Science.gov

Sample records for additional open source

  1. Open Source Molecular Modeling

    PubMed Central

    Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

    2016-01-01

    The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. PMID:27631126

  2. Creating Open Source Conversation

    ERIC Educational Resources Information Center

    Sheehan, Kate

    2009-01-01

    Darien Library, where the author serves as head of knowledge and learning services, launched a new website on September 1, 2008. The website is built with Drupal, an open source content management system (CMS). In this article, the author describes how she and her colleagues overhauled the library's website to provide an open source content…

  3. Open source molecular modeling.

    PubMed

    Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

    2016-09-01

    The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.

  4. Open source molecular modeling.

    PubMed

    Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

    2016-09-01

    The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. PMID:27631126

  5. Recent Additions in the Modeling Capabilities of an Open-Source Wave Energy Converter Design Tool: Preprint

    SciTech Connect

    Tom, N.; Lawson, M.; Yu, Y. H.

    2015-04-20

    WEC-Sim is a midfidelity numerical tool for modeling wave energy conversion devices. The code uses the MATLAB SimMechanics package to solve multibody dynamics and models wave interactions using hydrodynamic coefficients derived from frequency-domain boundary-element methods. This paper presents the new modeling features introduced in the latest release of WEC-Sim. The first feature discussed conversion of the fluid memory kernel to a state-space form. This enhancement offers a substantial computational benefit after the hydrodynamic body-to-body coefficients are introduced and the number of interactions increases exponentially with each additional body. Additional features include the ability to calculate the wave-excitation forces based on the instantaneous incident wave angle, allowing the device to weathervane, as well as import a user-defined wave elevation time series. A review of the hydrodynamic theory for each feature is provided and the successful implementation is verified using test cases.

  6. Open-Source Colorimeter

    PubMed Central

    Anzalone, Gerald C.; Glover, Alexandra G.; Pearce, Joshua M.

    2013-01-01

    The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories. PMID:23604032

  7. Open Source in Education

    ERIC Educational Resources Information Center

    Lakhan, Shaheen E.; Jhunjhunwala, Kavita

    2008-01-01

    Educational institutions have rushed to put their academic resources and services online, beginning the global community onto a common platform and awakening the interest of investors. Despite continuing technical challenges, online education shows great promise. Open source software offers one approach to addressing the technical problems in…

  8. Evaluating Open Source Portals

    ERIC Educational Resources Information Center

    Goh, Dion; Luyt, Brendan; Chua, Alton; Yee, See-Yong; Poh, Kia-Ngoh; Ng, How-Yeu

    2008-01-01

    Portals have become indispensable for organizations of all types trying to establish themselves on the Web. Unfortunately, there have only been a few evaluative studies of portal software and even fewer of open source portal software. This study aims to add to the available literature in this important area by proposing and testing a checklist for…

  9. Open-source colorimeter.

    PubMed

    Anzalone, Gerald C; Glover, Alexandra G; Pearce, Joshua M

    2013-01-01

    The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories.

  10. Open-Source GIS

    SciTech Connect

    Vatsavai, Raju; Burk, Thomas E; Lime, Steve

    2012-01-01

    The components making up an Open Source GIS are explained in this chapter. A map server (Sect. 30.1) can broadly be defined as a software platform for dynamically generating spatially referenced digital map products. The University of Minnesota MapServer (UMN Map Server) is one such system. Its basic features are visualization, overlay, and query. Section 30.2 names and explains many of the geospatial open source libraries, such as GDAL and OGR. The other libraries are FDO, JTS, GEOS, JCS, MetaCRS, and GPSBabel. The application examples include derived GIS-software and data format conversions. Quantum GIS, its origin and its applications explained in detail in Sect. 30.3. The features include a rich GUI, attribute tables, vector symbols, labeling, editing functions, projections, georeferencing, GPS support, analysis, and Web Map Server functionality. Future developments will address mobile applications, 3-D, and multithreading. The origins of PostgreSQL are outlined and PostGIS discussed in detail in Sect. 30.4. It extends PostgreSQL by implementing the Simple Feature standard. Section 30.5 details the most important open source licenses such as the GPL, the LGPL, the MIT License, and the BSD License, as well as the role of the Creative Commons.

  11. How Is Open Source Special?

    ERIC Educational Resources Information Center

    Kapor, Mitchell

    2005-01-01

    Open source software projects involve the production of goods, but in software projects, the "goods" consist of information. The open source model is an alternative to the conventional centralized, command-and-control way in which things are usually made. In contrast, open source projects are genuinely decentralized and transparent. Transparent…

  12. The HYPE Open Source Community

    NASA Astrophysics Data System (ADS)

    Strömbäck, L.; Pers, C.; Isberg, K.; Nyström, K.; Arheimer, B.

    2013-12-01

    The Hydrological Predictions for the Environment (HYPE) model is a dynamic, semi-distributed, process-based, integrated catchment model. It uses well-known hydrological and nutrient transport concepts and can be applied for both small and large scale assessments of water resources and status. In the model, the landscape is divided into classes according to soil type, vegetation and altitude. The soil representation is stratified and can be divided in up to three layers. Water and substances are routed through the same flow paths and storages (snow, soil, groundwater, streams, rivers, lakes) considering turn-over and transformation on the way towards the sea. HYPE has been successfully used in many hydrological applications at SMHI. For Europe, we currently have three different models; The S-HYPE model for Sweden; The BALT-HYPE model for the Baltic Sea; and the E-HYPE model for the whole Europe. These models simulate hydrological conditions and nutrients for their respective areas and are used for characterization, forecasts, and scenario analyses. Model data can be downloaded from hypeweb.smhi.se. In addition, we provide models for the Arctic region, the Arab (Middle East and Northern Africa) region, India, the Niger River basin, the La Plata Basin. This demonstrates the applicability of the HYPE model for large scale modeling in different regions of the world. An important goal with our work is to make our data and tools available as open data and services. For this aim we created the HYPE Open Source Community (OSC) that makes the source code of HYPE available for anyone interested in further development of HYPE. The HYPE OSC (hype.sourceforge.net) is an open source initiative under the Lesser GNU Public License taken by SMHI to strengthen international collaboration in hydrological modeling and hydrological data production. The hypothesis is that more brains and more testing will result in better models and better code. The code is transparent and can be changed

  13. An Open Source Simulation System

    NASA Technical Reports Server (NTRS)

    Slack, Thomas

    2005-01-01

    An investigation into the current state of the art of open source real time programming practices. This document includes what technologies are available, how easy is it to obtain, configure, and use them, and some performance measures done on the different systems. A matrix of vendors and their products is included as part of this investigation, but this is not an exhaustive list, and represents only a snapshot of time in a field that is changing rapidly. Specifically, there are three approaches investigated: 1. Completely open source on generic hardware, downloaded from the net. 2. Open source packaged by a vender and provided as free evaluation copy. 3. Proprietary hardware with pre-loaded proprietary source available software provided by the vender as for our evaluation.

  14. NGSI student activities in open source information analysis in support of the training program of the U.S. DOE laboratories for the entry into force of the additional protocol

    SciTech Connect

    Sandoval, M Analisa; Uribe, Eva C; Sandoval, Marisa N; Boyer, Brian D; Stevens, Rebecca S

    2009-01-01

    In 2008 a joint team from Los Alamos National Laboratory (LANL) and Brookhaven National Laboratory (BNL) consisting of specialists in training of IAEA inspectors in the use of complementary access activities formulated a training program to prepare the U.S. Doe laboratories for the entry into force of the Additional Protocol. As a major part of the support of the activity, LANL summer interns provided open source information analysis to the LANL-BNL mock inspection team. They were a part of the Next Generation Safeguards Initiative's (NGSI) summer intern program aimed at producing the next generation of safeguards specialists. This paper describes how they used open source information to 'backstop' the LANL-BNL team's effort to construct meaningful Additional Protocol Complementary Access training scenarios for each of the three DOE laboratories, Lawrence Livermore National Laboratory, Idaho National Laboratory, and Oak Ridge National Laboratory.

  15. THE OPEN SOURCING OF EPANET

    EPA Science Inventory

    A proposal was made at the 2009 EWRI Congress in Kansas City, MO to establish an Open Source Project (OSP) for the widely used EPANET pipe network analysis program. This would be an ongoing collaborative effort among a group of geographically dispersed advisors and developers, wo...

  16. Open Standards, Open Source, and Open Innovation: Harnessing the Benefits of Openness

    ERIC Educational Resources Information Center

    Committee for Economic Development, 2006

    2006-01-01

    Digitization of information and the Internet have profoundly expanded the capacity for openness. This report details the benefits of openness in three areas--open standards, open-source software, and open innovation--and examines the major issues in the debate over whether openness should be encouraged or not. The report explains each of these…

  17. AKM in Open Source Communities

    NASA Astrophysics Data System (ADS)

    Stamelos, Ioannis; Kakarontzas, George

    Previous chapters in this book have dealt with Architecture Knowledge Management in traditional Closed Source Software (CSS) projects. This chapterwill attempt to examine the ways that knowledge is shared among participants in Free Libre Open Source Software (FLOSS 1) projects and how architectural knowledge is managed w.r.t. CSS. FLOSS projects are organized and developed in a fundamentally different way than CSS projects. FLOSS projects simply do not develop code as CSS projects do. As a consequence, their knowledge management mechanisms are also based on different concepts and tools.

  18. Web accessibility and open source software.

    PubMed

    Obrenović, Zeljko

    2009-07-01

    A Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long-term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional functionalities, for which existing browsers tend to provide only partial solutions. Although functionality for Web accessibility can be found as open source and free software components, their reuse and integration is complex because they were developed in diverse implementation environments, following standards and conventions incompatible with the Web. To address these problems, we have started several activities that aim at exploiting the potential of open-source software for Web accessibility. The first of these activities is the development of Adaptable Multi-Interface COmmunicator (AMICO):WEB, an infrastructure that facilitates efficient reuse and integration of open source software components into the Web environment. The main contribution of AMICO:WEB is in enabling the syntactic and semantic interoperability between Web extension mechanisms and a variety of integration mechanisms used by open source and free software components. Its design is based on our experiences in solving practical problems where we have used open source components to improve accessibility of rich media Web applications. The second of our activities involves improving education, where we have used our platform to teach students how to build advanced accessibility solutions from diverse open-source software. We are also partially involved in the recently started Eclipse projects called Accessibility Tools Framework (ACTF), the aim of which is development of extensible infrastructure, upon which developers can build a variety of utilities that help to evaluate and enhance the accessibility of applications and content for people with disabilities. In this article we briefly report on these activities.

  19. The Commercial Open Source Business Model

    NASA Astrophysics Data System (ADS)

    Riehle, Dirk

    Commercial open source software projects are open source software projects that are owned by a single firm that derives a direct and significant revenue stream from the software. Commercial open source at first glance represents an economic paradox: How can a firm earn money if it is making its product available for free as open source? This paper presents the core properties of com mercial open source business models and discusses how they work. Using a commercial open source approach, firms can get to market faster with a superior product at lower cost than possible for traditional competitors. The paper shows how these benefits accrue from an engaged and self-supporting user community. Lacking any prior comprehensive reference, this paper is based on an analysis of public statements by practitioners of commercial open source. It forges the various anecdotes into a coherent description of revenue generation strategies and relevant business functions.

  20. Open Source Library Management Systems: A Multidimensional Evaluation

    ERIC Educational Resources Information Center

    Balnaves, Edmund

    2008-01-01

    Open source library management systems have improved steadily in the last five years. They now present a credible option for small to medium libraries and library networks. An approach to their evaluation is proposed that takes account of three additional dimensions that only open source can offer: the developer and support community, the source…

  1. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    PubMed

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  2. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    PubMed

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule. PMID:26914653

  3. The HYPE Open Source Community

    NASA Astrophysics Data System (ADS)

    Strömbäck, Lena; Arheimer, Berit; Pers, Charlotta; Isberg, Kristina

    2013-04-01

    The Hydrological Predictions for the Environment (HYPE) model is a dynamic, semi-distributed, process-based, integrated catchment model (Lindström et al., 2010). It uses well-known hydrological and nutrient transport concepts and can be applied for both small and large scale assessments of water resources and status. In the model, the landscape is divided into classes according to soil type, vegetation and altitude. The soil representation is stratified and can be divided in up to three layers. Water and substances are routed through the same flow paths and storages (snow, soil, groundwater, streams, rivers, lakes) considering turn-over and transformation on the way towards the sea. In Sweden, the model is used by water authorities to fulfil the Water Framework Directive and the Marine Strategy Framework Directive. It is used for characterization, forecasts, and scenario analyses. Model data can be downloaded for free from three different HYPE applications: Europe (www.smhi.se/e-hype), Baltic Sea basin (www.smhi.se/balt-hype), and Sweden (vattenweb.smhi.se) The HYPE OSC (hype.sourceforge.net) is an open source initiative under the Lesser GNU Public License taken by SMHI to strengthen international collaboration in hydrological modelling and hydrological data production. The hypothesis is that more brains and more testing will result in better models and better code. The code is transparent and can be changed and learnt from. New versions of the main code will be delivered frequently. The main objective of the HYPE OSC is to provide public access to a state-of-the-art operational hydrological model and to encourage hydrologic expertise from different parts of the world to contribute to model improvement. HYPE OSC is open to everyone interested in hydrology, hydrological modelling and code development - e.g. scientists, authorities, and consultancies. The HYPE Open Source Community was initiated in November 2011 by a kick-off and workshop with 50 eager participants

  4. Open source software to control Bioflo bioreactors.

    PubMed

    Burdge, David A; Libourel, Igor G L

    2014-01-01

    Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW. PMID:24667828

  5. Open source software to control Bioflo bioreactors.

    PubMed

    Burdge, David A; Libourel, Igor G L

    2014-01-01

    Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.

  6. Open Source Software to Control Bioflo Bioreactors

    PubMed Central

    Burdge, David A.; Libourel, Igor G. L.

    2014-01-01

    Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW. PMID:24667828

  7. Free for All: Open Source Software

    ERIC Educational Resources Information Center

    Schneider, Karen

    2008-01-01

    Open source software has become a catchword in libraryland. Yet many remain unclear about open source's benefits--or even what it is. So what is open source software (OSS)? It's software that is free in every sense of the word: free to download, free to use, and free to view or modify. Most OSS is distributed on the Web and one doesn't need to…

  8. Open-source hardware for medical devices

    PubMed Central

    2016-01-01

    Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device. PMID:27158528

  9. The 2016 Bioinformatics Open Source Conference (BOSC)

    PubMed Central

    Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

    2016-01-01

    Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science. PMID:27781083

  10. 7 Questions to Ask Open Source Vendors

    ERIC Educational Resources Information Center

    Raths, David

    2012-01-01

    With their budgets under increasing pressure, many campus IT directors are considering open source projects for the first time. On the face of it, the savings can be significant. Commercial emergency-planning software can cost upward of six figures, for example, whereas the open source Kuali Ready might run as little as $15,000 per year when…

  11. Open Source 2010: Reflections on 2007

    ERIC Educational Resources Information Center

    Wheeler, Brad

    2007-01-01

    Colleges and universities and commercial firms have demonstrated great progress in realizing the vision proffered for "Open Source 2007," and 2010 will mark even greater progress. Although much work remains in refining open source for higher education applications, the signals are now clear: the collaborative development of software can provide…

  12. OpenADR Open Source Toolkit: Developing Open Source Software for the Smart Grid

    SciTech Connect

    McParland, Charles

    2011-02-01

    Demand response (DR) is becoming an increasingly important part of power grid planning and operation. The advent of the Smart Grid, which mandates its use, further motivates selection and development of suitable software protocols to enable DR functionality. The OpenADR protocol has been developed and is being standardized to serve this goal. We believe that the development of a distributable, open source implementation of OpenADR will benefit this effort and motivate critical evaluation of its capabilities, by the wider community, for providing wide-scale DR services

  13. "Open-Sourcing" Personal Learning

    ERIC Educational Resources Information Center

    Fiedler, Sebastian H.D.

