ project

NASA Astrophysics Data System (ADS)

Haehner, Urs; Solca, Raffaele; Staar, Peter; Alvarez, Gonzalo; Maier, Thomas; Summers, Michael; Schulthess, Thomas

We present the first open release of the DCA++ project, a highly scalable and efficient research code to solve quantum many-body problems with cutting edge quantum cluster algorithms. The implemented dynamical cluster approximation (DCA) and its DCA+ extension with a continuous self-energy capture nonlocal correlations in strongly correlated electron systems thereby allowing insight into high-Tc superconductivity. With the increasing heterogeneity of modern machines, DCA++ provides portable performance on conventional and emerging new architectures, such as hybrid CPU-GPU and Xeon Phi, sustaining multiple petaflops on ORNL's Titan and CSCS' Piz Daint. Moreover, we will describe how best practices in software engineering can be applied to make software development sustainable and scalable in a research group. Software testing and documentation not only prevent productivity collapse, but more importantly, they are necessary for correctness, credibility and reproducibility of scientific results. This research used resources of the Oak Ridge Leadership Computing Facility (OLCF) awarded by the INCITE program, and of the Swiss National Supercomputing Center. OLCF is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.

IDEAL: Images Across Domains, Experiments, Algorithms and Learning

NASA Astrophysics Data System (ADS)

Ushizima, Daniela M.; Bale, Hrishikesh A.; Bethel, E. Wes; Ercius, Peter; Helms, Brett A.; Krishnan, Harinarayan; Grinberg, Lea T.; Haranczyk, Maciej; Macdowell, Alastair A.; Odziomek, Katarzyna; Parkinson, Dilworth Y.; Perciano, Talita; Ritchie, Robert O.; Yang, Chao

2016-11-01

Research across science domains is increasingly reliant on image-centric data. Software tools are in high demand to uncover relevant, but hidden, information in digital images, such as those coming from faster next generation high-throughput imaging platforms. The challenge is to analyze the data torrent generated by the advanced instruments efficiently, and provide insights such as measurements for decision-making. In this paper, we overview work performed by an interdisciplinary team of computational and materials scientists, aimed at designing software applications and coordinating research efforts connecting (1) emerging algorithms for dealing with large and complex datasets; (2) data analysis methods with emphasis in pattern recognition and machine learning; and (3) advances in evolving computer architectures. Engineering tools around these efforts accelerate the analyses of image-based recordings, improve reusability and reproducibility, scale scientific procedures by reducing time between experiments, increase efficiency, and open opportunities for more users of the imaging facilities. This paper describes our algorithms and software tools, showing results across image scales, demonstrating how our framework plays a role in improving image understanding for quality control of existent materials and discovery of new compounds.

The Weatherization Assistant User's Manual (Version 8.9)

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

Gettings, Michael B.; Malhotra, Mini; Ternes, Mark P.

The Weatherization Assistant is a Windows-based energy audit software tool that was developed by Oak Ridge National Laboratory (ORNL) to help states and their local weatherization agencies implement the U.S. Department of Energy (DOE) Weatherization Assistance Program. The Weatherization Assistant is an umbrella program for two individual energy audits or measure selection programs: the National Energy Audit Tool (NEAT) for site-built single-family homes and the Manufactured Home Energy Audit (MHEA) for mobile homes. The Weatherization Assistant User's Manual documents the operation of the user interface for Version 8.9 of the software. This includes how to install and setup the software,more » navigate through the program, and initiate an energy audit. All of the user interface forms associated with the software and the data fields on these forms are described in detail. The manual is intended to be a training manual for new users of the Weatherization Assistant and as a reference manual for experienced users.« less

A Randomized Trial Comparing Classical Participatory Design to VandAID, an Interactive CrowdSourcing Platform to Facilitate User-centered Design.

PubMed

Dufendach, Kevin R; Koch, Sabine; Unertl, Kim M; Lehmann, Christoph U

2017-10-26

Early involvement of stakeholders in the design of medical software is particularly important due to the need to incorporate complex knowledge and actions associated with clinical work. Standard user-centered design methods include focus groups and participatory design sessions with individual stakeholders, which generally limit user involvement to a small number of individuals due to the significant time investments from designers and end users. The goal of this project was to reduce the effort for end users to participate in co-design of a software user interface by developing an interactive web-based crowdsourcing platform. In a randomized trial, we compared a new web-based crowdsourcing platform to standard participatory design sessions. We developed an interactive, modular platform that allows responsive remote customization and design feedback on a visual user interface based on user preferences. The responsive canvas is a dynamic HTML template that responds in real time to user preference selections. Upon completion, the design team can view the user's interface creations through an administrator portal and download the structured selections through a REDCap interface. We have created a software platform that allows users to customize a user interface and see the results of that customization in real time, receiving immediate feedback on the impact of their design choices. Neonatal clinicians used the new platform to successfully design and customize a neonatal handoff tool. They received no specific instruction and yet were able to use the software easily and reported high usability. VandAID, a new web-based crowdsourcing platform, can involve multiple users in user-centered design simultaneously and provides means of obtaining design feedback remotely. The software can provide design feedback at any stage in the design process, but it will be of greatest utility for specifying user requirements and evaluating iterative designs with multiple options.

NASA Tech Briefs, October 2003

NASA Technical Reports Server (NTRS)

2003-01-01

Topics covered include: Cryogenic Temperature-Gradient Foam/Substrate Tensile Tester; Flight Test of an Intelligent Flight-Control System; Slat Heater Boxes for Thermal Vacuum Testing; System for Testing Thermal Insulation of Pipes; Electrical-Impedance-Based Ice-Thickness Gauges; Simulation System for Training in Laparoscopic Surgery; Flasher Powered by Photovoltaic Cells and Ultracapacitors; Improved Autoassociative Neural Networks; Toroidal-Core Microinductors Biased by Permanent Magnets; Using Correlated Photons to Suppress Background Noise; Atmospheric-Fade-Tolerant Tracking and Pointing in Wireless Optical Communication; Curved Focal-Plane Arrays Using Back-Illuminated High-Purity Photodetectors; Software for Displaying Data from Planetary Rovers; Software for Refining or Coarsening Computational Grids; Software for Diagnosis of Multiple Coordinated Spacecraft; Software Helps Retrieve Information Relevant to the User; Software for Simulating a Complex Robot; Software for Planning Scientific Activities on Mars; Software for Training in Pre-College Mathematics; Switching and Rectification in Carbon-Nanotube Junctions; Scandia-and-Yttria-Stabilized Zirconia for Thermal Barriers; Environmentally Safer, Less Toxic Fire-Extinguishing Agents; Multiaxial Temperature- and Time-Dependent Failure Model; Cloverleaf Vibratory Microgyroscope with Integrated Post; Single-Vector Calibration of Wind-Tunnel Force Balances; Microgyroscope with Vibrating Post as Rotation Transducer; Continuous Tuning and Calibration of Vibratory Gyroscopes; Compact, Pneumatically Actuated Filter Shuttle; Improved Bearingless Switched-Reluctance Motor; Fluorescent Quantum Dots for Biological Labeling; Growing Three-Dimensional Corneal Tissue in a Bioreactor; Scanning Tunneling Optical Resonance Microscopy; The Micro-Arcsecond Metrology Testbed; Detecting Moving Targets by Use of Soliton Resonances; and Finite-Element Methods for Real-Time Simulation of Surgery.

Modular modeling system for building distributed hydrologic models with a user-friendly software package

NASA Astrophysics Data System (ADS)

Wi, S.; Ray, P. A.; Brown, C.

2015-12-01

A software package developed to facilitate building distributed hydrologic models in a modular modeling system is presented. The software package provides a user-friendly graphical user interface that eases its practical use in water resources-related research and practice. The modular modeling system organizes the options available to users when assembling models according to the stages of hydrological cycle, such as potential evapotranspiration, soil moisture accounting, and snow/glacier melting processes. The software is intended to be a comprehensive tool that simplifies the task of developing, calibrating, validating, and using hydrologic models through the inclusion of intelligent automation to minimize user effort, and reduce opportunities for error. Processes so far automated include the definition of system boundaries (i.e., watershed delineation), climate and geographical input generation, and parameter calibration. Built-in post-processing toolkits greatly improve the functionality of the software as a decision support tool for water resources system management and planning. Example post-processing toolkits enable streamflow simulation at ungauged sites with predefined model parameters, and perform climate change risk assessment by means of the decision scaling approach. The software is validated through application to watersheds representing a variety of hydrologic regimes.

Software design for analysis of multichannel intracardial and body surface electrocardiograms.

PubMed

Potse, Mark; Linnenbank, André C; Grimbergen, Cornelis A

2002-11-01

Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the needs of a diverse group of researchers. It can handle a large variety of recording configurations. It allows for interactive usage through a fast and robust user interface, and batch processing for the analysis of large amounts of data. The package is user-extensible, includes routines for both common and experimental data processing tasks, and works on several computer platforms. The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide.

Make safety awareness a priority: Use a login software in your research facility

DOE PAGES

Camino, Fernando E.