    2014-01-01

    This article offers a critical reflection on the contemporary Open Educational Resource (OER) movement, its unquestioned investment in a collective "content fetish" and an educational "problem description" that focuses on issues of scarcity, access, and availability of quality materials. It also argues that OER proponents fail…

  14. The 2015 Bioinformatics Open Source Conference (BOSC 2015)

    PubMed Central

    Harris, Nomi L.; Cock, Peter J. A.; Lapp, Hilmar

    2016-01-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule. PMID:26914653

  15. OpenStudio: An Open Source Integrated Analysis Platform; Preprint

    SciTech Connect

    Guglielmetti, R.; Macumber, D.; Long, N.

    2011-12-01

    High-performance buildings require an integrated design approach for all systems to work together optimally; systems integration needs to be incorporated in the earliest stages of design for efforts to be cost and energy-use effective. Building designers need a full-featured software framework to support rigorous, multidisciplinary building simulation. An open source framework - the OpenStudio Software Development Kit (SDK) - is being developed to address this need. In this paper, we discuss the needs that drive OpenStudio's system architecture and goals, provide a development status report (the SDK is currently in alpha release), and present a brief case study that illustrates its utility and flexibility.

  16. Open source electronic health records and chronic disease management

    PubMed Central

    Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

    2014-01-01

    Objective To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC). Methods and Materials The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR. Results Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients. Discussion The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems. Conclusions The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC. PMID:23813566

  17. The Open Source Snowpack modelling ecosystem

    NASA Astrophysics Data System (ADS)

    Bavay, Mathias; Fierz, Charles; Egger, Thomas; Lehning, Michael

    2016-04-01

    As a large number of numerical snow models are available, a few stand out as quite mature and widespread. One such model is SNOWPACK, the Open Source model that is developed at the WSL Institute for Snow and Avalanche Research SLF. Over the years, various tools have been developed around SNOWPACK in order to expand its use or to integrate additional features. Today, the model is part of a whole ecosystem that has evolved to both offer seamless integration and high modularity so each tool can easily be used outside the ecosystem. Many of these Open Source tools experience their own, autonomous development and are successfully used in their own right in other models and applications. There is Alpine3D, the spatially distributed version of SNOWPACK, that forces it with terrain-corrected radiation fields and optionally with blowing and drifting snow. This model can be used on parallel systems (either with OpenMP or MPI) and has been used for applications ranging from climate change to reindeer herding. There is the MeteoIO pre-processing library that offers fully integrated data access, data filtering, data correction, data resampling and spatial interpolations. This library is now used by several other models and applications. There is the SnopViz snow profile visualization library and application that supports both measured and simulated snow profiles (relying on the CAAML standard) as well as time series. This JavaScript application can be used standalone without any internet connection or served on the web together with simulation results. There is the OSPER data platform effort with a data management service (build on the Global Sensor Network (GSN) platform) as well as a data documenting system (metadata management as a wiki). There are several distributed hydrological models for mountainous areas in ongoing development that require very little information about the soil structure based on the assumption that in step terrain, the most relevant information is

  18. Open source bioimage informatics for cell biology.

    PubMed

    Swedlow, Jason R; Eliceiri, Kevin W

    2009-11-01

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

  19. Open-source 3D-printable optics equipment.

    PubMed

    Zhang, Chenlong; Anzalone, Nicholas C; Faria, Rodrigo P; Pearce, Joshua M

    2013-01-01

    Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods.

  20. Open-Source 3D-Printable Optics Equipment

    PubMed Central

    Zhang, Chenlong; Anzalone, Nicholas C.; Faria, Rodrigo P.; Pearce, Joshua M.

    2013-01-01

    Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods. PMID:23544104

  1. Open-source 3D-printable optics equipment.

    PubMed

    Zhang, Chenlong; Anzalone, Nicholas C; Faria, Rodrigo P; Pearce, Joshua M

    2013-01-01

    Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods. PMID:23544104

  2. The SAMI2 Open Source Project

    NASA Astrophysics Data System (ADS)

    Huba, J. D.; Joyce, G.

    2001-05-01

    In the past decade, the Open Source Model for software development has gained popularity and has had numerous major achievements: emacs, Linux, the Gimp, and Python, to name a few. The basic idea is to provide the source code of the model or application, a tutorial on its use, and a feedback mechanism with the community so that the model can be tested, improved, and archived. Given the success of the Open Source Model, we believe it may prove valuable in the development of scientific research codes. With this in mind, we are `Open Sourcing' the low to mid-latitude ionospheric model that has recently been developed at the Naval Research Laboratory: SAMI2 (Sami2 is Another Model of the Ionosphere). The model is comprehensive and uses modern numerical techniques. The structure and design of SAMI2 make it relatively easy to understand and modify: the numerical algorithms are simple and direct, and the code is reasonably well-written. Furthermore, SAMI2 is designed to run on personal computers; prohibitive computational resources are not necessary, thereby making the model accessible and usable by virtually all researchers. For these reasons, SAMI2 is an excellent candidate to explore and test the open source modeling paradigm in space physics research. We will discuss various topics associated with this project. Research supported by the Office of Naval Research.

  3. Web Server Security on Open Source Environments

    NASA Astrophysics Data System (ADS)

    Gkoutzelis, Dimitrios X.; Sardis, Manolis S.

    Administering critical resources has never been more difficult that it is today. In a changing world of software innovation where major changes occur on a daily basis, it is crucial for the webmasters and server administrators to shield their data against an unknown arsenal of attacks in the hands of their attackers. Up until now this kind of defense was a privilege of the few, out-budgeted and low cost solutions let the defender vulnerable to the uprising of innovating attacking methods. Luckily, the digital revolution of the past decade left its mark, changing the way we face security forever: open source infrastructure today covers all the prerequisites for a secure web environment in a way we could never imagine fifteen years ago. Online security of large corporations, military and government bodies is more and more handled by open source application thus driving the technological trend of the 21st century in adopting open solutions to E-Commerce and privacy issues. This paper describes substantial security precautions in facing privacy and authentication issues in a totally open source web environment. Our goal is to state and face the most known problems in data handling and consequently propose the most appealing techniques to face these challenges through an open solution.

  4. Open Access, Open Source and Digital Libraries: A Current Trend in University Libraries around the World

    ERIC Educational Resources Information Center

    Krishnamurthy, M.

    2008-01-01

    Purpose: The purpose of this paper is to describe the open access and open source movement in the digital library world. Design/methodology/approach: A review of key developments in the open access and open source movement is provided. Findings: Open source software and open access to research findings are of great use to scholars in developing…

  5. The Emergence of Open-Source Software in China

    ERIC Educational Resources Information Center

    Pan, Guohua; Bonk, Curtis J.

    2007-01-01

    The open-source software movement is gaining increasing momentum in China. Of the limited numbers of open-source software in China, "Red Flag Linux" stands out most strikingly, commanding 30 percent share of Chinese software market. Unlike the spontaneity of open-source movement in North America, open-source software development in China, such as…

  6. Communal Resources in Open Source Software Development

    ERIC Educational Resources Information Center

    Spaeth, Sebastian; Haefliger, Stefan; von Krogh, Georg; Renzl, Birgit

    2008-01-01

    Introduction: Virtual communities play an important role in innovation. The paper focuses on the particular form of collective action in virtual communities underlying as Open Source software development projects. Method: Building on resource mobilization theory and private-collective innovation, we propose a theory of collective action in…

  7. Implementing Rakim: Open Source Chat Reference Software

    ERIC Educational Resources Information Center

    Caraway, Shawn; Payne, Susan

    2005-01-01

    This article describes the conception, implementation, and current status of Rakim open source software at Midlands Technical college in Columbia, SC. Midlands Technical College (MTC) is a 2-year school in Columbia, S.C. It has two large campuses and three smaller campuses. Although the library functions as a single unit, there are separate…

  8. Open-source syringe pump library.

    PubMed

    Wijnen, Bas; Hunt, Emily J; Anzalone, Gerald C; Pearce, Joshua M

    2014-01-01

    This article explores a new open-source method for developing and manufacturing high-quality scientific equipment suitable for use in virtually any laboratory. A syringe pump was designed using freely available open-source computer aided design (CAD) software and manufactured using an open-source RepRap 3-D printer and readily available parts. The design, bill of materials and assembly instructions are globally available to anyone wishing to use them. Details are provided covering the use of the CAD software and the RepRap 3-D printer. The use of an open-source Rasberry Pi computer as a wireless control device is also illustrated. Performance of the syringe pump was assessed and the methods used for assessment are detailed. The cost of the entire system, including the controller and web-based control interface, is on the order of 5% or less than one would expect to pay for a commercial syringe pump having similar performance. The design should suit the needs of a given research activity requiring a syringe pump including carefully controlled dosing of reagents, pharmaceuticals, and delivery of viscous 3-D printer media among other applications. PMID:25229451

  9. Of Birkenstocks and Wingtips: Open Source Licenses

    ERIC Educational Resources Information Center

    Gandel, Paul B.; Wheeler, Brad

    2005-01-01

    The notion of collaborating to create open source applications for higher education is rapidly gaining momentum. From course management systems to ERP financial systems, higher education institutions are working together to explore whether they can in fact build a better mousetrap. As Lois Brooks, of Stanford University, recently observed, the…

  10. Open-Source Syringe Pump Library

    PubMed Central

    Wijnen, Bas; Hunt, Emily J.; Anzalone, Gerald C.; Pearce, Joshua M.

    2014-01-01

    This article explores a new open-source method for developing and manufacturing high-quality scientific equipment suitable for use in virtually any laboratory. A syringe pump was designed using freely available open-source computer aided design (CAD) software and manufactured using an open-source RepRap 3-D printer and readily available parts. The design, bill of materials and assembly instructions are globally available to anyone wishing to use them. Details are provided covering the use of the CAD software and the RepRap 3-D printer. The use of an open-source Rasberry Pi computer as a wireless control device is also illustrated. Performance of the syringe pump was assessed and the methods used for assessment are detailed. The cost of the entire system, including the controller and web-based control interface, is on the order of 5% or less than one would expect to pay for a commercial syringe pump having similar performance. The design should suit the needs of a given research activity requiring a syringe pump including carefully controlled dosing of reagents, pharmaceuticals, and delivery of viscous 3-D printer media among other applications. PMID:25229451

  11. Open source OCR framework using mobile devices

    NASA Astrophysics Data System (ADS)

    Zhou, Steven Zhiying; Gilani, Syed Omer; Winkler, Stefan

    2008-02-01

    Mobile phones have evolved from passive one-to-one communication device to powerful handheld computing device. Today most new mobile phones are capable of capturing images, recording video, and browsing internet and do much more. Exciting new social applications are emerging on mobile landscape, like, business card readers, sing detectors and translators. These applications help people quickly gather the information in digital format and interpret them without the need of carrying laptops or tablet PCs. However with all these advancements we find very few open source software available for mobile phones. For instance currently there are many open source OCR engines for desktop platform but, to our knowledge, none are available on mobile platform. Keeping this in perspective we propose a complete text detection and recognition system with speech synthesis ability, using existing desktop technology. In this work we developed a complete OCR framework with subsystems from open source desktop community. This includes a popular open source OCR engine named Tesseract for text detection & recognition and Flite speech synthesis module, for adding text-to-speech ability.

  12. An open-source laser electronics suite

    NASA Astrophysics Data System (ADS)

    Pisenti, Neal C.; Reschovsky, Benjamin J.; Barker, Daniel S.; Restelli, Alessandro; Campbell, Gretchen K.

    2016-05-01

    We present an integrated set of open-source electronics for controlling external-cavity diode lasers and other instruments in the laboratory. The complete package includes a low-noise circuit for driving high-voltage piezoelectric actuators, an ultra-stable current controller based on the design of, and a high-performance, multi-channel temperature controller capable of driving thermo-electric coolers or resistive heaters. Each circuit (with the exception of the temperature controller) is designed to fit in a Eurocard rack equipped with a low-noise linear power supply capable of driving up to 5 A at +/- 15 V. A custom backplane allows signals to be shared between modules, and a digital communication bus makes the entire rack addressable by external control software over TCP/IP. The modular architecture makes it easy for additional circuits to be designed and integrated with existing electronics, providing a low-cost, customizable alternative to commercial systems without sacrificing performance.

  13. a Framework for AN Open Source Geospatial Certification Model

    NASA Astrophysics Data System (ADS)

    Khan, T. U. R.; Davis, P.; Behr, F.-J.

    2016-06-01

    The geospatial industry is forecasted to have an enormous growth in the forthcoming years and an extended need for well-educated workforce. Hence ongoing education and training play an important role in the professional life. Parallel, in the geospatial and IT arena as well in the political discussion and legislation Open Source solutions, open data proliferation, and the use of open standards have an increasing significance. Based on the Memorandum of Understanding between International Cartographic Association, OSGeo Foundation, and ISPRS this development led to the implementation of the ICA-OSGeo-Lab imitative with its mission "Making geospatial education and opportunities accessible to all". Discussions in this initiative and the growth and maturity of geospatial Open Source software initiated the idea to develop a framework for a worldwide applicable Open Source certification approach. Generic and geospatial certification approaches are already offered by numerous organisations, i.e., GIS Certification Institute, GeoAcademy, ASPRS, and software vendors, i. e., Esri, Oracle, and RedHat. They focus different fields of expertise and have different levels and ways of examination which are offered for a wide range of fees. The development of the certification framework presented here is based on the analysis of diverse bodies of knowledge concepts, i.e., NCGIA Core Curriculum, URISA Body Of Knowledge, USGIF Essential Body Of Knowledge, the "Geographic Information: Need to Know", currently under development, and the Geospatial Technology Competency Model (GTCM). The latter provides a US American oriented list of the knowledge, skills, and abilities required of workers in the geospatial technology industry and influenced essentially the framework of certification. In addition to the theoretical analysis of existing resources the geospatial community was integrated twofold. An online survey about the relevance of Open Source was performed and evaluated with 105

  14. Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

    PubMed Central

    2011-01-01

    Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community. PMID:21999342

  15. 16. INTERIOR OF BEDROOM NO. 3 (1965 ADDITION). OPEN DOOR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    16. INTERIOR OF BEDROOM NO. 3 (1965 ADDITION). OPEN DOOR LEADS TO BEDROOM NO. 2. WALLS AND CEILING IN THIS ROOM DO NOT HAVE THE DECORATIVE WOOD STRIPPING FOUND IN THE ORIGINAL PORTIONS OF THE HOUSE. VIEW TO NORTHEAST. - Bishop Creek Hydroelectric System, Plant 4, Worker Cottage, Bishop Creek, Bishop, Inyo County, CA

  16. Open Source, Open Standards, and Health Care Information Systems

    PubMed Central

    2011-01-01

    Recognition of the improvements in patient safety, quality of patient care, and efficiency that health care information systems have the potential to bring has led to significant investment. Globally the sale of health care information systems now represents a multibillion dollar industry. As policy makers, health care professionals, and patients, we have a responsibility to maximize the return on this investment. To this end we analyze alternative licensing and software development models, as well as the role of standards. We describe how licensing affects development. We argue for the superiority of open source licensing to promote safer, more effective health care information systems. We claim that open source licensing in health care information systems is essential to rational procurement strategy. PMID:21447469

  17. Computer Forensics Education - the Open Source Approach

    NASA Astrophysics Data System (ADS)

    Huebner, Ewa; Bem, Derek; Cheung, Hon

    In this chapter we discuss the application of the open source software tools in computer forensics education at tertiary level. We argue that open source tools are more suitable than commercial tools, as they provide the opportunity for students to gain in-depth understanding and appreciation of the computer forensic process as opposed to familiarity with one software product, however complex and multi-functional. With the access to all source programs the students become more than just the consumers of the tools as future forensic investigators. They can also examine the code, understand the relationship between the binary images and relevant data structures, and in the process gain necessary background to become the future creators of new and improved forensic software tools. As a case study we present an advanced subject, Computer Forensics Workshop, which we designed for the Bachelor's degree in computer science at the University of Western Sydney. We based all laboratory work and the main take-home project in this subject on open source software tools. We found that without exception more than one suitable tool can be found to cover each topic in the curriculum adequately. We argue that this approach prepares students better for forensic field work, as they gain confidence to use a variety of tools, not just a single product they are familiar with.