2017-01-21

We report on a facility login software, whose objective is to improve safety in multi-user research facilities. Its most important safety features are: 1) blocks users from entering the lab after being absent for more than a predetermined number of days; 2) gives users a random safety quiz question, which they need to answer satisfactorily in order to use the facility; 3) blocks unauthorized users from using the facility afterhours; and 4) displays the current users in the facility. Besides restricting access to unauthorized users, the software keeps users mindful of key safety concepts. In addition, integration of the softwaremore » with a door controller system can convert it into an effective physical safety mechanism. Depending on DOE approval, the code may be available as open source.« less

Make safety awareness a priority: Use a login software in your research facility

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

Camino, Fernando E.

We report on a facility login software, whose objective is to improve safety in multi-user research facilities. Its most important safety features are: 1) blocks users from entering the lab after being absent for more than a predetermined number of days; 2) gives users a random safety quiz question, which they need to answer satisfactorily in order to use the facility; 3) blocks unauthorized users from using the facility afterhours; and 4) displays the current users in the facility. Besides restricting access to unauthorized users, the software keeps users mindful of key safety concepts. In addition, integration of the softwaremore » with a door controller system can convert it into an effective physical safety mechanism. Depending on DOE approval, the code may be available as open source.« less

Enhancing User Customization through Novel Software Architecture for Utility Scale Solar Siting Software

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

Brant Peery; Sam Alessi; Randy Lee

2014-06-01

There is a need for a spatial decision support application that allows users to create customized metrics for comparing proposed locations of a new solar installation. This document discusses how PVMapper was designed to overcome the customization problem through the development of loosely coupled spatial and decision components in a JavaScript plugin architecture. This allows the user to easily add functionality and data to the system. The paper also explains how PVMapper provides the user with a dynamic and customizable decision tool that enables them to visually modify the formulas that are used in the decision algorithms that convert datamore » to comparable metrics. The technologies that make up the presentation and calculation software stack are outlined. This document also explains the architecture that allows the tool to grow through custom plugins created by the software users. Some discussion is given on the difficulties encountered while designing the system.« less

GeMS: an advanced software package for designing synthetic genes.

PubMed

Jayaraj, Sebastian; Reid, Ralph; Santi, Daniel V

2005-01-01

A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.

Two Mechanisms to Avoid Control Conflicts Resulting from Uncoordinated Intent

NASA Technical Reports Server (NTRS)

Mishkin, Andrew H.; Dvorak, Daniel L.; Wagner, David A.; Bennett, Matthew B.

2013-01-01

This software implements a real-time access control protocol that is intended to make all connected users aware of the presence of other connected users, and which of them is currently in control of the system. Here, "in control" means that a single user is authorized and enabled to issue instructions to the system. The software The software also implements a goal scheduling mechanism that can detect situations where plans for the operation of a target system proposed by different users overlap and interact in conflicting ways. In such situations, the system can either simply report the conflict (rejecting one goal or the entire plan), or reschedule the goals in a way that does not conflict. The access control mechanism (and associated control protocol) is unique. Other access control mechanisms are generally intended to authenticate users, or exclude unauthorized access. This software does neither, and would likely depend on having some other mechanism to support those requirements.

GEOSTATISTICS FOR WASTE MANAGEMENT: A USER'S MANUAL FOR THE GEOPACK (VERSION 1.0) GEOSTATISTICAL SOFTWARE SYSTEM

EPA Science Inventory

GEOPACK, a comprehensive user-friendly geostatistical software system, was developed to help in the analysis of spatially correlated data. The software system was developed to be used by scientists, engineers, regulators, etc., with little experience in geostatistical techniques...

A software for managing chemical processes in a multi-user laboratory

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

Camino, Fernando E.

Here, we report a software for logging chemical processes in a multi-user laboratory, which implements a work flow designed to reduce hazardous situations associated with the disposal of chemicals in incompatible waste containers. The software allows users to perform only those processes displayed in their list of authorized chemical processes and provides the location and label code of waste containers, among other useful information. The software has been used for six years in the cleanroom of the Center for Functional Nanomaterials at Brookhaven National Laboratory and has been an important factor for the excellent safety record of the Center.

A software for managing chemical processes in a multi-user laboratory

DOE PAGES

Camino, Fernando E.

2016-10-26

Here, we report a software for logging chemical processes in a multi-user laboratory, which implements a work flow designed to reduce hazardous situations associated with the disposal of chemicals in incompatible waste containers. The software allows users to perform only those processes displayed in their list of authorized chemical processes and provides the location and label code of waste containers, among other useful information. The software has been used for six years in the cleanroom of the Center for Functional Nanomaterials at Brookhaven National Laboratory and has been an important factor for the excellent safety record of the Center.

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.

User's manual for the VAX-Gerber link software package. Revision 1. 0

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

Isobe, G.W.

1985-10-01

This manual provides a user the information necessary to run the VAX-Gerber link software package. It is expected that the user already knows how to login to the VAX, and is familiar with the Gerber Photo Plotter. It is also highly desirable that the user be familiar with the full screen editor on the VAX, EDT.

Making interdisciplinary solid Earth modeling and analysis tools accessible in a diverse undergraduate and graduate classroom

NASA Astrophysics Data System (ADS)

Becker, T. W.

2011-12-01

I present results from ongoing, NSF-CAREER funded educational and research efforts that center around making numerical tools in seismology and geodynamics more accessible to a broader audience. The goal is not only to train students in quantitative, interdisciplinary research, but also to make methods more easily accessible to practitioners across disciplines. I describe the two main efforts that were funded, the Solid Earth Research and Teaching Environment (SEATREE, geosys.usc.edu/projects/seatree/), and a new Numerical Methods class. SEATREE is a modular and user-friendly software framework to facilitate using solid Earth research tools in the undergraduate and graduate classroom and for interdisciplinary, scientific collaboration. We use only open-source software, and most programming is done in the Python computer language. We strive to make use of modern software design and development concepts while remaining compatible with traditional scientific coding and existing, legacy software. Our goals are to provide a fully contained, yet transparent package that lets users operate in an easy, graphically supported "black box" mode, while also allowing to look under the hood, for example to conduct numerous forward models to explore parameter space. SEATREE currently has several implemented modules, including on global mantle flow, 2D phase velocity tomography, and 2D mantle convection and was used at the University of Southern California, Los Angeles, and at a 2010 CIDER summer school tutorial. SEATREE was developed in collaboration with engineering and computer science undergraduate students, some of which have gone on to work in Earth Science projects. In the long run, we envision SEATREE to contribute to new ways of sharing scientific research, and making (numerical) experiments truly reproducible again. The other project is a set of lecture notes and Matlab exercises on Numerical Methods in solid Earth, focusing on finite difference and element methods. The class has been taught several times at USC to a broad audience of Earth science students with very diverse levels of exposure to math and physics. It is our goal to bring everyone up to speed and empower students, and we have seen structural geology students with very little exposure to math go on to construct their own numerical models of pTt-paths in a core-complex setting. This exemplifies the goal of teaching students to both be able to put together simple numerical models from scratch, and, perhaps more importantly, to truly understand the basic concepts, capabilities, and pitfalls of the more powerful community codes that are being increasingly used. SEATREE and the Numerical Methods class material are freely available at geodynamics.usc.edu/~becker.

Accelerating scientific discovery : 2007 annual report.

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

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

2008-11-14

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

FastQuery: A Parallel Indexing System for Scientific Data

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

Chou, Jerry; Wu, Kesheng; Prabhat,

2011-07-29

Modern scientific datasets present numerous data management and analysis challenges. State-of-the- art index and query technologies such as FastBit can significantly improve accesses to these datasets by augmenting the user data with indexes and other secondary information. However, a challenge is that the indexes assume the relational data model but the scientific data generally follows the array data model. To match the two data models, we design a generic mapping mechanism and implement an efficient input and output interface for reading and writing the data and their corresponding indexes. To take advantage of the emerging many-core architectures, we also developmore » a parallel strategy for indexing using threading technology. This approach complements our on-going MPI-based parallelization efforts. We demonstrate the flexibility of our software by applying it to two of the most commonly used scientific data formats, HDF5 and NetCDF. We present two case studies using data from a particle accelerator model and a global climate model. We also conducted a detailed performance study using these scientific datasets. The results show that FastQuery speeds up the query time by a factor of 2.5x to 50x, and it reduces the indexing time by a factor of 16 on 24 cores.« 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...

Usability study of clinical exome analysis software: top lessons learned and recommendations.