  18. From open source communications to knowledge

    NASA Astrophysics Data System (ADS)

    Preece, Alun; Roberts, Colin; Rogers, David; Webberley, Will; Innes, Martin; Braines, Dave

    2016-05-01

    Rapid processing and exploitation of open source information, including social media sources, in order to shorten decision-making cycles, has emerged as an important issue in intelligence analysis in recent years. Through a series of case studies and natural experiments, focussed primarily upon policing and counter-terrorism scenarios, we have developed an approach to information foraging and framing to inform decision making, drawing upon open source intelligence, in particular Twitter, due to its real-time focus and frequent use as a carrier for links to other media. Our work uses a combination of natural language (NL) and controlled natural language (CNL) processing to support information collection from human sensors, linking and schematising of collected information, and the framing of situational pictures. We illustrate the approach through a series of vignettes, highlighting (1) how relatively lightweight and reusable knowledge models (schemas) can rapidly be developed to add context to collected social media data, (2) how information from open sources can be combined with reports from trusted observers, for corroboration or to identify con icting information; and (3) how the approach supports users operating at or near the tactical edge, to rapidly task information collection and inform decision-making. The approach is supported by bespoke software tools for social media analytics and knowledge management.

  19. Open Source GIS based integrated watershed management

    NASA Astrophysics Data System (ADS)

    Byrne, J. M.; Lindsay, J.; Berg, A. A.

    2013-12-01

    Optimal land and water management to address future and current resource stresses and allocation challenges requires the development of state-of-the-art geomatics and hydrological modelling tools. Future hydrological modelling tools should be of high resolution, process based with real-time capability to assess changing resource issues critical to short, medium and long-term enviromental management. The objective here is to merge two renowned, well published resource modeling programs to create an source toolbox for integrated land and water management applications. This work will facilitate a much increased efficiency in land and water resource security, management and planning. Following an 'open-source' philosophy, the tools will be computer platform independent with source code freely available, maximizing knowledge transfer and the global value of the proposed research. The envisioned set of water resource management tools will be housed within 'Whitebox Geospatial Analysis Tools'. Whitebox, is an open-source geographical information system (GIS) developed by Dr. John Lindsay at the University of Guelph. The emphasis of the Whitebox project has been to develop a user-friendly interface for advanced spatial analysis in environmental applications. The plugin architecture of the software is ideal for the tight-integration of spatially distributed models and spatial analysis algorithms such as those contained within the GENESYS suite. Open-source development extends knowledge and technology transfer to a broad range of end-users and builds Canadian capability to address complex resource management problems with better tools and expertise for managers in Canada and around the world. GENESYS (Generate Earth Systems Science input) is an innovative, efficient, high-resolution hydro- and agro-meteorological model for complex terrain watersheds developed under the direction of Dr. James Byrne. GENESYS is an outstanding research and applications tool to address

  20. Comparison of open source visual analytics toolkits.

    SciTech Connect

    Crossno, Patricia Joyce; Harger, John R.

    2010-11-01

    We present the results of the first stage of a two-stage evaluation of open source visual analytics packages. This stage is a broad feature comparison over a range of open source toolkits. Although we had originally intended to restrict ourselves to comparing visual analytics toolkits, we quickly found that very few were available. So we expanded our study to include information visualization, graph analysis, and statistical packages. We examine three aspects of each toolkit: visualization functions, analysis capabilities, and development environments. With respect to development environments, we look at platforms, language bindings, multi-threading/parallelism, user interface frameworks, ease of installation, documentation, and whether the package is still being actively developed.

  1. Open Source Real Time Operating Systems Overview

    SciTech Connect

    Straumann, Till

    2001-12-11

    Modern control systems applications are often built on top of a real time operating system (RTOS) which provides the necessary hardware abstraction as well as scheduling, networking and other services. Several open source RTOS solutions are publicly available, which is very attractive, both from an economic (no licensing fees) as well as from a technical (control over the source code) point of view. This contribution gives an overview of the RTLinux and RTEMS systems (architecture, development environment, API etc.). Both systems feature most popular CPUs, several APIs (including Posix), networking, portability and optional commercial support. Some performance figures are presented, focusing on interrupt latency and context switching delay.

  2. Open Source Approach to Urban Growth Simulation

    NASA Astrophysics Data System (ADS)

    Petrasova, A.; Petras, V.; Van Berkel, D.; Harmon, B. A.; Mitasova, H.; Meentemeyer, R. K.

    2016-06-01

    Spatial patterns of land use change due to urbanization and its impact on the landscape are the subject of ongoing research. Urban growth scenario simulation is a powerful tool for exploring these impacts and empowering planners to make informed decisions. We present FUTURES (FUTure Urban - Regional Environment Simulation) - a patch-based, stochastic, multi-level land change modeling framework as a case showing how what was once a closed and inaccessible model benefited from integration with open source GIS.We will describe our motivation for releasing this project as open source and the advantages of integrating it with GRASS GIS, a free, libre and open source GIS and research platform for the geospatial domain. GRASS GIS provides efficient libraries for FUTURES model development as well as standard GIS tools and graphical user interface for model users. Releasing FUTURES as a GRASS GIS add-on simplifies the distribution of FUTURES across all main operating systems and ensures the maintainability of our project in the future. We will describe FUTURES integration into GRASS GIS and demonstrate its usage on a case study in Asheville, North Carolina. The developed dataset and tutorial for this case study enable researchers to experiment with the model, explore its potential or even modify the model for their applications.

  3. OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

    PubMed

    Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

    2016-08-30

    High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease. PMID:27575624

  4. OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

    PubMed

    Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

    2016-08-30

    High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

  5. Open source portal to distributed image repositories

    NASA Astrophysics Data System (ADS)

    Tao, Wenchao; Ratib, Osman M.; Kho, Hwa; Hsu, Yung-Chao; Wang, Cun; Lee, Cason; McCoy, J. M.

    2004-04-01

    In large institution PACS, patient data may often reside in multiple separate systems. While most systems tend to be DICOM compliant, none of them offer the flexibility of seamless integration of multiple DICOM sources through a single access point. We developed a generic portal system with a web-based interactive front-end as well as an application programming interface (API) that allows both web users and client applications to query and retrieve image data from multiple DICOM sources. A set of software tools was developed to allow accessing several DICOM archives through a single point of access. An interactive web-based front-end allows user to search image data seamlessly from the different archives and display the results or route the image data to another DICOM compliant destination. An XML-based API allows other software programs to easily benefit from this portal to query and retrieve image data as well. Various techniques are employed to minimize the performance overhead inherent in the DICOM. The system is integrated with a hospital-wide HIPAA-compliant authentication and auditing service that provides centralized management of access to patient medical records. The system is provided under open source free licensing and developed using open-source components (Apache Tomcat for web server, MySQL for database, OJB for object/relational data mapping etc.). The portal paradigm offers a convenient and effective solution for accessing multiple image data sources in a given healthcare enterprise and can easily be extended to multi-institution through appropriate security and encryption mechanisms.

  6. Beyond Open Source: According to Jim Hirsch, Open Technology, Not Open Source, Is the Wave of the Future

    ERIC Educational Resources Information Center

    Villano, Matt

    2006-01-01

    This article presents an interview with Jim Hirsch, an associate superintendent for technology at Piano Independent School District in Piano, Texas. Hirsch serves as a liaison for the open technologies committee of the Consortium for School Networking. In this interview, he shares his opinion on the significance of open source in K-12.

  7. Open Source Testing Capability for Geospatial Software

    NASA Astrophysics Data System (ADS)

    Bermudez, L. E.

    2013-12-01

    Geospatial Software enables scientists to discover, access and process information for better understanding of the Earth. Hundreds, if not thousands, of geospatial software packages exist today. Many of these implement open standards. The OGC Implementation Statistics page [1] reports, for example, more than 450 software products that implement the OGC Web Map Service (WMS) 1.1.1 standard. Even though organizations voluntarily report their products as implementing the WMS standard, not all of these implementations can interoperate with each other. For example, a WMS client may not interact with all these WMS servers in the same functional way. Making the software work with other software, even when implementing the same standard, still remains a challenge, and the main reason is that not all implementations implement the standard correctly. The Open Geospatial Consortium (OGC) Compliance Program provides a testing infrastructure to test for the correct implementation of OGC standards in interfaces and encodings that enable communication between geospatial clients and servers. The OGC testing tool and the tests are all freely available, including the source code and access to the testing facility. The Test, Evaluation, And Measurement (TEAM) Engine is a test harness that executes test suites written using the OGC Compliance Testing Language (CTL) or the TestNG framework. TEAM Engine is available in Sourceforge. OGC hosts an official stable [2] deployment of TEAM Engine with the approved test suites. OGC also hosts a Beta TEAM Engine [3] with the tests in Beta and with new TEAM Engine functionality. Both deployments are freely available to everybody. The OGC testing infrastructure not only enables developers to test OGC standards, but it can be configured to test profiles of OGC standards and community-developed application agreements. These agreements can be any interface and encoding agreement, not only OGC based. The OGC Compliance Program is thus an important

  8. Open Knee: Open Source Modeling and Simulation in Knee Biomechanics.

    PubMed

    Erdemir, Ahmet

    2016-02-01

    Virtual representations of the knee joint can provide clinicians, scientists, and engineers the tools to explore mechanical functions of the knee and its tissue structures in health and disease. Modeling and simulation approaches such as finite element analysis also provide the possibility to understand the influence of surgical procedures and implants on joint stresses and tissue deformations. A large number of knee joint models are described in the biomechanics literature. However, freely accessible, customizable, and easy-to-use models are scarce. Availability of such models can accelerate clinical translation of simulations, where labor-intensive reproduction of model development steps can be avoided. Interested parties can immediately utilize readily available models for scientific discovery and clinical care. Motivated by this gap, this study aims to describe an open source and freely available finite element representation of the tibiofemoral joint, namely Open Knee, which includes the detailed anatomical representation of the joint's major tissue structures and their nonlinear mechanical properties and interactions. Three use cases illustrate customization potential of the model, its predictive capacity, and its scientific and clinical utility: prediction of joint movements during passive flexion, examining the role of meniscectomy on contact mechanics and joint movements, and understanding anterior cruciate ligament mechanics. A summary of scientific and clinically directed studies conducted by other investigators are also provided. The utilization of this open source model by groups other than its developers emphasizes the premise of model sharing as an accelerator of simulation-based medicine. Finally, the imminent need to develop next-generation knee models is noted. These are anticipated to incorporate individualized anatomy and tissue properties supported by specimen-specific joint mechanics data for evaluation, all acquired in vitro from varying age

  9. Color science demonstration kit from open source hardware and software

    NASA Astrophysics Data System (ADS)

    Zollers, Michael W.

    2014-09-01

    Color science is perhaps the most universally tangible discipline within the optical sciences for people of all ages. Excepting a small and relatively well-understood minority, we can see that the world around us consists of a multitude of colors; yet, describing the "what", "why", and "how" of these colors is not an easy task, especially without some sort of equally colorful visual aids. While static displays (e.g., poster boards, etc.) serve their purpose, there is a growing trend, aided by the recent permeation of small interactive devices into our society, for interactive and immersive learning. However, for the uninitiated, designing software and hardware for this purpose may not be within the purview of all optical scientists and engineers. Enter open source. Open source "anything" are those tools and designs -- hardware or software -- that are available and free to use, often without any restrictive licensing. Open source software may be familiar to some, but the open source hardware movement is relatively new. These are electronic circuit board designs that are provided for free and can be implemented in physical hardware by anyone. This movement has led to the availability of some relatively inexpensive, but quite capable, computing power for the creation of small devices. This paper will showcase the design and implementation of the software and hardware that was used to create an interactive demonstration kit for color. Its purpose is to introduce and demonstrate the concepts of color spectra, additive color, color rendering, and metamers.

  10. Open Source Live Distributions for Computer Forensics

    NASA Astrophysics Data System (ADS)

    Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

    Current distributions of open source forensic software provide digital investigators with a large set of heterogeneous tools. Their use is not always focused on the target and requires high technical expertise. We present a new GNU/Linux live distribution, named CAINE (Computer Aided INvestigative Environment) that contains a collection of tools wrapped up into a user friendly environment. The CAINE forensic framework introduces novel important features, aimed at filling the interoperability gap across different forensic tools. Moreover, it provides a homogeneous graphical interface that drives digital investigators during the acquisition and analysis of electronic evidence, and it offers a semi-automatic mechanism for the creation of the final report.

  11. The Emergence of Open-Source Software in North America

    ERIC Educational Resources Information Center

    Pan, Guohua; Bonk, Curtis J.

    2007-01-01

    Unlike conventional models of software development, the open source model is based on the collaborative efforts of users who are also co-developers of the software. Interest in open source software has grown exponentially in recent years. A "Google" search for the phrase open source in early 2005 returned 28.8 million webpage hits, while less than…

  12. Behind Linus's Law: Investigating Peer Review Processes in Open Source

    ERIC Educational Resources Information Center

    Wang, Jing

    2013-01-01

    Open source software has revolutionized the way people develop software, organize collaborative work, and innovate. The numerous open source software systems that have been created and adopted over the past decade are influential and vital in all aspects of work and daily life. The understanding of open source software development can enhance its…

  13. An Analysis of Open Source Security Software Products Downloads

    ERIC Educational Resources Information Center

    Barta, Brian J.

    2014-01-01

    Despite the continued demand for open source security software, a gap in the identification of success factors related to the success of open source security software persists. There are no studies that accurately assess the extent of this persistent gap, particularly with respect to the strength of the relationships of open source software…

  14. The Open Source Teaching Project (OSTP): Research Note.

    ERIC Educational Resources Information Center

    Hirst, Tony

    The Open Source Teaching Project (OSTP) is an attempt to apply a variant of the successful open source software approach to the development of educational materials. Open source software is software licensed in such a way as to allow anyone the right to modify and use it. From such a simple premise, a whole industry has arisen, most notably in the…

  15. Open Source Service Agent (OSSA) in the intelligence community's Open Source Architecture

    NASA Technical Reports Server (NTRS)

    Fiene, Bruce F.

    1994-01-01

    The Community Open Source Program Office (COSPO) has developed an architecture for the intelligence community's new Open Source Information System (OSIS). The architecture is a multi-phased program featuring connectivity, interoperability, and functionality. OSIS is based on a distributed architecture concept. The system is designed to function as a virtual entity. OSIS will be a restricted (non-public), user configured network employing Internet communications. Privacy and authentication will be provided through firewall protection. Connection to OSIS can be made through any server on the Internet or through dial-up modems provided the appropriate firewall authentication system is installed on the client.

  16. Open-source solutions for SPIMage processing.

    PubMed

    Schmied, Christopher; Stamataki, Evangelia; Tomancak, Pavel

    2014-01-01

    Light sheet microscopy is an emerging technique allowing comprehensive visualization of dynamic biological processes, at high spatial and temporal resolution without significant damage to the sample by the imaging process itself. It thus lends itself to time-lapse observation of fluorescently labeled molecular markers over long periods of time in a living specimen. In combination with sample rotation light sheet microscopy and in particular its selective plane illumination microscopy (SPIM) flavor, enables imaging of relatively large specimens, such as embryos of animal model organisms, in their entirety. The benefits of SPIM multiview imaging come to the cost of image data postprocessing necessary to deliver the final output that can be analyzed. Here, we provide a set of practical recipes that walk biologists through the complex processes of SPIM data registration, fusion, deconvolution, and time-lapse registration using publicly available open-source tools. We explain, in plain language, the basic principles behind SPIM image-processing algorithms that should enable users to make informed decisions during parameter tuning of the various processing steps applied to their own datasets. Importantly, the protocols presented here are applicable equally to processing of multiview SPIM data from the commercial Zeiss Lightsheet Z.1 microscope and from the open-access SPIM platforms such as OpenSPIM. PMID:24974045

  17. Spatial rainfall data in open source environment

    NASA Astrophysics Data System (ADS)

    Schuurmans, Hanneke; Maarten Verbree, Jan; Leijnse, Hidde; van Heeringen, Klaas-Jan; Uijlenhoet, Remko; Bierkens, Marc; van de Giesen, Nick; Gooijer, Jan; van den Houten, Gert

    2013-04-01

    Since January 2013 The Netherlands have access to innovative high-quality rainfall data that is used for watermanagers. This product is innovative because of the following reasons. (i) The product is developed in a 'golden triangle' construction - corporation between government, business and research. (ii) Second the rainfall products are developed according to the open-source GPL license. The initiative comes from a group of water boards in the Netherlands that joined their forces to fund the development of a new rainfall product. Not only data from Dutch radar stations (as is currently done by the Dutch meteorological organization KNMI) is used but also data from radars in Germany and Belgium. After a radarcomposite is made, it is adjusted according to data from raingauges (ground truth). This results in 9 different rainfall products that give for each moment the best rainfall data. Specific knowledge is necessary to develop these kind of data. Therefore a pool of experts (KNMI, Deltares and 3 universities) participated in the development. The philosophy of the developers (being corporations) is that products like this should be developed in open source. This way knowledge is shared and the whole community is able to make suggestions for improvement. In our opinion this is the only way to make real progress in product development. Furthermore the financial resources of government organizations are optimized. More info (in Dutch): www.nationaleregenradar.nl

  18. Open Source Hardware for DIY Environmental Sensing

    NASA Astrophysics Data System (ADS)

    Aufdenkampe, A. K.; Hicks, S. D.; Damiano, S. G.; Montgomery, D. S.