PubMed

Shyr, Casper; Kushniruk, Andre; Wasserman, Wyeth W

2014-10-01

New DNA sequencing technologies have revolutionized the search for genetic disruptions. Targeted sequencing of all protein coding regions of the genome, called exome analysis, is actively used in research-oriented genetics clinics, with the transition to exomes as a standard procedure underway. This transition is challenging; identification of potentially causal mutation(s) amongst ∼10(6) variants requires specialized computation in combination with expert assessment. This study analyzes the usability of user interfaces for clinical exome analysis software. There are two study objectives: (1) To ascertain the key features of successful user interfaces for clinical exome analysis software based on the perspective of expert clinical geneticists, (2) To assess user-system interactions in order to reveal strengths and weaknesses of existing software, inform future design, and accelerate the clinical uptake of exome analysis. Surveys, interviews, and cognitive task analysis were performed for the assessment of two next-generation exome sequence analysis software packages. The subjects included ten clinical geneticists who interacted with the software packages using the "think aloud" method. Subjects' interactions with the software were recorded in their clinical office within an urban research and teaching hospital. All major user interface events (from the user interactions with the packages) were time-stamped and annotated with coding categories to identify usability issues in order to characterize desired features and deficiencies in the user experience. We detected 193 usability issues, the majority of which concern interface layout and navigation, and the resolution of reports. Our study highlights gaps in specific software features typical within exome analysis. The clinicians perform best when the flow of the system is structured into well-defined yet customizable layers for incorporation within the clinical workflow. The results highlight opportunities to dramatically accelerate clinician analysis and interpretation of patient genomic data. We present the first application of usability methods to evaluate software interfaces in the context of exome analysis. Our results highlight how the study of user responses can lead to identification of usability issues and challenges and reveal software reengineering opportunities for improving clinical next-generation sequencing analysis. While the evaluation focused on two distinctive software tools, the results are general and should inform active and future software development for genome analysis software. As large-scale genome analysis becomes increasingly common in healthcare, it is critical that efficient and effective software interfaces are provided to accelerate clinical adoption of the technology. Implications for improved design of such applications are discussed. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

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

Svetlana Shasharina

The goal of the Center for Technology for Advanced Scientific Component Software is to fundamentally changing the way scientific software is developed and used by bringing component-based software development technologies to high-performance scientific and engineering computing. The role of Tech-X work in TASCS project is to provide an outreach to accelerator physics and fusion applications by introducing TASCS tools into applications, testing tools in the applications and modifying the tools to be more usable.

Astro-WISE: Chaining to the Universe

NASA Astrophysics Data System (ADS)

Valentijn, E. A.; McFarland, J. P.; Snigula, J.; Begeman, K. G.; Boxhoorn, D. R.; Rengelink, R.; Helmich, E.; Heraudeau, P.; Verdoes Kleijn, G.; Vermeij, R.; Vriend, W.-J.; Tempelaar, M. J.; Deul, E.; Kuijken, K.; Capaccioli, M.; Silvotti, R.; Bender, R.; Neeser, M.; Saglia, R.; Bertin, E.; Mellier, Y.

2007-10-01

The recent explosion of recorded digital data and its processed derivatives threatens to overwhelm researchers when analysing their experimental data or looking up data items in archives and file systems. While current hardware developments allow the acquisition, processing and storage of hundreds of terabytes of data at the cost of a modern sports car, the software systems to handle these data are lagging behind. This problem is very general and is well recognized by various scientific communities; several large projects have been initiated, e.g., DATAGRID/EGEE {http://www.eu-egee.org/} federates compute and storage power over the high-energy physical community, while the international astronomical community is building an Internet geared Virtual Observatory {http://www.euro-vo.org/pub/} (Padovani 2006) connecting archival data. These large projects either focus on a specific distribution aspect or aim to connect many sub-communities and have a relatively long trajectory for setting standards and a common layer. Here, we report first light of a very different solution (Valentijn & Kuijken 2004) to the problem initiated by a smaller astronomical IT community. It provides an abstract scientific information layer which integrates distributed scientific analysis with distributed processing and federated archiving and publishing. By designing new abstractions and mixing in old ones, a Science Information System with fully scalable cornerstones has been achieved, transforming data systems into knowledge systems. This break-through is facilitated by the full end-to-end linking of all dependent data items, which allows full backward chaining from the observer/researcher to the experiment. Key is the notion that information is intrinsic in nature and thus is the data acquired by a scientific experiment. The new abstraction is that software systems guide the user to that intrinsic information by forcing full backward and forward chaining in the data modelling.

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.

GEOSTATISTICS FOR WASTE MANAGEMENT: A USER'S MANUEL FOR THE GEOPACK (VERSION 1.0) GEOSTATISTICAL SOFTWARE SYSTEM

EPA Science Inventory

A comprehensive, user-friendly geostatistical software system called GEOPACk has been developed. The purpose of this software is to make available the programs necessary to undertake a geostatistical analysis of spatially correlated data. The programs were written so that they ...

User-Centered Design Guidelines for Collaborative Software for Intelligence Analysis

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

Scholtz, Jean; Endert, Alexander

In this position paper we discuss the necessity of using User-Centered Design (UCD) methods in order to design collaborative software for the intelligence community. We discuss a number of studies of collaboration in the intelligence community and use this information to provide some guidelines for collaboration software.

A Web-Based Earth-Systems Knowledge Portal and Collaboration Platform

NASA Astrophysics Data System (ADS)

D'Agnese, F. A.; Turner, A. K.

2010-12-01

In support of complex water-resource sustainability projects in the Great Basin region of the United States, Earth Knowledge, Inc. has developed several web-based data management and analysis platforms that have been used by its scientists, clients, and public to facilitate information exchanges, collaborations, and decision making. These platforms support accurate water-resource decision-making by combining second-generation internet (Web 2.0) technologies with traditional 2D GIS and web-based 2D and 3D mapping systems such as Google Maps, and Google Earth. Most data management and analysis systems use traditional software systems to address the data needs and usage behavior of the scientific community. In contrast, these platforms employ more accessible open-source and “off-the-shelf” consumer-oriented, hosted web-services. They exploit familiar software tools using industry standard protocols, formats, and APIs to discover, process, fuse, and visualize earth, engineering, and social science datasets. Thus, they respond to the information needs and web-interface expectations of both subject-matter experts and the public. Because the platforms continue to gather and store all the contributions of their broad-spectrum of users, each new assessment leverages the data, information, and expertise derived from previous investigations. In the last year, Earth Knowledge completed a conceptual system design and feasibility study for a platform, which has a Knowledge Portal providing access to users wishing to retrieve information or knowledge developed by the science enterprise and a Collaboration Environment Module, a framework that links the user-access functions to a Technical Core supporting technical and scientific analyses including Data Management, Analysis and Modeling, and Decision Management, and to essential system administrative functions within an Administrative Module. The over-riding technical challenge is the design and development of a single technical platform that is accessed through a flexible series of knowledge portal and collaboration environment styles reflecting the information needs and user expectations of a diverse community of users. Recent investigations have defined the information needs and expectations of the major end-users and also have reviewed and assessed a wide variety of modern web-based technologies. Combining these efforts produced design specifications and recommendations for the selection and integration of web- and client-based tools. When fully developed, the resulting platform will: -Support new, advanced information systems and decision environments that take full advantage of multiple data sources and platforms; -Provide a distribution network tailored to the timely delivery of products to a broad range of users that are needed to support applications in disaster management, resource management, energy, and urban sustainability; -Establish new integrated multiple-user requirements and knowledge databases that support researchers and promote infusion of successful technologies into existing processes; and -Develop new decision support strategies and presentation methodologies for applied earth science applications to reduce risk, cost, and time.

Multi-year Content Analysis of User Facility Related Publications

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

Patton, Robert M; Stahl, Christopher G; Hines, Jayson

2013-01-01

Scientific user facilities provide resources and support that enable scientists to conduct experiments or simulations pertinent to their respective research. Consequently, it is critical to have an informed understanding of the impact and contributions that these facilities have on scientific discoveries. Leveraging insight into scientific publications that acknowledge the use of these facilities enables more informed decisions by facility management and sponsors in regard to policy, resource allocation, and influencing the direction of science as well as more effectively understand the impact of a scientific user facility. This work discusses preliminary results of mining scientific publications that utilized resources atmore » the Oak Ridge Leadership Computing Facility (OLCF) at Oak Ridge National Laboratory (ORNL). These results show promise in identifying and leveraging multi-year trends and providing a higher resolution view of the impact that a scientific user facility may have on scientific discoveries.« less

Proceedings of the Second Software Architecture Technology User Network (SATURN) Workshop

DTIC Science & Technology

2006-08-01

Proceedings of the Second Software Architecture Technology User Network (SATURN) Workshop Robert L. Nord August 2006 TECHNICAL REPORT CMU...SEI-2006-TR-010 ESC-TR-2006-010 Software Architecture Technology Initiative Unlimited distribution subject to the copyright. This report was...Participants 3 3 Presentations 5 3.1 SATURN Opening Presentation: Future Directions of the Software Architecture Technology Initiative 5 3.2 Keynote

Tool for Statistical Analysis and Display of Landing Sites

NASA Technical Reports Server (NTRS)

Wawrzyniak, Geoffrey; Kennedy, Brian; Knocke, Philip; Michel, John

2006-01-01

MarsLS is a software tool for analyzing statistical dispersion of spacecraft-landing sites and displaying the results of its analyses. Originally intended for the Mars Explorer Rover (MER) mission, MarsLS is also applicable to landing sites on Earth and non-MER sites on Mars. MarsLS is a collection of interdependent MATLAB scripts that utilize the MATLAB graphical-user-interface software environment to display landing-site data (see figure) on calibrated image-maps of the Martian or other terrain. The landing-site data comprise latitude/longitude pairs generated by Monte Carlo runs of other computer programs that simulate entry, descent, and landing. Using these data, MarsLS can compute a landing-site ellipse a standard means of depicting the area within which the spacecraft can be expected to land with a given probability. MarsLS incorporates several features for the user s convenience, including capabilities for drawing lines and ellipses, overlaying kilometer or latitude/longitude grids, drawing and/or specifying lines and/or points, entering notes, defining and/or displaying polygons to indicate hazards or areas of interest, and evaluating hazardous and/or scientifically interesting areas. As part of such an evaluation, MarsLS can compute the probability of landing in a specified polygonal area.

A Comparative Study of Point Cloud Data Collection and Processing

NASA Astrophysics Data System (ADS)

Pippin, J. E.; Matheney, M.; Gentle, J. N., Jr.; Pierce, S. A.; Fuentes-Pineda, G.

2016-12-01

Over the past decade, there has been dramatic growth in the acquisition of publicly funded high-resolution topographic data for scientific, environmental, engineering and planning purposes. These data sets are valuable for applications of interest across a large and varied user community. However, because of the large volumes of data produced by high-resolution mapping technologies and expense of aerial data collection, it is often difficult to collect and distribute these datasets. Furthermore, the data can be technically challenging to process, requiring software and computing resources not readily available to many users. This study presents a comparison of advanced computing hardware and software that is used to collect and process point cloud datasets, such as LIDAR scans. Activities included implementation and testing of open source libraries and applications for point cloud data processing such as, Meshlab, Blender, PDAL, and PCL. Additionally, a suite of commercial scale applications, Skanect and Cloudcompare, were applied to raw datasets. Handheld hardware solutions, a Structure Scanner and Xbox 360 Kinect V1, were tested for their ability to scan at three field locations. The resultant data projects successfully scanned and processed subsurface karst features ranging from small stalactites to large rooms, as well as a surface waterfall feature. Outcomes support the feasibility of rapid sensing in 3D at field scales.

AstroImageJ: Image Processing and Photometric Extraction for Ultra-precise Astronomical Light Curves

NASA Astrophysics Data System (ADS)

Collins, Karen A.; Kielkopf, John F.; Stassun, Keivan G.; Hessman, Frederic V.

2017-02-01

ImageJ is a graphical user interface (GUI) driven, public domain, Java-based, software package for general image processing traditionally used mainly in life sciences fields. The image processing capabilities of ImageJ are useful and extendable to other scientific fields. Here we present AstroImageJ (AIJ), which provides an astronomy specific image display environment and tools for astronomy specific image calibration and data reduction. Although AIJ maintains the general purpose image processing capabilities of ImageJ, AIJ is streamlined for time-series differential photometry, light curve detrending and fitting, and light curve plotting, especially for applications requiring ultra-precise light curves (e.g., exoplanet transits). AIJ reads and writes standard Flexible Image Transport System (FITS) files, as well as other common image formats, provides FITS header viewing and editing, and is World Coordinate System aware, including an automated interface to the astrometry.net web portal for plate solving images. AIJ provides research grade image calibration and analysis tools with a GUI driven approach, and easily installed cross-platform compatibility. It enables new users, even at the level of undergraduate student, high school student, or amateur astronomer, to quickly start processing, modeling, and plotting astronomical image data with one tightly integrated software package.

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences.

PubMed

Shieh, Fwu-Shan; Jongeneel, Patrick; Steffen, Jamin D; Lin, Selena; Jain, Surbhi; Song, Wei; Su, Ying-Hsiu

2017-01-01

Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq's pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community.

SURE (Science User Resource Expert): A science planning and scheduling assistant for a resource based environment

NASA Technical Reports Server (NTRS)

Thalman, Nancy E.; Sparn, Thomas P.

1990-01-01

SURE (Science User Resource Expert) is one of three components that compose the SURPASS (Science User Resource Planning and Scheduling System). This system is a planning and scheduling tool which supports distributed planning and scheduling, based on resource allocation and optimization. Currently SURE is being used within the SURPASS by the UARS (Upper Atmospheric Research Satellite) SOLSTICE instrument to build a daily science plan and activity schedule and in a prototyping effort with NASA GSFC to demonstrate distributed planning and scheduling for the SOLSTICE II instrument on the EOS platform. For the SOLSTICE application the SURE utilizes a rule-based system. Development of a rule-based program using Ada CLIPS as opposed to using conventional programming, allows for capture of the science planning and scheduling heuristics in rules and provides flexibility in inserting or removing rules as the scientific objectives and mission constraints change. The SURE system's role as a component in the SURPASS, the purpose of the SURE planning and scheduling tool, the SURE knowledge base, and the software architecture of the SURE component are described.

User-friendly InSAR Data Products: Fast and Simple Timeseries (FAST) Processing

NASA Astrophysics Data System (ADS)

Zebker, H. A.

2017-12-01

Interferometric Synthetic Aperture Radar (InSAR) methods provide high resolution maps of surface deformation applicable to many scientific, engineering and management studies. Despite its utility, the specialized skills and computer resources required for InSAR analysis remain as barriers for truly widespread use of the technique. Reduction of radar scenes to maps of temporal deformation evolution requires not only detailed metadata describing the exact radar and surface acquisition geometries, but also a software package that can combine these for the specific scenes of interest. Furthermore, the radar range-Doppler radar coordinate system itself is confusing, so that many users find it hard to incorporate even useful products in their customary analyses. And finally, the sheer data volume needed to represent interferogram time series makes InSAR analysis challenging for many analysis systems. We show here that it is possible to deliver radar data products to users that address all of these difficulties, so that the data acquired by large, modern satellite systems are ready to use in more natural coordinates, without requiring further processing, and in as small volume as possible.

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences

PubMed Central

Shieh, Fwu-Shan; Jongeneel, Patrick; Steffen, Jamin D.; Lin, Selena; Jain, Surbhi; Song, Wei

2017-01-01

Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq’s pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community. PMID:28829778

The VISPA internet platform for outreach, education and scientific research in various experiments

NASA Astrophysics Data System (ADS)

van Asseldonk, D.; Erdmann, M.; Fischer, B.; Fischer, R.; Glaser, C.; Heidemann, F.; Müller, G.; Quast, T.; Rieger, M.; Urban, M.; Welling, C.

2015-12-01

VISPA provides a graphical front-end to computing infrastructures giving its users all functionality needed for working conditions comparable to a personal computer. It is a framework that can be extended with custom applications to support individual needs, e.g. graphical interfaces for experiment-specific software. By design, VISPA serves as a multipurpose platform for many disciplines and experiments as demonstrated in the following different use-cases. A GUI to the analysis framework OFFLINE of the Pierre Auger collaboration, submission and monitoring of computing jobs, university teaching of hundreds of students, and outreach activity, especially in CERN's open data initiative. Serving heterogeneous user groups and applications gave us lots of experience. This helps us in maturing the system, i.e. improving the robustness and responsiveness, and the interplay of the components. Among the lessons learned are the choice of a file system, the implementation of websockets, efficient load balancing, and the fine-tuning of existing technologies like the RPC over SSH. We present in detail the improved server setup and report on the performance, the user acceptance and the realized applications of the system.

Collaborative Planning of Robotic Exploration

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Backes, Paul; Powell, Mark; Vona, Marsette; Steinke, Robert

2004-01-01

The Science Activity Planner (SAP) software system includes an uplink-planning component, which enables collaborative planning of activities to be undertaken by an exploratory robot on a remote planet or on Earth. Included in the uplink-planning component is the SAP-Uplink Browser, which enables users to load multiple spacecraft activity plans into a single window, compare them, and merge them. The uplink-planning component includes a subcomponent that implements the Rover Markup Language Activity Planning format (RML-AP), based on the Extensible Markup Language (XML) format that enables the representation, within a single document, of planned spacecraft and robotic activities together with the scientific reasons for the activities. Each such document is highly parseable and can be validated easily. Another subcomponent of the uplink-planning component is the Activity Dictionary Markup Language (ADML), which eliminates the need for two mission activity dictionaries - one in a human-readable format and one in a machine-readable format. Style sheets that have been developed along with the ADML format enable users to edit one dictionary in a user-friendly environment without compromising

Endnote Web tutorial for BJCVS/RBCCV

PubMed Central

de Oliveira, Marcos Aurélio Barboza; dos Santos, Carlos Alberto; Brandi, Antônio Carlos; Botelho, Paulo Henrique Husseini; Sciarra, Adília Maria Pires; Braile, Domingo Marcolino

2015-01-01

At present, many useful tools for reference management are available for use. They can be either off-line softwares or accessible Websites to all users in the internet. Their target is to facilitate the production of scientific text. But, to accomplish that, the featured bibliographic style should be effectively inserted, and the program has to be free. Here in this tutorial, we present Endnote Web®, a bibliographic reference management program comprising these two requirements: it contains the Brazilian Journal of Cardiovascular Surgery reference format and its use is free for charge after sign-in in IP registered terminal in Web of Science®. PMID:26107457

SBOL Visual: A Graphical Language for Genetic Designs

DOE PAGES

Quinn, Jacqueline Y.; Cox, Robert Sidney; Adler, Aaron; ...

2015-12-03

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. We report that it consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.

SBOL Visual: A Graphical Language for Genetic Designs

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

Quinn, Jacqueline Y.; Cox, Robert Sidney; Adler, Aaron

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. We report that it consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.