    2014-12-01

    The Arduino open source electronics platform has been very popular within the DIY (Do It Yourself) community for several years, and it is now providing environmental science researchers with an inexpensive alternative to commercial data logging and transmission hardware. Here we present the designs for our latest series of custom Arduino-based dataloggers, which include wireless communication options like self-meshing radio networks and cellular phone modules. The main Arduino board uses a custom interface board to connect to various research-grade sensors to take readings of turbidity, dissolved oxygen, water depth and conductivity, soil moisture, solar radiation, and other parameters. Sensors with SDI-12 communications can be directly interfaced to the logger using our open Arduino-SDI-12 software library (https://github.com/StroudCenter/Arduino-SDI-12). Different deployment options are shown, like rugged enclosures to house the loggers and rigs for mounting the sensors in both fresh water and marine environments. After the data has been collected and transmitted by the logger, the data is received by a mySQL-PHP stack running on a web server that can be accessed from anywhere in the world. Once there, the data can be visualized on web pages or served though REST requests and Water One Flow (WOF) services. Since one of the main benefits of using open source hardware is the easy collaboration between users, we are introducing a new web platform for discussion and sharing of ideas and plans for hardware and software designs used with DIY environmental sensors and data loggers.

  19. An Open Source Tool to Test Interoperability

    NASA Astrophysics Data System (ADS)

    Bermudez, L. E.

    2012-12-01

    Scientists interact with information at various levels from gathering of the raw observed data to accessing portrayed processed quality control data. Geoinformatics tools help scientist on the acquisition, storage, processing, dissemination and presentation of geospatial information. Most of the interactions occur in a distributed environment between software components that take the role of either client or server. The communication between components includes protocols, encodings of messages and managing of errors. Testing of these communication components is important to guarantee proper implementation of standards. The communication between clients and servers can be adhoc or follow standards. By following standards interoperability between components increase while reducing the time of developing new software. The Open Geospatial Consortium (OGC), not only coordinates the development of standards but also, within the Compliance Testing Program (CITE), provides a testing infrastructure to test clients and servers. The OGC Web-based Test Engine Facility, based on TEAM Engine, allows developers to test Web services and clients for correct implementation of OGC standards. TEAM Engine is a JAVA open source facility, available at Sourceforge that can be run via command line, deployed in a web servlet container or integrated in developer's environment via MAVEN. The TEAM Engine uses the Compliance Test Language (CTL) and TestNG to test HTTP requests, SOAP services and XML instances against Schemas and Schematron based assertions of any type of web service, not only OGC services. For example, the OGC Web Feature Service (WFS) 1.0.0 test has more than 400 test assertions. Some of these assertions includes conformance of HTTP responses, conformance of GML-encoded data; proper values for elements and attributes in the XML; and, correct error responses. This presentation will provide an overview of TEAM Engine, introduction of how to test via the OGC Testing web site and

  20. Developing an Open Source Option for NASA Software

    NASA Technical Reports Server (NTRS)

    Moran, Patrick J.; Parks, John W. (Technical Monitor)

    2003-01-01

    We present arguments in favor of developing an Open Source option for NASA software; in particular we discuss how Open Source is compatible with NASA's mission. We compare and contrast several of the leading Open Source licenses, and propose one - the Mozilla license - for use by NASA. We also address some of the related issues for NASA with respect to Open Source. In particular, we discuss some of the elements in the External Release of NASA Software document (NPG 2210.1A) that will likely have to be changed in order to make Open Source a reality withm the agency.

  1. An open source simulator for water management

    NASA Astrophysics Data System (ADS)

    Knox, Stephen; Meier, Philipp; Selby, Philip; Mohammed, Khaled; Khadem, Majed; Padula, Silvia; Harou, Julien; Rosenberg, David; Rheinheimer, David

    2015-04-01

    Descriptive modelling of water resource systems requires the representation of different aspects in one model: the physical system including hydrological inputs and engineered infrastructure, and human management, including social, economic and institutional behaviours and constraints. Although most water resource systems share some characteristics such as the ability to represent them as a network of nodes and links, geographical, institutional and other differences mean that invariably each water system functions in a unique way. A diverse group is developing an open source simulation framework which will allow model developers to build generalised water management models that are customised to the institutional, physical and economical components they are seeking to model. The framework will allow the simulation of complex individual and institutional behaviour required for the assessment of real-world resource systems. It supports the spatial and hierarchical structures commonly found in water resource systems. The individual infrastructures can be operated by different actors while policies are defined at a regional level by one or more institutional actors. The framework enables building multi-agent system simulators in which developers can define their own agent types and add their own decision making code. Developers using the framework have two main tasks: (i) Extend the core classes to represent the aspects of their particular system, and (ii) write model structure files. Both are done in Python. For task one, users must either write new decision making code for each class or link to an existing code base to provide functionality to each of these extension classes. The model structure file links these extension classes in a standardised way to the network topology. The framework will be open-source and written in Python and is to be available directly for download through standard installer packages. Many water management model developers are unfamiliar

  2. Modular Open-Source Software for Item Factor Analysis

    PubMed Central

    Pritikin, Joshua N.; Hunter, Micheal D.; Boker, Steven

    2015-01-01

    This paper introduces an Item Factor Analysis (IFA) module for OpenMx, a free, open-source, and modular statistical modeling package that runs within the R programming environment on GNU/Linux, Mac OS X, and Microsoft Windows. The IFA module offers a novel model specification language that is well suited to programmatic generation and manipulation of models. Modular organization of the source code facilitates the easy addition of item models, item parameter estimation algorithms, optimizers, test scoring algorithms, and fit diagnostics all within an integrated framework. Three short example scripts are presented for fitting item parameters, latent distribution parameters, and a multiple group model. The availability of both IFA and structural equation modeling in the same software is a step toward the unification of these two methodologies. PMID:27065479

  3. An Affordable Open-Source Turbidimeter

    PubMed Central

    Kelley, Christopher D.; Krolick, Alexander; Brunner, Logan; Burklund, Alison; Kahn, Daniel; Ball, William P.; Weber-Shirk, Monroe

    2014-01-01

    Turbidity is an internationally recognized criterion for assessing drinking water quality, because the colloidal particles in turbid water may harbor pathogens, chemically reduce oxidizing disinfectants, and hinder attempts to disinfect water with ultraviolet radiation. A turbidimeter is an electronic/optical instrument that assesses turbidity by measuring the scattering of light passing through a water sample containing such colloidal particles. Commercial turbidimeters cost hundreds or thousands of dollars, putting them beyond the reach of low-resource communities around the world. An affordable open-source turbidimeter based on a single light-to-frequency sensor was designed and constructed, and evaluated against a portable commercial turbidimeter. The final product, which builds on extensive published research, is intended to catalyze further developments in affordable water and sanitation monitoring. PMID:24759114

  4. An open source business model for malaria.

    PubMed

    Årdal, Christine; Røttingen, John-Arne

    2015-01-01

    Greater investment is required in developing new drugs and vaccines against malaria in order to eradicate malaria. These precious funds must be carefully managed to achieve the greatest impact. We evaluate existing efforts to discover and develop new drugs and vaccines for malaria to determine how best malaria R&D can benefit from an enhanced open source approach and how such a business model may operate. We assess research articles, patents, clinical trials and conducted a smaller survey among malaria researchers. Our results demonstrate that the public and philanthropic sectors are financing and performing the majority of malaria drug/vaccine discovery and development, but are then restricting access through patents, 'closed' publications and hidden away physical specimens. This makes little sense since it is also the public and philanthropic sector that purchases the drugs and vaccines. We recommend that a more "open source" approach is taken by making the entire value chain more efficient through greater transparency which may lead to more extensive collaborations. This can, for example, be achieved by empowering an existing organization like the Medicines for Malaria Venture (MMV) to act as a clearing house for malaria-related data. The malaria researchers that we surveyed indicated that they would utilize such registry data to increase collaboration. Finally, we question the utility of publicly or philanthropically funded patents for malaria medicines, where little to no profits are available. Malaria R&D benefits from a publicly and philanthropically funded architecture, which starts with academic research institutions, product development partnerships, commercialization assistance through UNITAID and finally procurement through mechanisms like The Global Fund to Fight AIDS, Tuberculosis and Malaria and the U.S.' President's Malaria Initiative. We believe that a fresh look should be taken at the cost/benefit of patents particularly related to new malaria

  5. OpenMx: An Open Source Extended Structural Equation Modeling Framework

    ERIC Educational Resources Information Center

    Boker, Steven; Neale, Michael; Maes, Hermine; Wilde, Michael; Spiegel, Michael; Brick, Timothy; Spies, Jeffrey; Estabrook, Ryne; Kenny, Sarah; Bates, Timothy; Mehta, Paras; Fox, John

    2011-01-01

    OpenMx is free, full-featured, open source, structural equation modeling (SEM) software. OpenMx runs within the "R" statistical programming environment on Windows, Mac OS-X, and Linux computers. The rationale for developing OpenMx is discussed along with the philosophy behind the user interface. The OpenMx data structures are introduced--these…

  6. An Open Source Business Model for Malaria

    PubMed Central

    Årdal, Christine; Røttingen, John-Arne

    2015-01-01

    Greater investment is required in developing new drugs and vaccines against malaria in order to eradicate malaria. These precious funds must be carefully managed to achieve the greatest impact. We evaluate existing efforts to discover and develop new drugs and vaccines for malaria to determine how best malaria R&D can benefit from an enhanced open source approach and how such a business model may operate. We assess research articles, patents, clinical trials and conducted a smaller survey among malaria researchers. Our results demonstrate that the public and philanthropic sectors are financing and performing the majority of malaria drug/vaccine discovery and development, but are then restricting access through patents, ‘closed’ publications and hidden away physical specimens. This makes little sense since it is also the public and philanthropic sector that purchases the drugs and vaccines. We recommend that a more “open source” approach is taken by making the entire value chain more efficient through greater transparency which may lead to more extensive collaborations. This can, for example, be achieved by empowering an existing organization like the Medicines for Malaria Venture (MMV) to act as a clearing house for malaria-related data. The malaria researchers that we surveyed indicated that they would utilize such registry data to increase collaboration. Finally, we question the utility of publicly or philanthropically funded patents for malaria medicines, where little to no profits are available. Malaria R&D benefits from a publicly and philanthropically funded architecture, which starts with academic research institutions, product development partnerships, commercialization assistance through UNITAID and finally procurement through mechanisms like The Global Fund to Fight AIDS, Tuberculosis and Malaria and the U.S.’ President’s Malaria Initiative. We believe that a fresh look should be taken at the cost/benefit of patents particularly related to new

  7. The case for open-source software in drug discovery.

    PubMed

    DeLano, Warren L

    2005-02-01

    Widespread adoption of open-source software for network infrastructure, web servers, code development, and operating systems leads one to ask how far it can go. Will "open source" spread broadly, or will it be restricted to niches frequented by hopeful hobbyists and midnight hackers? Here we identify reasons for the success of open-source software and predict how consumers in drug discovery will benefit from new open-source products that address their needs with increased flexibility and in ways complementary to proprietary options.

  8. Closed-Loop, Open-Source Electrophysiology

    PubMed Central

    Rolston, John D.; Gross, Robert E.; Potter, Steve M.

    2010-01-01

    Multiple extracellular microelectrodes (multi-electrode arrays, or MEAs) effectively record rapidly varying neural signals, and can also be used for electrical stimulation. Multi-electrode recording can serve as artificial output (efferents) from a neural system, while complex spatially and temporally targeted stimulation can serve as artificial input (afferents) to the neuronal network. Multi-unit or local field potential (LFP) recordings can not only be used to control real world artifacts, such as prostheses, computers or robots, but can also trigger or alter subsequent stimulation. Real-time feedback stimulation may serve to modulate or normalize aberrant neural activity, to induce plasticity, or to serve as artificial sensory input. Despite promising closed-loop applications, commercial electrophysiology systems do not yet take advantage of the bidirectional capabilities of multi-electrodes, especially for use in freely moving animals. We addressed this lack of tools for closing the loop with NeuroRighter, an open-source system including recording hardware, stimulation hardware, and control software with a graphical user interface. The integrated system is capable of multi-electrode recording and simultaneous patterned microstimulation (triggered by recordings) with minimal stimulation artifact. The potential applications of closed-loop systems as research tools and clinical treatments are broad; we provide one example where epileptic activity recorded by a multi-electrode probe is used to trigger targeted stimulation, via that probe, to freely moving rodents. PMID:20859448

  9. Closed-loop, open-source electrophysiology.

    PubMed

    Rolston, John D; Gross, Robert E; Potter, Steve M

    2010-01-01

    Multiple extracellular microelectrodes (multi-electrode arrays, or MEAs) effectively record rapidly varying neural signals, and can also be used for electrical stimulation. Multi-electrode recording can serve as artificial output (efferents) from a neural system, while complex spatially and temporally targeted stimulation can serve as artificial input (afferents) to the neuronal network. Multi-unit or local field potential (LFP) recordings can not only be used to control real world artifacts, such as prostheses, computers or robots, but can also trigger or alter subsequent stimulation. Real-time feedback stimulation may serve to modulate or normalize aberrant neural activity, to induce plasticity, or to serve as artificial sensory input. Despite promising closed-loop applications, commercial electrophysiology systems do not yet take advantage of the bidirectional capabilities of multi-electrodes, especially for use in freely moving animals. We addressed this lack of tools for closing the loop with NeuroRighter, an open-source system including recording hardware, stimulation hardware, and control software with a graphical user interface. The integrated system is capable of multi-electrode recording and simultaneous patterned microstimulation (triggered by recordings) with minimal stimulation artifact. The potential applications of closed-loop systems as research tools and clinical treatments are broad; we provide one example where epileptic activity recorded by a multi-electrode probe is used to trigger targeted stimulation, via that probe, to freely moving rodents. PMID:20859448

  10. XNAT Central: Open sourcing imaging research data.

    PubMed

    Herrick, Rick; Horton, William; Olsen, Timothy; McKay, Michael; Archie, Kevin A; Marcus, Daniel S

    2016-01-01

    XNAT Central is a publicly accessible medical imaging data repository based on the XNAT open-source imaging informatics platform. It hosts a wide variety of research imaging data sets. The primary motivation for creating XNAT Central was to provide a central repository to host and provide access to a wide variety of neuroimaging data. In this capacity, XNAT Central hosts a number of data sets from research labs and investigative efforts from around the world, including the OASIS Brains imaging studies, the NUSDAST study of schizophrenia, and more. Over time, XNAT Central has expanded to include imaging data from many different fields of research, including oncology, orthopedics, cardiology, and animal studies, but continues to emphasize neuroimaging data. Through the use of XNAT's DICOM metadata extraction capabilities, XNAT Central provides a searchable repository of imaging data that can be referenced by groups, labs, or individuals working in many different areas of research. The future development of XNAT Central will be geared towards greater ease of use as a reference library of heterogeneous neuroimaging data and associated synthetic data. It will also become a tool for making data available supporting published research and academic articles.

  11. Zherlock: an open source data analysis software.

    PubMed

    Alsberg, B K; Kirkhus, L; Hagen, R; Knudsen, O; Tangstad, T; Anderssen, E

    2003-01-01

    Zherlock is an open source software that provides state-of-the-art data analysis tools to the user in an intuitive and flexible way. It is a front-end to different numerical "engines" to produce a seamless integration of algorithms written in different computer languages. Of particular interest is creating an interface to high-level scientific languages such as Octave (a Matlab clone) and R (an S-PLUS clone) to enable efficient porting of new data analytical methods. Zherlock uses advanced scientific visualization tools in 2-D and 3-D and has been extended to work on virtual reality (VR) systems. Central to Zherlock is a visual programming environment (VPE) which enables diagram based programming. These diagrams consist of nodes and connection lines where each node is an operator or a method and lines describe the flow of data between nodes. A VPE is chosen for Zherlock because it forms an effective way to control the processing pipeline in complex data analyses. The VPE is similar in functionality to other programs such as IRIS Explorer, AVS or LabVIEW. PMID:14758979

  12. ENKI - An Open Source environmental modelling platfom

    NASA Astrophysics Data System (ADS)

    Kolberg, S.; Bruland, O.

    2012-04-01

    The ENKI software framework for implementing spatio-temporal models is now released under the LGPL license. Originally developed for evaluation and comparison of distributed hydrological model compositions, ENKI can be used for simulating any time-evolving process over a spatial domain. The core approach is to connect a set of user specified subroutines into a complete simulation model, and provide all administrative services needed to calibrate and run that model. This includes functionality for geographical region setup, all file I/O, calibration and uncertainty estimation etc. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines and various model compositions in a fixed framework. The open-source license and modular design of ENKI will also facilitate rapid dissemination of new methods to institutions engaged in operational water resource management. ENKI uses a plug-in structure to invoke separately compiled subroutines, separately built as dynamic-link libraries (dlls). The source code of an ENKI routine is highly compact, with a narrow framework-routine interface allowing the main program to recognise the number, types, and names of the routine's variables. The framework then exposes these variables to the user within the proper context, ensuring that distributed maps coincide spatially, time series exist for input variables, states are initialised, GIS data sets exist for static map data, manually or automatically calibrated values for parameters etc. By using function calls and memory data structures to invoke routines and facilitate information flow, ENKI provides good performance. For a typical distributed hydrological model setup in a spatial domain of 25000 grid cells, 3-4 time steps simulated per second should be expected. Future adaptation to parallel processing may further increase this speed. New modifications to ENKI include a full separation of API and user interface

  13. OpenCFU, a new free and open-source software to count cell colonies and other circular objects.

    PubMed

    Geissmann, Quentin

    2013-01-01

    Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.

  14. Open Source Initiative Powers Real-Time Data Streams

    NASA Technical Reports Server (NTRS)

    2014-01-01

    Under an SBIR contract with Dryden Flight Research Center, Creare Inc. developed a data collection tool called the Ring Buffered Network Bus. The technology has now been released under an open source license and is hosted by the Open Source DataTurbine Initiative. DataTurbine allows anyone to stream live data from sensors, labs, cameras, ocean buoys, cell phones, and more.

  15. Open Source for Knowledge and Learning Management: Strategies beyond Tools

    ERIC Educational Resources Information Center

    Lytras, Miltiadis, Ed.; Naeve, Ambjorn, Ed.

    2007-01-01

    In the last years, knowledge and learning management have made a significant impact on the IT research community. "Open Source for Knowledge and Learning Management: Strategies Beyond Tools" presents learning and knowledge management from a point of view where the basic tools and applications are provided by open source technologies. This book…

  16. Integrating an Automatic Judge into an Open Source LMS

    ERIC Educational Resources Information Center

    Georgouli, Katerina; Guerreiro, Pedro

    2011-01-01

    This paper presents the successful integration of the evaluation engine of Mooshak into the open source learning management system Claroline. Mooshak is an open source online automatic judge that has been used for international and national programming competitions. although it was originally designed for programming competitions, Mooshak has also…

  17. Open-Source Unionism: New Workers, New Strategies

    ERIC Educational Resources Information Center

    Schmid, Julie M.

    2004-01-01

    In "Open-Source Unionism: Beyond Exclusive Collective Bargaining," published in fall 2002 in the journal Working USA, labor scholars Richard B. Freeman and Joel Rogers use the term "open-source unionism" to describe a form of unionization that uses Web technology to organize in hard-to-unionize workplaces. Rather than depend on the traditional…

  18. Open Source Communities in Technical Writing: Local Exigence, Global Extensibility

    ERIC Educational Resources Information Center

    Conner, Trey; Gresham, Morgan; McCracken, Jill

    2011-01-01

    By offering open-source software (OSS)-based networks as an affordable technology alternative, we partnered with a nonprofit community organization. In this article, we narrate the client-based experiences of this partnership, highlighting the ways in which OSS and open-source culture (OSC) transformed our students' and our own expectations of…

  19. Migrations of the Mind: The Emergence of Open Source Education

    ERIC Educational Resources Information Center

    Glassman, Michael; Bartholomew, Mitchell; Jones, Travis

    2011-01-01

    The authors describe an Open Source approach to education. They define Open Source Education (OSE) as a teaching and learning framework where the use and presentation of information is non-hierarchical, malleable, and subject to the needs and contributions of students as they become "co-owners" of the course. The course transforms itself into an…

  20. Open Source as Appropriate Technology for Global Education

    ERIC Educational Resources Information Center

    Carmichael, Patrick; Honour, Leslie

    2002-01-01

    Economic arguments for the adoption of "open source" software in business have been widely discussed. In this paper we draw on personal experience in the UK, South Africa and Southeast Asia to forward compelling reasons why open source software should be considered as an appropriate and affordable alternative to the currently prevailing dependency…

  1. Getting Open Source Software into Schools: Strategies and Challenges

    ERIC Educational Resources Information Center

    Hepburn, Gary; Buley, Jan

    2006-01-01

    In this article Gary Hepburn and Jan Buley outline different approaches to implementing open source software (OSS) in schools; they also address the challenges that open source advocates should anticipate as they try to convince educational leaders to adopt OSS. With regard to OSS implementation, they note that schools have a flexible range of…

  2. Open source software engineering for geoscientific modeling applications

    NASA Astrophysics Data System (ADS)

    Bilke, L.; Rink, K.; Fischer, T.; Kolditz, O.

    2012-12-01

    , static analysis tools) - Informs developers on errors (via email) - Generates source code documentation - Provides binaries for end users These points enhance the software development process considerably. Firstly, platform independence is maintained. Additionally, errors in the source code can be tracked down easily. Lastly, developers gain access to code analysis tools and up-to-date source code documentation.; Overview of the OpenGeoSys software engineering workflow

  3. Integrating HCI Specialists into Open Source Software Development Projects

    NASA Astrophysics Data System (ADS)

    Hedberg, Henrik; Iivari, Netta

    Typical open source software (OSS) development projects are organized around technically talented developers, whose communication is based on technical aspects and source code. Decision-making power is gained through proven competence and activity in the project, and non-technical end-user opinions are too many times neglected. In addition, also human-computer interaction (HCI) specialists have encountered difficulties in trying to participate in OSS projects, because there seems to be no clear authority and responsibility for them. In this paper, based on HCI and OSS literature, we introduce an extended OSS development project organization model that adds a new level of communication and roles for attending human aspects of software. The proposed model makes the existence of HCI specialists visible in the projects, and promotes interaction between developers and the HCI specialists in the course of a project.

  4. Clarity: an open-source manager for laboratory automation.

    PubMed

    Delaney, Nigel F; Rojas Echenique, José I; Marx, Christopher J

    2013-04-01

    Software to manage automated laboratories, when interfaced with hardware instruments, gives users a way to specify experimental protocols and schedule activities to avoid hardware conflicts. In addition to these basics, modern laboratories need software that can run multiple different protocols in parallel and that can be easily extended to interface with a constantly growing diversity of techniques and instruments. We present Clarity, a laboratory automation manager that is hardware agnostic, portable, extensible, and open source. Clarity provides critical features including remote monitoring, robust error reporting by phone or email, and full state recovery in the event of a system crash. We discuss the basic organization of Clarity, demonstrate an example of its implementation for the automated analysis of bacterial growth, and describe how the program can be extended to manage new hardware. Clarity is mature, well documented, actively developed, written in C# for the Common Language Infrastructure, and is free and open-source software. These advantages set Clarity apart from currently available laboratory automation programs. The source code and documentation for Clarity is available at http://code.google.com/p/osla/.

  5. Learning from hackers: open-source clinical trials.

    PubMed

    Dunn, Adam G; Day, Richard O; Mandl, Kenneth D; Coiera, Enrico

    2012-05-01

    Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. A similar gap was addressed in the software industry by their open-source software movement. Here, we examine how the social and technical principles of the movement can guide the growth of an open-source clinical trial community.

  6. Efficient Open Source Lidar for Desktop Users

    NASA Astrophysics Data System (ADS)

    Flanagan, Jacob P.

    Lidar --- Light Detection and Ranging --- is a remote sensing technology that utilizes a device similar to a rangefinder to determine a distance to a target. A laser pulse is shot at an object and the time it takes for the pulse to return in measured. The distance to the object is easily calculated using the speed property of light. For lidar, this laser is moved (primarily in a rotational movement usually accompanied by a translational movement) and records the distances to objects several thousands of times per second. From this, a 3 dimensional structure can be procured in the form of a point cloud. A point cloud is a collection of 3 dimensional points with at least an x, a y and a z attribute. These 3 attributes represent the position of a single point in 3 dimensional space. Other attributes can be associated with the points that include properties such as the intensity of the return pulse, the color of the target or even the time the point was recorded. Another very useful, post processed attribute is point classification where a point is associated with the type of object the point represents (i.e. ground.). Lidar has gained popularity and advancements in the technology has made its collection easier and cheaper creating larger and denser datasets. The need to handle this data in a more efficiently manner has become a necessity; The processing, visualizing or even simply loading lidar can be computationally intensive due to its very large size. Standard remote sensing and geographical information systems (GIS) software (ENVI, ArcGIS, etc.) was not originally built for optimized point cloud processing and its implementation is an afterthought and therefore inefficient. Newer, more optimized software for point cloud processing (QTModeler, TopoDOT, etc.) usually lack more advanced processing tools, requires higher end computers and are very costly. Existing open source lidar approaches the loading and processing of lidar in an iterative fashion that requires

  7. TLSpy: An Open-Source Addition to Terrestrial Lidar Workflows

    NASA Astrophysics Data System (ADS)

    Frechette, J. D.; Weissmann, G. S.; Wawrzyniec, T. F.

    2008-12-01

    Terrestrial lidar scanners (TLS) that capture three dimensional (3D) geometry with cm scale precision present many new opportunities in the Earth Sciences and related fields. However, the lack of domain specific tools impedes full and efficient utilization of the information contained in these datasets. Most processing and analysis is performed using a variety of manufacturing, surveying, airborne lidar, and GIS software. Although much overlap exists, inevitably some needs are not addressed by these applications. TLSpy provides a plugin driven framework with 3D visualization capabilities that encourages researchers to fill these gaps. The goal is to free researchers from the intellectual overhead imposed by user and data interface design, enabling rapid development of TLS specific processing and analysis algorithms. We present two plugins as examples of problems that TLSpy is being applied to. The first plugin corrects for the strong influence of target orientation on TLS measured reflectance intensities. It calculates the distribution of incidence angles and intensities in an input scan and assists the user in fitting a reflectance model to the distribution. The model is then used to normalize input intensities, minimizing the impact of surface orientation and simplifying the extraction of quantitative data from reflectance measurements. Although reasonable default models can be determined the large number of factors influencing reflectance values require that the plugin be designed for maximum flexibility, allowing the user to adjust all model parameters and define new reflectance models as needed. The second plugin helps eliminate multipath reflections from water surfaces. Characterized by a lower intensity mirror image of the subaerial bank appearing below the water surface, these reflections are a common problem in scans containing water. These erroneous reflections can be removed by manually selecting points that lie on the waterline, fitting a plane to the points, and deleting points below that plane. This plugin simplifies the process by automatically identifying waterline points using characteristic changes in geometry and intensity. Automatic identification is often faster and more reliable than manual identification, however, manual control is retained as a fallback for degenerate cases.

  8. OpenOrb: Open-source asteroid orbit computation software including statistical ranging

    NASA Astrophysics Data System (ADS)

    Granvik, M.; Virtanen, J.; Oszkiewicz, D.; Muinonen, K.

    2009-01-01

    We are making an open-source asteroid orbit computation software package called OpenOrb publicly available. OpenOrb is built on a well-established Bayesian inversion theory, which means that it is to a large part complementary to orbit-computation packages currently available. In particular, OpenOrb is the first package that contains tools for rigorously estimating the uncertainties resulting from the inverse problem of computing orbital elements using scarce astrometry. In addition to the well-known least-squares method, OpenOrb also contains both Monte-Carlo (MC) and Markov-Chain MC (MCMC; Oszkiewicz et al. [2009]) versions of the statistical ranging method. Ranging allows the user to obtain sampled, non-Gaussian orbital-element probability-density functions and is therefore optimized for cases where the amount of astrometry is scarce or spans a relatively short time interval. Ranging-based methods have successfully been applied to a variety of different problems such as rigorous ephemeris prediction, orbital element distribution studies for transneptunian objects, the computation of invariant collision probabilities between near-Earth objects and the Earth, detection of linkages between astrometric asteroid observations within an apparition as well as between apparitions, and in the rigorous analysis of the impact of orbital arc length and/or astrometric uncertainty on the uncertainty of the resulting orbits. Tools for making ephemeris predictions and for classifying objects based on their orbits are also available in OpenOrb. As an example, we use OpenOrb in the search for candidate retrograde and/or high-inclination objects similar to 2008 KV42 in the known population of transneptunian objects that have an observational time span shorter than 30 days.

  9. 10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... REQUIREMENTS FOR WELL LOGGING Equipment § 39.43 Inspection, maintenance, and opening of a source or source holder. (a) Each licensee shall visually check source holders, logging tools, and source handling tools... holders, logging tools, injection tools, source handling tools, storage containers, transport...

  10. Spatial Information Processing: Standards-Based Open Source Visualization Technology

    NASA Astrophysics Data System (ADS)

    Hogan, P.

    2009-12-01

    elements. World Wind therefore changed its mission from providing a single information browser to enabling a whole class of 3D geographic applications. Instead of creating a single program, World Wind is a suite of components that can be selectively used in any number of programs. World Wind technology can be a part of any application, or it can be a window in a web page. Or it can be extended with additional functionalities by application and web developers. World Wind makes it possible to include virtual globe visualization and server technology in support of any objective. The world community can continually benefit from advances made in the technology by NASA in concert with the world community. 3. OPEN SOURCE AND OPEN STANDARDS NASA World Wind is NASA Open Source software. This means that the source code is fully accessible for anyone to freely use, even in association with proprietary technology. Imagery and other data provided by the World Wind servers reside in the public domain, including the data server technology itself. This allows others to deliver their own geospatial data and to provide custom solutions based on users specific needs.

  11. Guidelines for the implementation of an open source information system

    SciTech Connect

    Doak, J.; Howell, J.A.

    1995-08-01

    This work was initially performed for the International Atomic Energy Agency (IAEA) to help with the Open Source Task of the 93 + 2 Initiative; however, the information should be of interest to anyone working with open sources. The authors cover all aspects of an open source information system (OSIS) including, for example, identifying relevant sources, understanding copyright issues, and making information available to analysts. They foresee this document as a reference point that implementors of a system could augment for their particular needs. The primary organization of this document focuses on specific aspects, or components, of an OSIS; they describe each component and often make specific recommendations for its implementation. This document also contains a section discussing the process of collecting open source data and a section containing miscellaneous information. The appendix contains a listing of various providers, producers, and databases that the authors have come across in their research.