The UCLan SDO Data Hub

NASA Astrophysics Data System (ADS)

Dalla, S.; Walsh, R. W.; Chapman, S. A.; Marsh, M.; Regnier, S.; Bewsher, D.; Brown, D. S.; Kelly, J.; Laitinen, T.; Alexander, C.

2010-12-01

A data pipeline for the distribution of SDO data products has been developed throughout a number of countries in the US, Europe and Asia. The UK node within this pipeline is at the University of Central Lancashire (UCLan), where a data center has been established to host a rolling AIA and HMI archive, aimed at supplying data to the country's large solar scientific community. This presentation will describe the hardware and software structures of the archive, as well as the best practice identified and feedback received from users of the facility. We will also discuss algorithms that are run locally in order to identify solar features and events.

SBOL Visual: A Graphical Language for Genetic Designs

PubMed Central

Adler, Aaron; Beal, Jacob; Bhatia, Swapnil; Cai, Yizhi; Chen, Joanna; Clancy, Kevin; Galdzicki, Michal; Hillson, Nathan J.; Le Novère, Nicolas; Maheshwari, Akshay J.; McLaughlin, James Alastair; Myers, Chris J.; P, Umesh; Pocock, Matthew; Rodriguez, Cesar; Soldatova, Larisa; Stan, Guy-Bart V.; Swainston, Neil; Wipat, Anil; Sauro, Herbert M.

2015-01-01

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual. PMID:26633141

OPM: The Open Porous Media Initiative

NASA Astrophysics Data System (ADS)

Flemisch, B.; Flornes, K. M.; Lie, K.; Rasmussen, A.

2011-12-01

The principal objective of the Open Porous Media (OPM) initiative is to develop a simulation suite that is capable of modeling industrially and scientifically relevant flow and transport processes in porous media and bridge the gap between the different application areas of porous media modeling, including reservoir mechanics, CO2 sequestration, biological systems, and product development of engineered media. The OPM initiative will provide a long-lasting, efficient, and well-maintained open-source software for flow and transport in porous media built on modern software principles. The suite is released under the GNU General Public License (GPL). Our motivation is to provide a means to unite industry and public research on simulation of flow and transport in porous media. For academic users, we seek to provide a software infrastructure that facilitates testing of new ideas on models with industry-standard complexity, while at the same time giving the researcher control over discretization and solvers. Similarly, we aim to accelerate the technology transfer from academic institutions to professional companies by making new research results available as free software of professional standard. The OPM initiative is currently supported by six research groups in Norway and Germany and funded by existing grants from public research agencies as well as from Statoil Petroleum and Total E&P Norge. However, a full-scale development of the OPM initiative requires substantially more funding and involvement of more research groups and potential end users. In this talk, we will provide an overview of the current activities in the OPM initiative. Special emphasis will be given to the demonstration of the synergies achieved by combining the strengths of individual open-source software components. In particular, a new fully implicit solver developed within the DUNE-based simulator DuMux could be enhanced by the ability to read industry-standard Eclipse input files and to run on grids given in corner-point format. Examples taken from the SPE comparative solution projects and CO2 sequestration benchmarks illustrate the current capabilities of the simulation suite.

TEST (Toxicity Estimation Software Tool) Ver 4.1

EPA Science Inventory

The Toxicity Estimation Software Tool (T.E.S.T.) has been developed to allow users to easily estimate toxicity and physical properties using a variety of QSAR methodologies. T.E.S.T allows a user to estimate toxicity without requiring any external programs. Users can input a chem...

Scientific Visualization of Radio Astronomy Data using Gesture Interaction

NASA Astrophysics Data System (ADS)

Mulumba, P.; Gain, J.; Marais, P.; Woudt, P.

2015-09-01

MeerKAT in South Africa (Meer = More Karoo Array Telescope) will require software to help visualize, interpret and interact with multidimensional data. While visualization of multi-dimensional data is a well explored topic, little work has been published on the design of intuitive interfaces to such systems. More specifically, the use of non-traditional interfaces (such as motion tracking and multi-touch) has not been widely investigated within the context of visualizing astronomy data. We hypothesize that a natural user interface would allow for easier data exploration which would in turn lead to certain kinds of visualizations (volumetric, multidimensional). To this end, we have developed a multi-platform scientific visualization system for FITS spectral data cubes using VTK (Visualization Toolkit) and a natural user interface to explore the interaction between a gesture input device and multidimensional data space. Our system supports visual transformations (translation, rotation and scaling) as well as sub-volume extraction and arbitrary slicing of 3D volumetric data. These tasks were implemented across three prototypes aimed at exploring different interaction strategies: standard (mouse/keyboard) interaction, volumetric gesture tracking (Leap Motion controller) and multi-touch interaction (multi-touch monitor). A Heuristic Evaluation revealed that the volumetric gesture tracking prototype shows great promise for interfacing with the depth component (z-axis) of 3D volumetric space across multiple transformations. However, this is limited by users needing to remember the required gestures. In comparison, the touch-based gesture navigation is typically more familiar to users as these gestures were engineered from standard multi-touch actions. Future work will address a complete usability test to evaluate and compare the different interaction modalities against the different visualization tasks.

CHERNOLITTM. Chernobyl Bibliographic Search System

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

Caff, F., Jr.; Kennedy, R.A.; Mahaffey, J.A.

1992-03-02

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world`s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Chernobyl Bibliographic Search System

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

Carr, Jr, F.; Kennedy, R. A.; Mahaffey, J. A.

1992-05-11

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world''s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Software Authority Transition through Multiple Distributors

PubMed Central

Han, Kyusunk; Shon, Taeshik

2014-01-01

The rapid growth in the use of smartphones and tablets has changed the software distribution ecosystem. The trend today is to purchase software through application stores rather than from traditional offline markets. Smartphone and tablet users can install applications easily by purchasing from the online store deployed in their device. Several systems, such as Android or PC-based OS units, allow users to install software from multiple sources. Such openness, however, can promote serious threats, including malware and illegal usage. In order to prevent such threats, several stores use online authentication techniques. These methods can, however, also present a problem whereby even licensed users cannot use their purchased application. In this paper, we discuss these issues and provide an authentication method that will make purchased applications available to the registered user at all times. PMID:25143971

Software authority transition through multiple distributors.

PubMed

Han, Kyusunk; Shon, Taeshik

2014-01-01

The rapid growth in the use of smartphones and tablets has changed the software distribution ecosystem. The trend today is to purchase software through application stores rather than from traditional offline markets. Smartphone and tablet users can install applications easily by purchasing from the online store deployed in their device. Several systems, such as Android or PC-based OS units, allow users to install software from multiple sources. Such openness, however, can promote serious threats, including malware and illegal usage. In order to prevent such threats, several stores use online authentication techniques. These methods can, however, also present a problem whereby even licensed users cannot use their purchased application. In this paper, we discuss these issues and provide an authentication method that will make purchased applications available to the registered user at all times.

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.

Global Sensitivity Applied to Dynamic Combined Finite Discrete Element Methods for Fracture Simulation

NASA Astrophysics Data System (ADS)

Godinez, H. C.; Rougier, E.; Osthus, D.; Srinivasan, G.

2017-12-01

Fracture propagation play a key role for a number of application of interest to the scientific community. From dynamic fracture processes like spall and fragmentation in metals and detection of gas flow in static fractures in rock and the subsurface, the dynamics of fracture propagation is important to various engineering and scientific disciplines. In this work we implement a global sensitivity analysis test to the Hybrid Optimization Software Suite (HOSS), a multi-physics software tool based on the combined finite-discrete element method, that is used to describe material deformation and failure (i.e., fracture and fragmentation) under a number of user-prescribed boundary conditions. We explore the sensitivity of HOSS for various model parameters that influence how fracture are propagated through a material of interest. The parameters control the softening curve that the model relies to determine fractures within each element in the mesh, as well a other internal parameters which influence fracture behavior. The sensitivity method we apply is the Fourier Amplitude Sensitivity Test (FAST), which is a global sensitivity method to explore how each parameter influence the model fracture and to determine the key model parameters that have the most impact on the model. We present several sensitivity experiments for different combination of model parameters and compare against experimental data for verification.

An Overview of the GIS Weasel

USGS Publications Warehouse

Viger, Roland J.

2008-01-01

This fact sheet provides a high-level description of the GIS Weasel, a software system designed to aid users in preparing spatial information as input to lumped and distributed parameter environmental simulation models (ESMs). The GIS Weasel provides geographic information system (GIS) tools to help create maps of geographic features relevant to the application of a user?s ESM and to generate parameters from those maps. The operation of the GIS Weasel does not require a user to be a GIS expert, only that a user has an understanding of the spatial information requirements of the model. The GIS Weasel software system provides a GIS-based graphical user interface (GUI), C programming language executables, and general utility scripts. The software will run on any computing platform where ArcInfo Workstation (version 8.1 or later) and the GRID extension are accessible. The user controls the GIS Weasel by interacting with menus, maps, and tables.

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

A progress report on a NASA research program for embedded computer systems software

NASA Technical Reports Server (NTRS)

Foudriat, E. C.; Senn, E. H.; Will, R. W.; Straeter, T. A.

1979-01-01

The paper presents the results of the second stage of the Multipurpose User-oriented Software Technology (MUST) program. Four primary areas of activities are discussed: programming environment, HAL/S higher-order programming language support, the Integrated Verification and Testing System (IVTS), and distributed system language research. The software development environment is provided by the interactive software invocation system. The higher-order programming language (HOL) support chosen for consideration is HAL/S mainly because at the time it was one of the few HOLs with flight computer experience and it is the language used on the Shuttle program. The overall purpose of IVTS is to provide a 'user-friendly' software testing system which is highly modular, user controlled, and cooperative in nature.

Management, Analysis, and Visualization of Experimental and Observational Data – The Convergence of Data and Computing

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

Bethel, E. Wes; Greenwald, Martin; Kleese van Dam, Kerstin

Scientific user facilities—particle accelerators, telescopes, colliders, supercomputers, light sources, sequencing facilities, and more—operated by the U.S. Department of Energy (DOE) Office of Science (SC) generate ever increasing volumes of data at unprecedented rates from experiments, observations, and simulations. At the same time there is a growing community of experimentalists that require real-time data analysis feedback, to enable them to steer their complex experimental instruments to optimized scientific outcomes and new discoveries. Recent efforts in DOE-SC have focused on articulating the data-centric challenges and opportunities facing these science communities. Key challenges include difficulties coping with data size, rate, and complexity inmore » the context of both real-time and post-experiment data analysis and interpretation. Solutions will require algorithmic and mathematical advances, as well as hardware and software infrastructures that adequately support data-intensive scientific workloads. This paper presents the summary findings of a workshop held by DOE-SC in September 2015, convened to identify the major challenges and the research that is needed to meet those challenges.« less

Management, Analysis, and Visualization of Experimental and Observational Data -- The Convergence of Data and Computing

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

Bethel, E. Wes; Greenwald, Martin; Kleese van Dam, Kersten

Scientific user facilities---particle accelerators, telescopes, colliders, supercomputers, light sources, sequencing facilities, and more---operated by the U.S. Department of Energy (DOE) Office of Science (SC) generate ever increasing volumes of data at unprecedented rates from experiments, observations, and simulations. At the same time there is a growing community of experimentalists that require real-time data analysis feedback, to enable them to steer their complex experimental instruments to optimized scientific outcomes and new discoveries. Recent efforts in DOE-SC have focused on articulating the data-centric challenges and opportunities facing these science communities. Key challenges include difficulties coping with data size, rate, and complexity inmore » the context of both real-time and post-experiment data analysis and interpretation. Solutions will require algorithmic and mathematical advances, as well as hardware and software infrastructures that adequately support data-intensive scientific workloads. This paper presents the summary findings of a workshop held by DOE-SC in September 2015, convened to identify the major challenges and the research that is needed to meet those challenges.« less

User Manuals for a Primary Care Electronic Medical Record System: A Mixed Methods Study of User- and Vendor-Generated Documents.

PubMed

Shachak, Aviv; Dow, Rustam; Barnsley, Jan; Tu, Karen; Domb, Sharon; Jadad, Alejandro R; Lemieux-Charles, Louise

2013-06-04

Tutorials and user manuals are important forms of impersonal support for using software applications including electronic medical records (EMRs). Differences between user- and vendor documentation may indicate support needs, which are not sufficiently addressed by the official documentation, and reveal new elements that may inform the design of tutorials and user manuals. What are the differences between user-generated tutorials and manuals for an EMR and the official user manual from the software vendor? Effective design of tutorials and user manuals requires careful packaging of information, balance between declarative and procedural texts, an action and task-oriented approach, support for error recognition and recovery, and effective use of visual elements. No previous research compared these elements between formal and informal documents. We conducted an mixed methods study. Seven tutorials and two manuals for an EMR were collected from three family health teams and compared with the official user manual from the software vendor. Documents were qualitatively analyzed using a framework analysis approach in relation to the principles of technical documentation described above. Subsets of the data were quantitatively analyzed using cross-tabulation to compare the types of error information and visual cues in screen captures between user- and vendor-generated manuals. The user-developed tutorials and manuals differed from the vendor-developed manual in that they contained mostly procedural and not declarative information; were customized to the specific workflow, user roles, and patient characteristics; contained more error information related to work processes than to software usage; and used explicit visual cues on screen captures to help users identify window elements. These findings imply that to support EMR implementation, tutorials and manuals need to be customized and adapted to specific organizational contexts and workflows. The main limitation of the study is its generalizability. Future research should address this limitation and may explore alternative approaches to software documentation, such as modular manuals or participatory design.

Software For Design Of Life-Support Systems

NASA Technical Reports Server (NTRS)

Rudokas, Mary R.; Cantwell, Elizabeth R.; Robinson, Peter I.; Shenk, Timothy W.

1991-01-01

Design Assistant Workstation (DAWN) computer program is prototype of expert software system for analysis and design of regenerative, physical/chemical life-support systems that revitalize air, reclaim water, produce food, and treat waste. Incorporates both conventional software for quantitative mathematical modeling of physical, chemical, and biological processes and expert system offering user stored knowledge about materials and processes. Constructs task tree as it leads user through simulated process, offers alternatives, and indicates where alternative not feasible. Also enables user to jump from one design level to another.

"One-Stop Shopping" for Ocean Remote-Sensing and Model Data

NASA Technical Reports Server (NTRS)

Li, P. Peggy; Vu, Quoc; Chao, Yi; Li, Zhi-Jin; Choi, Jei-Kook

2006-01-01

OurOcean Portal 2.0 (http:// ourocean.jpl.nasa.gov) is a software system designed to enable users to easily gain access to ocean observation data, both remote-sensing and in-situ, configure and run an Ocean Model with observation data assimilated on a remote computer, and visualize both the observation data and the model outputs. At present, the observation data and models focus on the California coastal regions and Prince William Sound in Alaska. This system can be used to perform both real-time and retrospective analyses of remote-sensing data and model outputs. OurOcean Portal 2.0 incorporates state-of-the-art information technologies (IT) such as MySQL database, Java Web Server (Apache/Tomcat), Live Access Server (LAS), interactive graphics with Java Applet at the Client site and MatLab/GMT at the server site, and distributed computing. OurOcean currently serves over 20 real-time or historical ocean data products. The data are served in pre-generated plots or their native data format. For some of the datasets, users can choose different plotting parameters and produce customized graphics. OurOcean also serves 3D Ocean Model outputs generated by ROMS (Regional Ocean Model System) using LAS. The Live Access Server (LAS) software, developed by the Pacific Marine Environmental Laboratory (PMEL) of the National Oceanic and Atmospheric Administration (NOAA), is a configurable Web-server program designed to provide flexible access to geo-referenced scientific data. The model output can be views as plots in horizontal slices, depth profiles or time sequences, or can be downloaded as raw data in different data formats, such as NetCDF, ASCII, Binary, etc. The interactive visualization is provided by graphic software, Ferret, also developed by PMEL. In addition, OurOcean allows users with minimal computing resources to configure and run an Ocean Model with data assimilation on a remote computer. Users may select the forcing input, the data to be assimilated, the simulation period, and the output variables and submit the model to run on a backend parallel computer. When the run is complete, the output will be added to the LAS server for

Multimedia software to help caregivers cope.

PubMed

Chambers, Mary G; Connor, Samantha L; McGonigle, Mary; Diver, Mike G

2003-01-01

This report describes the design and evaluation of a software application to help carers cope when faced with caring problems and emergencies. The design process involved users at each stage to ensure the content of the software application was appropriate, and the research team carefully considered the requirements of disabled and elderly users. Focus group discussions and individual interviews were conducted in five European countries to ascertain the needs of caregivers in this area. The findings were used to design a three-part multimedia software application to help family caregivers prepare to cope with sudden, unexpected, and difficult situations that may arise during their time as a caregiver. This prototype then was evaluated via user trials and usability questionnaires to consider the usability and acceptance of the application and any changes that may be required. User acceptance of the software application was high, and the key features of usability such as content, appearance, and navigation were highly rated. In general, comments were positive and enthusiastic regarding the content of the software application and relevance to the caring situation. The software application has the potential to offer information and support to those who are caring for the elderly and disabled at home and to help them prepare for a crisis.

ISCE: A Modular, Reusable Library for Scalable SAR/InSAR Processing

NASA Astrophysics Data System (ADS)

Agram, P. S.; Lavalle, M.; Gurrola, E. M.; Sacco, G. F.; Rosen, P. A.