  12. Leveraging Open Source Technologies to Build Scientific Data Systems

    NASA Astrophysics Data System (ADS)

    Crichton, D. J.; Mattmann, C. A.; Hart, A.; Hughes, J. S.; Hardman, S.; Law, E.; Kelly, S.

    2011-12-01

    occurring between teams to ensure that high quality systems are being developed in cost effective ways. In addition, we have been careful to ensure that appropriate architectural boundaries have been observed to separate the common data management components in Apache OODT from the discipline specific requirements that need to be met in our software system deployments. Science, particularly Earth Science, is well positioned to embrace a collaborative software development model across institutions and agencies, both to share data and promote interoperability at a systems level, as well as to promote open source development for building and evolving fundamental software infrastructure components for data management. We believe that this paradigm shift is critical to improving both the capability and cost effectiveness of the systems, and that it will ultimately lead to improvements in software and data reuse.

  13. Open Source, Meet "User-Generated Science"

    ERIC Educational Resources Information Center

    Huwe, Terence K.

    2009-01-01

    This article discusses Research Blogging, a community-run nonprofit organization that is promoting a suite of blogging software to scholars. Research Blogging itself does two things. First, it extends an invitation to a community, and it is open to anyone. Second, it requires its users to follow guidelines. The combination of rigorous guidelines…

  14. OMPC: an Open-Source MATLAB-to-Python Compiler.

    PubMed

    Jurica, Peter; van Leeuwen, Cees

    2009-01-01

    Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

  15. Percolation model with an additional source of disorder

    NASA Astrophysics Data System (ADS)

    Kundu, Sumanta; Manna, S. S.

    2016-06-01

    The ranges of transmission of the mobiles in a mobile ad hoc network are not uniform in reality. They are affected by the temperature fluctuation in air, obstruction due to the solid objects, even the humidity difference in the environment, etc. How the varying range of transmission of the individual active elements affects the global connectivity in the network may be an important practical question to ask. Here a model of percolation phenomena, with an additional source of disorder, is introduced for a theoretical understanding of this problem. As in ordinary percolation, sites of a square lattice are occupied randomly with probability p . Each occupied site is then assigned a circular disk of random value R for its radius. A bond is defined to be occupied if and only if the radii R1 and R2 of the disks centered at the ends satisfy a certain predefined condition. In a very general formulation, one divides the R1-R2 plane into two regions by an arbitrary closed curve. One defines a point within one region as representing an occupied bond; otherwise it is a vacant bond. The study of three different rules under this general formulation indicates that the percolation threshold always varies continuously. This threshold has two limiting values, one is pc(sq) , the percolation threshold for the ordinary site percolation on the square lattice, and the other is unity. The approach of the percolation threshold to its limiting values are characterized by two exponents. In a special case, all lattice sites are occupied by disks of random radii R ∈{0 ,R0} and a percolation transition is observed with R0 as the control variable, similar to the site occupation probability.

  16. Percolation model with an additional source of disorder.

    PubMed

    Kundu, Sumanta; Manna, S S

    2016-06-01

    The ranges of transmission of the mobiles in a mobile ad hoc network are not uniform in reality. They are affected by the temperature fluctuation in air, obstruction due to the solid objects, even the humidity difference in the environment, etc. How the varying range of transmission of the individual active elements affects the global connectivity in the network may be an important practical question to ask. Here a model of percolation phenomena, with an additional source of disorder, is introduced for a theoretical understanding of this problem. As in ordinary percolation, sites of a square lattice are occupied randomly with probability p. Each occupied site is then assigned a circular disk of random value R for its radius. A bond is defined to be occupied if and only if the radii R_{1} and R_{2} of the disks centered at the ends satisfy a certain predefined condition. In a very general formulation, one divides the R_{1}-R_{2} plane into two regions by an arbitrary closed curve. One defines a point within one region as representing an occupied bond; otherwise it is a vacant bond. The study of three different rules under this general formulation indicates that the percolation threshold always varies continuously. This threshold has two limiting values, one is p_{c}(sq), the percolation threshold for the ordinary site percolation on the square lattice, and the other is unity. The approach of the percolation threshold to its limiting values are characterized by two exponents. In a special case, all lattice sites are occupied by disks of random radii R∈{0,R_{0}} and a percolation transition is observed with R_{0} as the control variable, similar to the site occupation probability.

  17. Percolation model with an additional source of disorder.

    PubMed

    Kundu, Sumanta; Manna, S S

    2016-06-01

    The ranges of transmission of the mobiles in a mobile ad hoc network are not uniform in reality. They are affected by the temperature fluctuation in air, obstruction due to the solid objects, even the humidity difference in the environment, etc. How the varying range of transmission of the individual active elements affects the global connectivity in the network may be an important practical question to ask. Here a model of percolation phenomena, with an additional source of disorder, is introduced for a theoretical understanding of this problem. As in ordinary percolation, sites of a square lattice are occupied randomly with probability p. Each occupied site is then assigned a circular disk of random value R for its radius. A bond is defined to be occupied if and only if the radii R_{1} and R_{2} of the disks centered at the ends satisfy a certain predefined condition. In a very general formulation, one divides the R_{1}-R_{2} plane into two regions by an arbitrary closed curve. One defines a point within one region as representing an occupied bond; otherwise it is a vacant bond. The study of three different rules under this general formulation indicates that the percolation threshold always varies continuously. This threshold has two limiting values, one is p_{c}(sq), the percolation threshold for the ordinary site percolation on the square lattice, and the other is unity. The approach of the percolation threshold to its limiting values are characterized by two exponents. In a special case, all lattice sites are occupied by disks of random radii R∈{0,R_{0}} and a percolation transition is observed with R_{0} as the control variable, similar to the site occupation probability. PMID:27415234

  18. Open source IPSEC software in manned and unmanned space missions

    NASA Astrophysics Data System (ADS)

    Edwards, Jacob

    Network security is a major topic of research because cyber attackers pose a threat to national security. Securing ground-space communications for NASA missions is important because attackers could endanger mission success and human lives. This thesis describes how an open source IPsec software package was used to create a secure and reliable channel for ground-space communications. A cost efficient, reproducible hardware testbed was also created to simulate ground-space communications. The testbed enables simulation of low-bandwidth and high latency communications links to experiment how the open source IPsec software reacts to these network constraints. Test cases were built that allowed for validation of the testbed and the open source IPsec software. The test cases also simulate using an IPsec connection from mission control ground routers to points of interest in outer space. Tested open source IPsec software did not meet all the requirements. Software changes were suggested to meet requirements.

  19. Open Source Solutions for Libraries: ABCD vs Koha

    ERIC Educational Resources Information Center

    Macan, Bojan; Fernandez, Gladys Vanesa; Stojanovski, Jadranka

    2013-01-01

    Purpose: The purpose of this study is to present an overview of the two open source (OS) integrated library systems (ILS)--Koha and ABCD (ISIS family), to compare their "next-generation library catalog" functionalities, and to give comparison of other important features available through ILS modules. Design/methodology/approach: Two open source…

  20. Modular Open-Source Software for Item Factor Analysis

    ERIC Educational Resources Information Center

    Pritikin, Joshua N.; Hunter, Micheal D.; Boker, Steven M.

    2015-01-01

    This article introduces an item factor analysis (IFA) module for "OpenMx," a free, open-source, and modular statistical modeling package that runs within the R programming environment on GNU/Linux, Mac OS X, and Microsoft Windows. The IFA module offers a novel model specification language that is well suited to programmatic generation…

  1. Managing Digital Archives Using Open Source Software Tools

    NASA Astrophysics Data System (ADS)

    Barve, S.; Dongare, S.

    2007-10-01

    This paper describes the use of open source software tools such as MySQL and PHP for creating database-backed websites. Such websites offer many advantages over ones built from static HTML pages. This paper will discuss how OSS tools are used and their benefits, and after the successful implementation of these tools how the library took the initiative in implementing an institutional repository using DSpace open source software.

  2. Using R to implement spatial analysis in open source environment

    NASA Astrophysics Data System (ADS)

    Shao, Yixi; Chen, Dong; Zhao, Bo

    2007-06-01

    R is an open source (GPL) language and environment for spatial analysis, statistical computing and graphics which provides a wide variety of statistical and graphical techniques, and is highly extensible. In the Open Source environment it plays an important role in doing spatial analysis. So, to implement spatial analysis in the Open Source environment which we called the Open Source geocomputation is using the R data analysis language integrated with GRASS GIS and MySQL or PostgreSQL. This paper explains the architecture of the Open Source GIS environment and emphasizes the role R plays in the aspect of spatial analysis. Furthermore, one apt illustration of the functions of R is given in this paper through the project of constructing CZPGIS (Cheng Zhou Population GIS) supported by Changzhou Government, China. In this project we use R to implement the geostatistics in the Open Source GIS environment to evaluate the spatial correlation of land price and estimate it by Kriging Interpolation. We also use R integrated with MapServer and php to show how R and other Open Source software cooperate with each other in WebGIS environment, which represents the advantages of using R to implement spatial analysis in Open Source GIS environment. And in the end, we points out that the packages for spatial analysis in R is still scattered and the limited memory is still a bottleneck when large sum of clients connect at the same time. Therefore further work is to group the extensive packages in order or design normative packages and make R cooperate better with other commercial software such as ArcIMS. Also we look forward to developing packages for land price evaluation.

  3. Open Source Software Licenses for Livermore National Laboratory

    SciTech Connect

    Busby, L.

    2000-08-10

    This paper attempts to develop supporting material in an effort to provide new options for licensing Laboratory-created software. Where employees and the Lab wish to release software codes as so-called ''Open Source'', they need, at a minimum, new licensing language for their released products. Several open source software licenses are reviewed to understand their common elements, and develop recommendations regarding new language.

  4. Open source data assimilation framework for hydrological modeling

    NASA Astrophysics Data System (ADS)

    Ridler, Marc; Hummel, Stef; van Velzen, Nils; Katrine Falk, Anne; Madsen, Henrik

    2013-04-01

    An open-source data assimilation framework is proposed for hydrological modeling. Data assimilation (DA) in hydrodynamic and hydrological forecasting systems has great potential to improve predictions and improve model result. The basic principle is to incorporate measurement information into a model with the aim to improve model results by error minimization. Great strides have been made to assimilate traditional in-situ measurements such as discharge, soil moisture, hydraulic head and snowpack into hydrologic models. More recently, remotely sensed data retrievals of soil moisture, snow water equivalent or snow cover area, surface water elevation, terrestrial water storage and land surface temperature have been successfully assimilated in hydrological models. The assimilation algorithms have become increasingly sophisticated to manage measurement and model bias, non-linear systems, data sparsity (time & space) and undetermined system uncertainty. It is therefore useful to use a pre-existing DA toolbox such as OpenDA. OpenDA is an open interface standard for (and free implementation of) a set of tools to quickly implement DA and calibration for arbitrary numerical models. The basic design philosophy of OpenDA is to breakdown DA into a set of building blocks programmed in object oriented languages. To implement DA, a model must interact with OpenDA to create model instances, propagate the model, get/set variables (or parameters) and free the model once DA is completed. An open-source interface for hydrological models exists capable of all these tasks: OpenMI. OpenMI is an open source standard interface already adopted by key hydrological model providers. It defines a universal approach to interact with hydrological models during simulation to exchange data during runtime, thus facilitating the interactions between models and data sources. The interface is flexible enough so that models can interact even if the model is coded in a different language, represent

  5. Open Source and ROI: Open Source Has Made Significant Leaps in Recent Years. What Does It Have to Offer Education?

    ERIC Educational Resources Information Center

    Guhlin, Miguel

    2007-01-01

    A switch to free open source software can minimize cost and allow funding to be diverted to equipment and other programs. For instance, the OpenOffice suite is an alternative to expensive basic application programs offered by major vendors. Many such programs on the market offer features seldom used in education but for which educators must pay.…

  6. Your Personal Analysis Toolkit - An Open Source Solution

    NASA Astrophysics Data System (ADS)

    Mitchell, T.

    2009-12-01

    Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

  7. The Imagery Exchange (TIE): Open Source Imagery Management System

    NASA Astrophysics Data System (ADS)

    Alarcon, C.; Huang, T.; Thompson, C. K.; Roberts, J. T.; Hall, J. R.; Cechini, M.; Schmaltz, J. E.; McGann, J. M.; Boller, R. A.; Murphy, K. J.; Bingham, A. W.

    2013-12-01

    The NASA's Global Imagery Browse Service (GIBS) is the Earth Observation System (EOS) imagery solution for delivering global, full-resolution satellite imagery in a highly responsive manner. GIBS consists of two major subsystems, OnEarth and The Imagery Exchange (TIE). TIE is the GIBS horizontally scaled imagery workflow manager component, an Open Archival Information System (OAIS) responsible for orchestrating the acquisition, preparation, generation, and archiving of imagery to be served by OnEarth. TIE is an extension of the Data Management and Archive System (DMAS), a high performance data management system developed at the Jet Propulsion Laboratory by leveraging open source tools and frameworks, which includes Groovy/Grails, Restlet, Apache ZooKeeper, Apache Solr, and other open source solutions. This presentation focuses on the application of Open Source technologies in developing a horizontally scaled data system like DMAS and TIE. As part of our commitment in contributing back to the open source community, TIE is in the process of being open sourced. This presentation will also cover our current effort in getting TIE in to the hands of the community from which we benefited from.

  8. Improving Data Catalogs with Free and Open Source Software

    NASA Astrophysics Data System (ADS)

    Schweitzer, R.; Hankin, S.; O'Brien, K.

    2013-12-01

    The Global Earth Observation Integrated Data Environment (GEO-IDE) is NOAA's effort to successfully integrate data and information with partners in the national US-Global Earth Observation System (US-GEO) and the international Global Earth Observation System of Systems (GEOSS). As part of the GEO-IDE, the Unified Access Framework (UAF) is working to build momentum towards the goal of increased data integration and interoperability. The UAF project is moving towards this goal with an approach that includes leveraging well known and widely used standards, as well as free and open source software. The UAF project shares the widely held conviction that the use of data standards is a key ingredient necessary to achieve interoperability. Many community-based consensus standards fail, though, due to poor compliance. Compliance problems emerge for many reasons: because the standards evolve through versions, because documentation is ambiguous or because individual data providers find the standard inadequate as-is to meet their special needs. In addition, minimalist use of standards will lead to a compliant service, but one which is of low quality. In this presentation, we will be discussing the UAF effort to build a catalog cleaning tool which is designed to crawl THREDDS catalogs, analyze the data available, and then build a 'clean' catalog of data which is standards compliant and has a uniform set of data access services available. These data services include, among others, OPeNDAP, Web Coverage Service (WCS) and Web Mapping Service (WMS). We will also discuss how we are utilizing free and open source software and services to both crawl, analyze and build the clean data catalog, as well as our efforts to help data providers improve their data catalogs. We'll discuss the use of open source software such as DataNucleus, Thematic Realtime Environmental Distributed Data Services (THREDDS), ncISO and the netCDF Java Common Data Model (CDM). We'll also demonstrate how we are

  9. No Strings Attached: Open Source Solutions

    ERIC Educational Resources Information Center

    Fredricks, Kathy

    2009-01-01

    Imagine downloading a new software application and not having to worry about licensing, finding dollars in the budget, or incurring additional maintenance costs. Imagine finding a Web design tool in the public domain--free for use. Imagine major universities that provide online courses with no strings attached. Imagine online textbooks without a…

  10. A Framework for the Systematic Collection of Open Source Intelligence

    SciTech Connect

    Pouchard, Line Catherine; Trien, Joseph P; Dobson, Jonathan D

    2009-01-01

    Following legislative directions, the Intelligence Community has been mandated to make greater use of Open Source Intelligence (OSINT). Efforts are underway to increase the use of OSINT but there are many obstacles. One of these obstacles is the lack of tools helping to manage the volume of available data and ascertain its credibility. We propose a unique system for selecting, collecting and storing Open Source data from the Web and the Open Source Center. Some data management tasks are automated, document source is retained, and metadata containing geographical coordinates are added to the documents. Analysts are thus empowered to search, view, store, and analyze Web data within a single tool. We present ORCAT I and ORCAT II, two implementations of the system.