2016-12-01

Traditional community SAR/InSAR processing software tools have primarily focused on differential interferometry and Solid Earth applications. The InSAR Scientific Computing Environment (ISCE) was specifically designed to support the Earth Sciences user community as well as large scale operational processing tasks, thanks to its two-layered (Python+C/Fortran) architecture and modular framework. ISCE is freely distributed as a source tarball, allowing advanced users to modify and extend it for their research purposes and developing exploratory applications, while providing a relatively simple user interface for novice users to perform routine data analysis efficiently. Modular design of the ISCE library also enables easier development of applications to address the needs of Ecosystems, Cryosphere and Disaster Response communities in addition to the traditional Solid Earth applications. In this talk, we would like to emphasize the broader purview of the ISCE library and some of its unique features that sets it apart from other freely available community software like GMTSAR and DORIS, including: Support for multiple geometry regimes - Native Doppler (ALOS-1) as well Zero Doppler (ESA missions) systems. Support for data acquired by airborne platforms - e.g, JPL's UAVSAR and AirMOSS, DLR's F-SAR. Radiometric Terrain Correction - Auxiliary output layers from the geometry modules include projection angles, incidence angles, shadow-layover masks. Dense pixel offsets - Parallelized amplitude cross correlation for cryosphere / ionospheric correction applications. Rubber sheeting - Pixel-by-pixel offsets fields for resampling slave imagery for geometric co-registration/ ionospheric corrections. Preliminary Tandem-X processing support - Bistatic geometry modules. Extensibility to support other non-Solid Earth missions - Modules can be directly adopted for use with other SAR missions, e.g., SWOT. Preliminary support for multi-dimensional data products- multi-polarization, multi-frequency, multi-temporal, multi-baseline stacks via the PLANT and GIAnT toolboxes. Rapid prototyping - Geometry manipulation functionality at the python level allows users to prototype and test processing modules at the interpreter level before optimal implementation in C/C++/Fortran.

Information management and analysis system for groundwater data in Thailand

NASA Astrophysics Data System (ADS)

Gill, D.; Luckananurung, P.

1992-01-01

The Ground Water Division of the Thai Department of Mineral Resources maintains a large archive of groundwater data with information on some 50,000 water wells. Each well file contains information on well location, well completion, borehole geology, water levels, water quality, and pumping tests. In order to enable efficient use of this information a computer-based system for information management and analysis was created. The project was sponsored by the United Nations Development Program and the Thai Department of Mineral Resources. The system was designed to serve users who lack prior training in automated data processing. Access is through a friendly user/system dialogue. Tasks are segmented into a number of logical steps, each of which is managed by a separate screen. Selective retrieval is possible by four different methods of area definition and by compliance with user-specified constraints on any combination of database variables. The main types of outputs are: (1) files of retrieved data, screened according to users' specifications; (2) an assortment of pre-formatted reports; (3) computed geochemical parameters and various diagrams of water chemistry derived therefrom; (4) bivariate scatter diagrams and linear regression analysis; (5) posting of data and computed results on maps; and (6) hydraulic aquifer characteristics as computed from pumping tests. Data are entered directly from formatted screens. Most records can be copied directly from hand-written documents. The database-management program performs data integrity checks in real time, enabling corrections at the time of input. The system software can be grouped into: (1) database administration and maintenance—these functions are carried out by the SIR/DBMS software package; (2) user communication interface for task definition and execution control—the interface is written in the operating system command language (VMS/DCL) and in FORTRAN 77; and (3) scientific data-processing programs, written in FORTRAN 77. The system was implemented on a DEC MicroVAX II computer.

qPortal: A platform for data-driven biomedical research.

PubMed

Mohr, Christopher; Friedrich, Andreas; Wojnar, David; Kenar, Erhan; Polatkan, Aydin Can; Codrea, Marius Cosmin; Czemmel, Stefan; Kohlbacher, Oliver; Nahnsen, Sven

2018-01-01

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software's strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on high-performance computing systems via coupling of workflow management systems. Integration of project and data management as well as workflow resources in one place present clear advantages over existing solutions.

The SISMA Project: A pre-operative seismic hazard monitoring system.

NASA Astrophysics Data System (ADS)

Massimiliano Chersich, M. C.; Amodio, A. A. Angelo; Francia, A. F. Andrea; Sparpaglione, C. S. Claudio

2009-04-01

Galileian Plus is currently leading the development, in collaboration with several Italian Universities, of the SISMA (Seismic Information System for Monitoring and Alert) Pilot Project financed by the Italian Space Agency. The system is devoted to the continuous monitoring of the seismic risk and is addressed to support the Italian Civil Protection decisional process. Completion of the Pilot Project is planned at the beginning of 2010. Main scientific paradigm of SISMA is an innovative deterministic approach integrating geophysical models, geodesy and active tectonics. This paper will give a general overview of project along with its progress status and a particular focus will be put on the architectural design details and to the software implementation choices. SISMA is built on top of a software infrastructure developed by Galileian Plus to integrate the scientific programs devoted to the update of seismic risk maps. The main characteristics of the system may be resumed as follow: automatic download of input data; integration of scientific programs; definition and scheduling of chains of processes; monitoring and control of the system through a graphical user interface (GUI); compatibility of the products with ESRI ArcGIS, by mean of post-processing conversion. a) automatic download of input data SISMA needs input data such as GNSS observations, updated seismic catalogue, SAR satellites orbits, etc. that are periodically updated and made available from remote servers through FTP and HTTP. This task is accomplished by a dedicated user configurable component. b) integration of scientific programs SISMA integrates many scientific programs written in different languages (Fortran, C, C++, Perl and Bash) and running into different operating systems. This design requirements lead to the development of a distributed system which is platform independent and is able to run any terminal-based program following few simple predefined rules. c) definition and scheduling of chains of processes Processes are bound each other, in the sense that the output of process "A" should be passed as input to process "B". In this case the process "B" must run automatically as soon as the required input is ready. In SISMA this issue is handled with the "data-driven" activation concept allowing specifying that a process should be started as soon as the needed input datum has been made available in the archive. Moreover SISMA may run processes on a "time-driven" base. The infrastructure of SISMA provides a configurable scheduler allowing the user to define the start time and the periodicity of such processes. d) monitoring and control The operator of the system needs to monitor and control every process running in the system. The SISMA infrastructure allows, through its GUI, the user to: view log messages of running and old processes; stop running processes; monitor processes executions; monitor resource status (available ram, network reachability, and available disk space) for every machine in the system. e) compatibility with ESRI Shapefiles Nearly all the SISMA data has some geographic information, and it is useful to integrate it in a Geographic Information System (GIS). Processors output are georeferred, but they are generated as ASCII files in a proprietary format, and thus cannot directly loaded in a GIS. The infrastructures provides a simple framework for adding filters that reads the data in the proprietary format and converts it to ESRI Shapefile format.

Proposal for a CLIPS software library

NASA Technical Reports Server (NTRS)

Porter, Ken

1991-01-01

This paper is a proposal to create a software library for the C Language Integrated Production System (CLIPS) expert system shell developed by NASA. Many innovative ideas for extending CLIPS were presented at the First CLIPS Users Conference, including useful user and database interfaces. CLIPS developers would benefit from a software library of reusable code. The CLIPS Users Group should establish a software library-- a course of action to make that happen is proposed. Open discussion to revise this library concept is essential, since only a group effort is likely to succeed. A response form intended to solicit opinions and support from the CLIPS community is included.

USER'S GUIDE: Strategic Waste Minimization Initiative (SWAMI) Version 2.0 - A Software Tool to Aid in Process Analysis for Pollution Prevention

EPA Science Inventory

The Strategic WAste Minimization Initiative (SWAMI) Software, Version 2.0 is a tool for using process analysis for identifying waste minimization opportunities within an industrial setting. The software requires user-supplied information for process definition, as well as materia...

Design and Pedagogical Issues in the Development of the InSight Series of Instructional Software.

ERIC Educational Resources Information Center

Baro, John A.; Lehmkulke, Stephen

1993-01-01

Design issues in development of InSight software for optometric education include choice of hardware, identification of audience, definition of scope and limitations of content, selection of user interface and programing environment, obtaining user feedback, and software distribution. Pedagogical issues include practicality and improvement on…

User Studies: Developing Learning Strategy Tool Software for Children.

ERIC Educational Resources Information Center

Fitzgerald, Gail E.; Koury, Kevin A.; Peng, Hsinyi

This paper is a report of user studies for developing learning strategy tool software for children. The prototype software demonstrated is designed for children with learning and behavioral disabilities. The tools consist of easy-to-use templates for creating organizational, memory, and learning approach guides for use in classrooms and at home.…

Information Leaks and Limitations of Role-Based Access Control Mechanisms: A Qualitative Exploratory Single Case Study

ERIC Educational Resources Information Center

Antony, Laljith

2016-01-01

Failing to prevent leaks of confidential and proprietary information to unauthorized users from software applications is a major challenge that companies face. Access control policies defined in software applications with access control mechanisms are unable to prevent information leaks from software applications to unauthorized users. Role-based…

System for Automated Geoscientific Analyses (SAGA) v. 2.1.4

NASA Astrophysics Data System (ADS)

Conrad, O.; Bechtel, B.; Bock, M.; Dietrich, H.; Fischer, E.; Gerlitz, L.; Wehberg, J.; Wichmann, V.; Böhner, J.