  11. The Future of ECHO: Evaluating Open Source Possibilities

    NASA Astrophysics Data System (ADS)

    Pilone, D.; Gilman, J.; Baynes, K.; Mitchell, A. E.

    2012-12-01

    NASA's Earth Observing System ClearingHOuse (ECHO) is a format agnostic metadata repository supporting over 3000 collections and 100M science granules. ECHO exposes FTP and RESTful Data Ingest APIs in addition to both SOAP and RESTful search and order capabilities. Built on top of ECHO is a human facing search and order web application named Reverb. ECHO processes hundreds of orders, tens of thousands of searches, and 1-2M ingest actions each week. As ECHO's holdings, metadata format support, and visibility have increased, the ECHO team has received requests by non-NASA entities for copies of ECHO that can be run locally against their data holdings. ESDIS and the ECHO Team have begun investigations into various deployment and Open Sourcing models that can balance the real constraints faced by the ECHO project with the benefits of providing ECHO capabilities to a broader set of users and providers. This talk will discuss several release and Open Source models being investigated by the ECHO team along with the impacts those models are expected to have on the project. We discuss: - Addressing complex deployment or setup issues for potential users - Models of vetting code contributions - Balancing external (public) user requests versus our primary partners - Preparing project code for public release, including navigating licensing issues related to leveraged libraries - Dealing with non-free project dependencies such as commercial databases - Dealing with sensitive aspects of project code such as database passwords, authentication approaches, security through obscurity, etc. - Ongoing support for the released code including increased testing demands, bug fixes, security fixes, and new features.

  12. Open Source Radiation Hardened by Design Technology

    NASA Technical Reports Server (NTRS)

    Shuler, Robert

    2016-01-01

    The proposed technology allows use of the latest microcircuit technology with lowest power and fastest speed, with minimal delay and engineering costs, through new Radiation Hardened by Design (RHBD) techniques that do not require extensive process characterization, technique evaluation and re-design at each Moore's Law generation. The separation of critical node groups is explicitly parameterized so it can be increased as microcircuit technologies shrink. The technology will be open access to radiation tolerant circuit vendors. INNOVATION: This technology would enhance computation intensive applications such as autonomy, robotics, advanced sensor and tracking processes, as well as low power applications such as wireless sensor networks. OUTCOME / RESULTS: 1) Simulation analysis indicates feasibility. 2)Compact voting latch 65 nanometer test chip designed and submitted for fabrication -7/2016. INFUSION FOR SPACE / EARTH: This technology may be used in any digital integrated circuit in which a high level of resistance to Single Event Upsets is desired, and has the greatest benefit outside low earth orbit where cosmic rays are numerous.

  13. Open Source Drug Discovery in Practice: A Case Study

    PubMed Central

    Årdal, Christine; Røttingen, John-Arne

    2012-01-01

    Background Open source drug discovery offers potential for developing new and inexpensive drugs to combat diseases that disproportionally affect the poor. The concept borrows two principle aspects from open source computing (i.e., collaboration and open access) and applies them to pharmaceutical innovation. By opening a project to external contributors, its research capacity may increase significantly. To date there are only a handful of open source R&D projects focusing on neglected diseases. We wanted to learn from these first movers, their successes and failures, in order to generate a better understanding of how a much-discussed theoretical concept works in practice and may be implemented. Methodology/Principal Findings A descriptive case study was performed, evaluating two specific R&D projects focused on neglected diseases. CSIR Team India Consortium's Open Source Drug Discovery project (CSIR OSDD) and The Synaptic Leap's Schistosomiasis project (TSLS). Data were gathered from four sources: interviews of participating members (n = 14), a survey of potential members (n = 61), an analysis of the websites and a literature review. Both cases have made significant achievements; however, they have done so in very different ways. CSIR OSDD encourages international collaboration, but its process facilitates contributions from mostly Indian researchers and students. Its processes are formal with each task being reviewed by a mentor (almost always offline) before a result is made public. TSLS, on the other hand, has attracted contributors internationally, albeit significantly fewer than CSIR OSDD. Both have obtained funding used to pay for access to facilities, physical resources and, at times, labor costs. TSLS releases its results into the public domain, whereas CSIR OSDD asserts ownership over its results. Conclusions/Significance Technically TSLS is an open source project, whereas CSIR OSDD is a crowdsourced project. However, both have enabled high quality

  14. Technology collaboration by means of an open source government

    NASA Astrophysics Data System (ADS)

    Berardi, Steven M.

    2009-05-01

    The idea of open source software originally began in the early 1980s, but it never gained widespread support until recently, largely due to the explosive growth of the Internet. Only the Internet has made this kind of concept possible, bringing together millions of software developers from around the world to pool their knowledge. The tremendous success of open source software has prompted many corporations to adopt the culture of open source and thus share information they previously held secret. The government, and specifically the Department of Defense (DoD), could also benefit from adopting an open source culture. In acquiring satellite systems, the DoD often builds walls between program offices, but installing doors between programs can promote collaboration and information sharing. This paper addresses the challenges and consequences of adopting an open source culture to facilitate technology collaboration for DoD space acquisitions. DISCLAIMER: The views presented here are the views of the author, and do not represent the views of the United States Government, United States Air Force, or the Missile Defense Agency.

  15. Comparison of open-source linear programming solvers.

    SciTech Connect

    Gearhart, Jared Lee; Adair, Kristin Lynn; Durfee, Justin David.; Jones, Katherine A.; Martin, Nathaniel; Detry, Richard Joseph

    2013-10-01

    When developing linear programming models, issues such as budget limitations, customer requirements, or licensing may preclude the use of commercial linear programming solvers. In such cases, one option is to use an open-source linear programming solver. A survey of linear programming tools was conducted to identify potential open-source solvers. From this survey, four open-source solvers were tested using a collection of linear programming test problems and the results were compared to IBM ILOG CPLEX Optimizer (CPLEX) [1], an industry standard. The solvers considered were: COIN-OR Linear Programming (CLP) [2], [3], GNU Linear Programming Kit (GLPK) [4], lp_solve [5] and Modular In-core Nonlinear Optimization System (MINOS) [6]. As no open-source solver outperforms CPLEX, this study demonstrates the power of commercial linear programming software. CLP was found to be the top performing open-source solver considered in terms of capability and speed. GLPK also performed well but cannot match the speed of CLP or CPLEX. lp_solve and MINOS were considerably slower and encountered issues when solving several test problems.

  16. Open-Source Selective Laser Sintering (OpenSLS) of Nylon and Biocompatible Polycaprolactone

    PubMed Central

    Paulsen, Samantha J.; Hwang, Daniel H.; Ta, Anderson H.; Yalacki, David R.; Schmidt, Tim; Miller, Jordan S.

    2016-01-01

    Selective Laser Sintering (SLS) is an additive manufacturing process that uses a laser to fuse powdered starting materials into solid 3D structures. Despite the potential for fabrication of complex, high-resolution structures with SLS using diverse starting materials (including biomaterials), prohibitive costs of commercial SLS systems have hindered the wide adoption of this technology in the scientific community. Here, we developed a low-cost, open-source SLS system (OpenSLS) and demonstrated its capacity to fabricate structures in nylon with sub-millimeter features and overhanging regions. Subsequently, we demonstrated fabrication of polycaprolactone (PCL) into macroporous structures such as a diamond lattice. Widespread interest in using PCL for bone tissue engineering suggests that PCL lattices are relevant model scaffold geometries for engineering bone. SLS of materials with large powder grain size (~500 μm) leads to part surfaces with high roughness, so we further introduced a simple vapor-smoothing technique to reduce the surface roughness of sintered PCL structures which further improves their elastic modulus and yield stress. Vapor-smoothed PCL can also be used for sacrificial templating of perfusable fluidic networks within orthogonal materials such as poly(dimethylsiloxane) silicone. Finally, we demonstrated that human mesenchymal stem cells were able to adhere, survive, and differentiate down an osteogenic lineage on sintered and smoothed PCL surfaces, suggesting that OpenSLS has the potential to produce PCL scaffolds useful for cell studies. OpenSLS provides the scientific community with an accessible platform for the study of laser sintering and the fabrication of complex geometries in diverse materials. PMID:26841023

  17. Evaluating open-source cloud computing solutions for geosciences

    NASA Astrophysics Data System (ADS)

    Huang, Qunying; Yang, Chaowei; Liu, Kai; Xia, Jizhe; Xu, Chen; Li, Jing; Gui, Zhipeng; Sun, Min; Li, Zhenglong

    2013-09-01

    Many organizations start to adopt cloud computing for better utilizing computing resources by taking advantage of its scalability, cost reduction, and easy to access characteristics. Many private or community cloud computing platforms are being built using open-source cloud solutions. However, little has been done to systematically compare and evaluate the features and performance of open-source solutions in supporting Geosciences. This paper provides a comprehensive study of three open-source cloud solutions, including OpenNebula, Eucalyptus, and CloudStack. We compared a variety of features, capabilities, technologies and performances including: (1) general features and supported services for cloud resource creation and management, (2) advanced capabilities for networking and security, and (3) the performance of the cloud solutions in provisioning and operating the cloud resources as well as the performance of virtual machines initiated and managed by the cloud solutions in supporting selected geoscience applications. Our study found that: (1) no significant performance differences in central processing unit (CPU), memory and I/O of virtual machines created and managed by different solutions, (2) OpenNebula has the fastest internal network while both Eucalyptus and CloudStack have better virtual machine isolation and security strategies, (3) Cloudstack has the fastest operations in handling virtual machines, images, snapshots, volumes and networking, followed by OpenNebula, and (4) the selected cloud computing solutions are capable for supporting concurrent intensive web applications, computing intensive applications, and small-scale model simulations without intensive data communication.

  18. Bioclipse: an open source workbench for chemo- and bioinformatics

    PubMed Central

    Spjuth, Ola; Helmus, Tobias; Willighagen, Egon L; Kuhn, Stefan; Eklund, Martin; Wagener, Johannes; Murray-Rust, Peter; Steinbeck, Christoph; Wikberg, Jarl ES

    2007-01-01

    Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at . PMID:17316423

  19. Additional muon calculations for the SLC positron source

    SciTech Connect

    Nelson, W.R.; McCall, R.C.

    1985-04-23

    This note is an update to the muon calculations presented in CN-221 and takes into account: (1) a more complete muon production and transport model, including an estimate of wide angle production based on experimental data, (2) additional earth shielding that will be added on top and both sides of the 2/3 tunnel areas, and (3) a detailed analysis of the earth profile as it pertains to shielding in the direction of the SLAC site boundary. The highest annual dose at the SLAC boundary is found to be 13 mrem/year (4000 hours of operation at 50 kW), and this occurs at a horizontal angle of 0 degrees and a vertical angle of 3.6 degrees relative to the incident beam direction. Although the shielding criteria is 10 mrem/year at the site boundary, the radiation transport model becomes somewhat conservative at large distances from the shield, which should bring the 13 mrem/year number actually well below the criteria. This point is also about 28 feet above the roadway. Extension of this line may strike the ground in the Christmas tree farm beyond the SLAC boundary but there will be additional attenuation due to distance. We do not recommend that any additional shielding be added at this time. 4 refs., 1 fig.

  20. Open source tools for ATR development and performance evaluation

    NASA Astrophysics Data System (ADS)

    Baumann, James M.; Dilsavor, Ronald L.; Stubbles, James; Mossing, John C.

    2002-07-01

    Early in almost every engineering project, a decision must be made about tools; should I buy off-the-shelf tools or should I develop my own. Either choice can involve significant cost and risk. Off-the-shelf tools may be readily available, but they can be expensive to purchase and to maintain licenses, and may not be flexible enough to satisfy all project requirements. On the other hand, developing new tools permits great flexibility, but it can be time- (and budget-) consuming, and the end product still may not work as intended. Open source software has the advantages of both approaches without many of the pitfalls. This paper examines the concept of open source software, including its history, unique culture, and informal yet closely followed conventions. These characteristics influence the quality and quantity of software available, and ultimately its suitability for serious ATR development work. We give an example where Python, an open source scripting language, and OpenEV, a viewing and analysis tool for geospatial data, have been incorporated into ATR performance evaluation projects. While this case highlights the successful use of open source tools, we also offer important insight into risks associated with this approach.

  1. Freeing Crop Genetics through the Open Source Seed Initiative

    PubMed Central

    Luby, Claire H.; Goldman, Irwin L.

    2016-01-01

    For millennia, seeds have been freely available to use for farming and plant breeding without restriction. Within the past century, however, intellectual property rights (IPRs) have threatened this tradition. In response, a movement has emerged to counter the trend toward increasing consolidation of control and ownership of plant germplasm. One effort, the Open Source Seed Initiative (OSSI, www.osseeds.org), aims to ensure access to crop genetic resources by embracing an open source mechanism that fosters exchange and innovation among farmers, plant breeders, and seed companies. Plant breeders across many sectors have taken the OSSI Pledge to create a protected commons of plant germplasm for future generations. PMID:27093567

  2. Human genome and open source: balancing ethics and business.

    PubMed

    Marturano, Antonio

    2011-01-01

    The Human Genome Project has been completed thanks to a massive use of computer techniques, as well as the adoption of the open-source business and research model by the scientists involved. This model won over the proprietary model and allowed a quick propagation and feedback of research results among peers. In this paper, the author will analyse some ethical and legal issues emerging by the use of such computer model in the Human Genome property rights. The author will argue that the Open Source is the best business model, as it is able to balance business and human rights perspectives.

  3. Open Source Next Generation Visualization Software for Interplanetary Missions

    NASA Technical Reports Server (NTRS)

    Trimble, Jay; Rinker, George

    2016-01-01

    Mission control is evolving quickly, driven by the requirements of new missions, and enabled by modern computing capabilities. Distributed operations, access to data anywhere, data visualization for spacecraft analysis that spans multiple data sources, flexible reconfiguration to support multiple missions, and operator use cases, are driving the need for new capabilities. NASA's Advanced Multi-Mission Operations System (AMMOS), Ames Research Center (ARC) and the Jet Propulsion Laboratory (JPL) are collaborating to build a new generation of mission operations software for visualization, to enable mission control anywhere, on the desktop, tablet and phone. The software is built on an open source platform that is open for contributions (http://nasa.github.io/openmct).

  4. Open source and DIY hardware for DNA nanotechnology labs

    PubMed Central

    Damase, Tulsi R.; Stephens, Daniel; Spencer, Adam; Allen, Peter B.

    2015-01-01

    A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%. PMID:26457320

  5. NASA's Open Source Software for Serving and Viewing Global Imagery

    NASA Astrophysics Data System (ADS)

    Roberts, J. T.; Alarcon, C.; Boller, R. A.; Cechini, M. F.; Gunnoe, T.; Hall, J. R.; Huang, T.; Ilavajhala, S.; King, J.; McGann, M.; Murphy, K. J.; Plesea, L.; Schmaltz, J. E.; Thompson, C. K.

    2014-12-01

    The NASA Global Imagery Browse Services (GIBS), which provide open access to an enormous archive of historical and near real time imagery from NASA supported satellite instruments, has also released most of its software to the general public as open source. The software packages, originally developed at the Jet Propulsion Laboratory and Goddard Space Flight Center, currently include: 1) the Meta Raster Format (MRF) GDAL driver—GDAL support for a specialized file format used by GIBS to store imagery within a georeferenced tile pyramid for exceptionally fast access; 2) OnEarth—a high performance Apache module used to serve tiles from MRF files via common web service protocols; 3) Worldview—a web mapping client to interactively browse global, full-resolution satellite imagery and download underlying data. Examples that show developers how to use GIBS with various mapping libraries and programs are also available. This stack of tools is intended to provide an out-of-the-box solution for serving any georeferenced imagery.Scientists as well as the general public can use the open source software for their own applications such as developing visualization interfaces for improved scientific understanding and decision support, hosting a repository of browse images to help find and discover satellite data, or accessing large datasets of geo-located imagery in an efficient manner. Open source users may also contribute back to NASA and the wider Earth Science community by taking an active role in evaluating and developing the software.This presentation will discuss the experiences of developing the software in an open source environment and useful lessons learned. To access the open source software repositories, please visit: https://github.com/nasa-gibs/

  6. Is Open Source the ERP Cure-All?

    ERIC Educational Resources Information Center

    Panettieri, Joseph C.