2015-07-01

The System for Automated Geoscientific Analyses (SAGA) is an open source geographic information system (GIS), mainly licensed under the GNU General Public License. Since its first release in 2004, SAGA has rapidly developed from a specialized tool for digital terrain analysis to a comprehensive and globally established GIS platform for scientific analysis and modeling. SAGA is coded in C++ in an object oriented design and runs under several operating systems including Windows and Linux. Key functional features of the modular software architecture comprise an application programming interface for the development and implementation of new geoscientific methods, a user friendly graphical user interface with many visualization options, a command line interpreter, and interfaces to interpreted languages like R and Python. The current version 2.1.4 offers more than 600 tools, which are implemented in dynamically loadable libraries or shared objects and represent the broad scopes of SAGA in numerous fields of geoscientific endeavor and beyond. In this paper, we inform about the system's architecture, functionality, and its current state of development and implementation. Furthermore, we highlight the wide spectrum of scientific applications of SAGA in a review of published studies, with special emphasis on the core application areas digital terrain analysis, geomorphology, soil science, climatology and meteorology, as well as remote sensing.

Transfer of computer software technology through workshops: The case of fish bioenergetics modeling

USGS Publications Warehouse

Johnson, B.L.

1992-01-01

A three-part program is proposed to promote the availability and use of computer software packages to fishery managers and researchers. The approach consists of journal articles that announce new technologies, technical reports that serve as user's guides, and hands-on workshops that provide direct instruction to new users. Workshops, which allow experienced users to directly instruct novices in software operation and application are important, but often neglected. The author's experience with organizing and conducting bioenergetics modeling workshops suggests the optimal workshop would take 2 days, have 10-15 participants, one computer for every two users, and one instructor for every 5-6 people.

Clinician user involvement in the real world: Designing an electronic tool to improve interprofessional communication and collaboration in a hospital setting.

PubMed

Tang, Terence; Lim, Morgan E; Mansfield, Elizabeth; McLachlan, Alexander; Quan, Sherman D

2018-02-01

User involvement is vital to the success of health information technology implementation. However, involving clinician users effectively and meaningfully in complex healthcare organizations remains challenging. The objective of this paper is to share our real-world experience of applying a variety of user involvement methods in the design and implementation of a clinical communication and collaboration platform aimed at facilitating care of complex hospitalized patients by an interprofessional team of clinicians. We designed and implemented an electronic clinical communication and collaboration platform in a large community teaching hospital. The design team consisted of both technical and healthcare professionals. Agile software development methodology was used to facilitate rapid iterative design and user input. We involved clinician users at all stages of the development lifecycle using a variety of user-centered, user co-design, and participatory design methods. Thirty-six software releases were delivered over 24 months. User involvement has resulted in improvement in user interface design, identification of software defects, creation of new modules that facilitated workflow, and identification of necessary changes to the scope of the project early on. A variety of user involvement methods were complementary and benefited the design and implementation of a complex health IT solution. Combining these methods with agile software development methodology can turn designs into functioning clinical system to support iterative improvement. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies.

PubMed

Calabria, Andrea; Spinozzi, Giulio; Benedicenti, Fabrizio; Tenderini, Erika; Montini, Eugenio

2015-01-01

Many biological laboratories that deal with genomic samples are facing the problem of sample tracking, both for pure laboratory management and for efficiency. Our laboratory exploits PCR techniques and Next Generation Sequencing (NGS) methods to perform high-throughput integration site monitoring in different clinical trials and scientific projects. Because of the huge amount of samples that we process every year, which result in hundreds of millions of sequencing reads, we need to standardize data management and tracking systems, building up a scalable and flexible structure with web-based interfaces, which are usually called Laboratory Information Management System (LIMS). We started collecting end-users' requirements, composed of desired functionalities of the system and Graphical User Interfaces (GUI), and then we evaluated available tools that could address our requirements, spanning from pure LIMS to Content Management Systems (CMS) up to enterprise information systems. Our analysis identified ADempiere ERP, an open source Enterprise Resource Planning written in Java J2EE, as the best software that also natively implements some highly desirable technological advances, such as the high usability and modularity that grants high use-case flexibility and software scalability for custom solutions. We extended and customized ADempiere ERP to fulfil LIMS requirements and we developed adLIMS. It has been validated by our end-users verifying functionalities and GUIs through test cases for PCRs samples and pre-sequencing data and it is currently in use in our laboratories. adLIMS implements authorization and authentication policies, allowing multiple users management and roles definition that enables specific permissions, operations and data views to each user. For example, adLIMS allows creating sample sheets from stored data using available exporting operations. This simplicity and process standardization may avoid manual errors and information backtracking, features that are not granted using track recording on files or spreadsheets. adLIMS aims to combine sample tracking and data reporting features with higher accessibility and usability of GUIs, thus allowing time to be saved on doing repetitive laboratory tasks, and reducing errors with respect to manual data collection methods. Moreover, adLIMS implements automated data entry, exploiting sample data multiplexing and parallel/transactional processing. adLIMS is natively extensible to cope with laboratory automation through platform-dependent API interfaces, and could be extended to genomic facilities due to the ERP functionalities.

Hardwood log defect photographic database, software and user's guide

Treesearch

R. Edward Thomas

2009-01-01

Computer software and user's guide for Hardwood Log Defect Photographic Database. The database contains photographs and information on external hardwood log defects and the corresponding internal characteristics. This database allows users to search for specific defect types, sizes, and locations by tree species. For every defect, the database contains photos of...

Library Automation Alternatives in 1996 and User Satisfaction Ratings of Library Users by Operating System.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Examines library automation product introductions and conversions to new operating systems. Compares user satisfaction ratings of the following library software packages: DOS/Windows, UNIX, Macintosh, and DEC VAX/VMS. Software is rated according to documentation, service/support, training, product reliability, product capabilities, ease of use,…

Section 4. The GIS Weasel User's Manual

USGS Publications Warehouse

Viger, Roland J.; Leavesley, George H.

2007-01-01

INTRODUCTION The GIS Weasel was designed to aid in the preparation of spatial information for input to lumped and distributed parameter hydrologic or other environmental models. The GIS Weasel provides geographic information system (GIS) tools to help create maps of geographic features relevant to a user's model and to generate parameters from those maps. The operation of the GIS Weasel does not require the user to be a GIS expert, only that the user have an understanding of the spatial information requirements of the environmental simulation model being used. The GIS Weasel software system uses a GIS-based graphical user interface (GUI), the C programming language, and external scripting languages. The software will run on any computing platform where ArcInfo Workstation (version 8.0.2 or later) and the GRID extension are accessible. The user controls the processing of the GIS Weasel by interacting with menus, maps, and tables. The purpose of this document is to describe the operation of the software. This document is not intended to describe the usage of this software in support of any particular environmental simulation model. Such guides are published separately.

Software for Partly Automated Recognition of Targets

NASA Technical Reports Server (NTRS)

Opitz, David; Blundell, Stuart; Bain, William; Morris, Matthew; Carlson, Ian; Mangrich, Mark; Selinsky, T.

2002-01-01

The Feature Analyst is a computer program for assisted (partially automated) recognition of targets in images. This program was developed to accelerate the processing of high-resolution satellite image data for incorporation into geographic information systems (GIS). This program creates an advanced user interface that embeds proprietary machine-learning algorithms in commercial image-processing and GIS software. A human analyst provides samples of target features from multiple sets of data, then the software develops a data-fusion model that automatically extracts the remaining features from selected sets of data. The program thus leverages the natural ability of humans to recognize objects in complex scenes, without requiring the user to explain the human visual recognition process by means of lengthy software. Two major subprograms are the reactive agent and the thinking agent. The reactive agent strives to quickly learn the user's tendencies while the user is selecting targets and to increase the user's productivity by immediately suggesting the next set of pixels that the user may wish to select. The thinking agent utilizes all available resources, taking as much time as needed, to produce the most accurate autonomous feature-extraction model possible.

A Comprehensive Software and Database Management System for Glomerular Filtration Rate Estimation by Radionuclide Plasma Sampling and Serum Creatinine Methods.

PubMed

Jha, Ashish Kumar

2015-01-01

Glomerular filtration rate (GFR) estimation by plasma sampling method is considered as the gold standard. However, this method is not widely used because the complex technique and cumbersome calculations coupled with the lack of availability of user-friendly software. The routinely used Serum Creatinine method (SrCrM) of GFR estimation also requires the use of online calculators which cannot be used without internet access. We have developed user-friendly software "GFR estimation software" which gives the options to estimate GFR by plasma sampling method as well as SrCrM. We have used Microsoft Windows(®) as operating system and Visual Basic 6.0 as the front end and Microsoft Access(®) as database tool to develop this software. We have used Russell's formula for GFR calculation by plasma sampling method. GFR calculations using serum creatinine have been done using MIRD, Cockcroft-Gault method, Schwartz method, and Counahan-Barratt methods. The developed software is performing mathematical calculations correctly and is user-friendly. This software also enables storage and easy retrieval of the raw data, patient's information and calculated GFR for further processing and comparison. This is user-friendly software to calculate the GFR by various plasma sampling method and blood parameter. This software is also a good system for storing the raw and processed data for future analysis.

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.

A Survey of Techniques for Security Architecture Analysis

DTIC Science & Technology

2003-05-01

to be corrected immediately. 49 DSTO-TR-1438 A software phenomenon is the "user innovation network", examples of such networks being "free" and "open...source" software projects. These networks have innovation development, production, distribution and consumption all being performed by users/self...manufacturers. "User innovation networks can function entirely independently of manufacturers because (1) at least some users have sufficient incentive to