    2008-01-01

    Conventional and hosted applications thrive, but open source ERP (enterprise resource planning) is coming on strong. In many ways, the evolution of the ERP market is littered with ironies. When Oracle began buying up customer relationship management (CRM) and ERP companies, some universities worried that they would be left with fewer choices and…

  7. Faculty/Student Surveys Using Open Source Software

    ERIC Educational Resources Information Center

    Kaceli, Sali

    2004-01-01

    This session will highlight an easy survey package which lets non-technical users create surveys, administer surveys, gather results, and view statistics. This is an open source application all managed online via a web browser. By using phpESP, the faculty is given the freedom of creating various surveys at their convenience and link them to their…

  8. Bioconductor: an open source framework for bioinformatics and computational biology.

    PubMed

    Reimers, Mark; Carey, Vincent J

    2006-01-01

    This chapter describes the Bioconductor project and details of its open source facilities for analysis of microarray and other high-throughput biological experiments. Particular attention is paid to concepts of container and workflow design, connections of biological metadata to statistical analysis products, support for statistical quality assessment, and calibration of inference uncertainty measures when tens of thousands of simultaneous statistical tests are performed.

  9. Analysing the Social Networks constituted by Open Source communities

    NASA Astrophysics Data System (ADS)

    Concas, Giulio; Lisci, Manuela; Pinna, Sandro; Porruvecchio, Guido; Uras, Selene

    2008-11-01

    In this study on Open Source communities, we examined some important aspects about communication among participants to developers mailing lists. We utilized Social Network Analysis approach to analyse this particular kind of communities, in order to better understand interaction among members, individuate communicational flows and discover whether there is a subsequential community coordination and control.

  10. Open Source Software: Fully Featured vs. "The Devil You Know"

    ERIC Educational Resources Information Center

    Hotrum, Michael; Ludwig, Brian; Baggaley, Jon

    2005-01-01

    The "ILIAS" learning management system (LMS) was evaluated, following its favourable rating in an independent evaluation study of open source software (OSS) products. The current review found "ILIAS" to have numerous features of value to distance education (DE) students and teachers, as well as problems for consideration in the system's ongoing…

  11. The Value of Open Source Software Tools in Qualitative Research

    ERIC Educational Resources Information Center

    Greenberg, Gary

    2011-01-01

    In an era of global networks, researchers using qualitative methods must consider the impact of any software they use on the sharing of data and findings. In this essay, I identify researchers' main areas of concern regarding the use of qualitative software packages for research. I then examine how open source software tools, wherein the publisher…

  12. Higher Education Sub-Cultures and Open Source Adoption

    ERIC Educational Resources Information Center

    van Rooij, Shahron Williams

    2011-01-01

    Successful adoption of new teaching and learning technologies in higher education requires the consensus of two sub-cultures, namely the technologist sub-culture and the academic sub-culture. This paper examines trends in adoption of open source software (OSS) for teaching and learning by comparing the results of a 2009 survey of 285 Chief…

  13. Chinese Localisation of Evergreen: An Open Source Integrated Library System

    ERIC Educational Resources Information Center

    Zou, Qing; Liu, Guoying

    2009-01-01

    Purpose: The purpose of this paper is to investigate various issues related to Chinese language localisation in Evergreen, an open source integrated library system (ILS). Design/methodology/approach: A Simplified Chinese version of Evergreen was implemented and tested and various issues such as encoding, indexing, searching, and sorting…

  14. Digital Preservation in Open-Source Digital Library Software

    ERIC Educational Resources Information Center

    Madalli, Devika P.; Barve, Sunita; Amin, Saiful

    2012-01-01

    Digital archives and digital library projects are being initiated all over the world for materials of different formats and domains. To organize, store, and retrieve digital content, many libraries as well as archiving centers are using either proprietary or open-source software. While it is accepted that print media can survive for centuries with…

  15. The Case for Open Source Software in Digital Forensics

    NASA Astrophysics Data System (ADS)

    Zanero, Stefano; Huebner, Ewa

    In this introductory chapter we discuss the importance of the use of open source software (OSS), and in particular of free software (FLOSS) in computer forensics investigations including the identification, capture, preservation and analysis of digital evidence; we also discuss the importance of OSS in computer forensics

  16. Open Source Projects in Software Engineering Education: A Mapping Study

    ERIC Educational Resources Information Center

    Nascimento, Debora M. C.; Almeida Bittencourt, Roberto; Chavez, Christina

    2015-01-01

    Context: It is common practice in academia to have students work with "toy" projects in software engineering (SE) courses. One way to make such courses more realistic and reduce the gap between academic courses and industry needs is getting students involved in open source projects (OSP) with faculty supervision. Objective: This study…

  17. Critical Analysis on Open Source LMSs Using FCA

    ERIC Educational Resources Information Center

    Sumangali, K.; Kumar, Ch. Aswani

    2013-01-01

    The objective of this paper is to apply Formal Concept Analysis (FCA) to identify the best open source Learning Management System (LMS) for an E-learning environment. FCA is a mathematical framework that represents knowledge derived from a formal context. In constructing the formal context, LMSs are treated as objects and their features as…

  18. Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

    PubMed

    Teleman, Johan; Chawade, Aakash; Sandin, Marianne; Levander, Fredrik; Malmström, Johan

    2016-07-01

    In bottom-up mass spectrometry (MS)-based proteomics, peptide isotopic and chromatographic traces (features) are frequently used for label-free quantification in data-dependent acquisition MS but can also be used for the improved identification of chimeric spectra or sample complexity characterization. Feature detection is difficult because of the high complexity of MS proteomics data from biological samples, which frequently causes features to intermingle. In addition, existing feature detection algorithms commonly suffer from compatibility issues, long computation times, or poor performance on high-resolution data. Because of these limitations, we developed a new tool, Dinosaur, with increased speed and versatility. Dinosaur has the functionality to sample algorithm computations through quality-control plots, which we call a plot trail. From the evaluation of this plot trail, we introduce several algorithmic improvements to further improve the robustness and performance of Dinosaur, with the detection of features for 98% of MS/MS identifications in a benchmark data set, and no other algorithm tested in this study passed 96% feature detection. We finally used Dinosaur to reimplement a published workflow for peptide identification in chimeric spectra, increasing chimeric identification from 26% to 32% over the standard workflow. Dinosaur is operating-system-independent and is freely available as open source on https://github.com/fickludd/dinosaur . PMID:27224449

  19. Open-Source Telemedicine Platform for Wireless Medical Video Communication

    PubMed Central

    Panayides, A.; Eleftheriou, I.; Pantziaris, M.

    2013-01-01

    An m-health system for real-time wireless communication of medical video based on open-source software is presented. The objective is to deliver a low-cost telemedicine platform which will allow for reliable remote diagnosis m-health applications such as emergency incidents, mass population screening, and medical education purposes. The performance of the proposed system is demonstrated using five atherosclerotic plaque ultrasound videos. The videos are encoded at the clinically acquired resolution, in addition to lower, QCIF, and CIF resolutions, at different bitrates, and four different encoding structures. Commercially available wireless local area network (WLAN) and 3.5G high-speed packet access (HSPA) wireless channels are used to validate the developed platform. Objective video quality assessment is based on PSNR ratings, following calibration using the variable frame delay (VFD) algorithm that removes temporal mismatch between original and received videos. Clinical evaluation is based on atherosclerotic plaque ultrasound video assessment protocol. Experimental results show that adequate diagnostic quality wireless medical video communications are realized using the designed telemedicine platform. HSPA cellular networks provide for ultrasound video transmission at the acquired resolution, while VFD algorithm utilization bridges objective and subjective ratings. PMID:23573082

  20. Open source tools for standardized privacy protection of medical images

    NASA Astrophysics Data System (ADS)

    Lien, Chung-Yueh; Onken, Michael; Eichelberg, Marco; Kao, Tsair; Hein, Andreas

    2011-03-01

    In addition to the primary care context, medical images are often useful for research projects and community healthcare networks, so-called "secondary use". Patient privacy becomes an issue in such scenarios since the disclosure of personal health information (PHI) has to be prevented in a sharing environment. In general, most PHIs should be completely removed from the images according to the respective privacy regulations, but some basic and alleviated data is usually required for accurate image interpretation. Our objective is to utilize and enhance these specifications in order to provide reliable software implementations for de- and re-identification of medical images suitable for online and offline delivery. DICOM (Digital Imaging and Communications in Medicine) images are de-identified by replacing PHI-specific information with values still being reasonable for imaging diagnosis and patient indexing. In this paper, this approach is evaluated based on a prototype implementation built on top of the open source framework DCMTK (DICOM Toolkit) utilizing standardized de- and re-identification mechanisms. A set of tools has been developed for DICOM de-identification that meets privacy requirements of an offline and online sharing environment and fully relies on standard-based methods.

  1. Open-source telemedicine platform for wireless medical video communication.

    PubMed

    Panayides, A; Eleftheriou, I; Pantziaris, M

    2013-01-01

    An m-health system for real-time wireless communication of medical video based on open-source software is presented. The objective is to deliver a low-cost telemedicine platform which will allow for reliable remote diagnosis m-health applications such as emergency incidents, mass population screening, and medical education purposes. The performance of the proposed system is demonstrated using five atherosclerotic plaque ultrasound videos. The videos are encoded at the clinically acquired resolution, in addition to lower, QCIF, and CIF resolutions, at different bitrates, and four different encoding structures. Commercially available wireless local area network (WLAN) and 3.5G high-speed packet access (HSPA) wireless channels are used to validate the developed platform. Objective video quality assessment is based on PSNR ratings, following calibration using the variable frame delay (VFD) algorithm that removes temporal mismatch between original and received videos. Clinical evaluation is based on atherosclerotic plaque ultrasound video assessment protocol. Experimental results show that adequate diagnostic quality wireless medical video communications are realized using the designed telemedicine platform. HSPA cellular networks provide for ultrasound video transmission at the acquired resolution, while VFD algorithm utilization bridges objective and subjective ratings. PMID:23573082

  2. Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

    PubMed

    Teleman, Johan; Chawade, Aakash; Sandin, Marianne; Levander, Fredrik; Malmström, Johan

    2016-07-01

    In bottom-up mass spectrometry (MS)-based proteomics, peptide isotopic and chromatographic traces (features) are frequently used for label-free quantification in data-dependent acquisition MS but can also be used for the improved identification of chimeric spectra or sample complexity characterization. Feature detection is difficult because of the high complexity of MS proteomics data from biological samples, which frequently causes features to intermingle. In addition, existing feature detection algorithms commonly suffer from compatibility issues, long computation times, or poor performance on high-resolution data. Because of these limitations, we developed a new tool, Dinosaur, with increased speed and versatility. Dinosaur has the functionality to sample algorithm computations through quality-control plots, which we call a plot trail. From the evaluation of this plot trail, we introduce several algorithmic improvements to further improve the robustness and performance of Dinosaur, with the detection of features for 98% of MS/MS identifications in a benchmark data set, and no other algorithm tested in this study passed 96% feature detection. We finally used Dinosaur to reimplement a published workflow for peptide identification in chimeric spectra, increasing chimeric identification from 26% to 32% over the standard workflow. Dinosaur is operating-system-independent and is freely available as open source on https://github.com/fickludd/dinosaur .

  3. Dinosaur: A Refined Open-Source Peptide MS Feature Detector

    PubMed Central

    2016-01-01

    In bottom-up mass spectrometry (MS)-based proteomics, peptide isotopic and chromatographic traces (features) are frequently used for label-free quantification in data-dependent acquisition MS but can also be used for the improved identification of chimeric spectra or sample complexity characterization. Feature detection is difficult because of the high complexity of MS proteomics data from biological samples, which frequently causes features to intermingle. In addition, existing feature detection algorithms commonly suffer from compatibility issues, long computation times, or poor performance on high-resolution data. Because of these limitations, we developed a new tool, Dinosaur, with increased speed and versatility. Dinosaur has the functionality to sample algorithm computations through quality-control plots, which we call a plot trail. From the evaluation of this plot trail, we introduce several algorithmic improvements to further improve the robustness and performance of Dinosaur, with the detection of features for 98% of MS/MS identifications in a benchmark data set, and no other algorithm tested in this study passed 96% feature detection. We finally used Dinosaur to reimplement a published workflow for peptide identification in chimeric spectra, increasing chimeric identification from 26% to 32% over the standard workflow. Dinosaur is operating-system-independent and is freely available as open source on https://github.com/fickludd/dinosaur. PMID:27224449

  4. A global, open-source database of flood protection standards

    NASA Astrophysics Data System (ADS)

    Scussolini, Paolo; Aerts, Jeroen; Jongman, Brenden; Bouwer, Laurens; Winsemius, Hessel; de Moel, Hans; Ward, Philip

    2016-04-01

    Accurate flood risk estimation is pivotal in that it enables risk-informed policies in disaster risk reduction, as emphasized in the recent Sendai framework for Disaster Risk Reduction. To improve our understanding of flood risk, models are now capable to provide actionable risk information on the (sub)global scale. Still the accuracy of their results is greatly limited by the lack of information on standards of protection to flood that are actually in place; and researchers thus take large assumptions on the extent of protection. With our work we propose a first global, open-source database of FLOod PROtection Standards, FLOPROS, covering a range of spatial scales. FLOPROS is structured in three layers of information, and merges them into one consistent database: 1) the Design layer contains empirical information about the standard of protection presently in place; 2) the Policy layer contains intended protection standards from normative documents; 3) the Model layer uses a validated numerical approach to calculate protection standards for areas not covered in the other layers. The FLOPROS database can be used for more accurate risk assessment exercises across scales. As the database should be continually updated to reflect new interventions, we invite researchers and practitioners to contribute information. Further, we look for partners within the risk community to participate in additional strategies to implement the amount and accuracy of information contained in this first version of FLOPROS.

  5. Gadgetron: an open source framework for medical image reconstruction.

    PubMed

    Hansen, Michael Schacht; Sørensen, Thomas Sangild

    2013-06-01

    This work presents a new open source framework for medical image reconstruction called the "Gadgetron." The framework implements a flexible system for creating streaming data processing pipelines where data pass through a series of modules or "Gadgets" from raw data to reconstructed images. The data processing pipeline is configured dynamically at run-time based on an extensible markup language configuration description. The framework promotes reuse and sharing of reconstruction modules and new Gadgets can be added to the Gadgetron framework through a plugin-like architecture without recompiling the basic framework infrastructure. Gadgets are typically implemented in C/C++, but the framework includes wrapper Gadgets that allow the user to implement new modules in the Python scripting language for rapid prototyping. In addition to the streaming framework infrastructure, the Gadgetron comes with a set of dedicated toolboxes in shared libraries for medical image reconstruction. This includes generic toolboxes for data-parallel (e.g., GPU-based) execution of compute-intensive components. The basic framework architecture is independent of medical imaging modality, but this article focuses on its application to Cartesian and non-Cartesian parallel magnetic resonance imaging.

  6. OpenFLUID: an open-source software environment for modelling fluxes in landscapes

    NASA Astrophysics Data System (ADS)

    Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

    2013-04-01

    Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network

  7. OpenDA: Open Source Generic Data Assimilation Environment and its Application in Geophysical Process Models

    NASA Astrophysics Data System (ADS)

    Weerts, A.; van Velzen, N.; Verlaan, M.; Sumihar, J.; Hummel, S.; El Serafy, G.; Dhondia, J.; Gerritsen, H.; Vermeer-Ooms, S.; Loots, E.; Markus, A.; Kockx, A.

    2011-12-01

    Data Assimilation techniques are essential elements in state-of-the-art development of models and their use in operational forecasting and real-time control in the fields of groundwater, surface water and soil systems. In meteorological and atmospheric sciences, steady improvements in numerical weather forecasting and climate prediction over the last couple of decades have been enabled to a large degree by the development of community-based models and data assimilation systems. The hydrologic community should learn from the experiences of the meteorological and atmospheric communities by accelerating the transition of hydrologic DA research into operations and developing community-supported, open-source modeling and forecasting systems and data assimilation tools. In 2010, a community based open source initiative named OpenDA was started. The openDA initiative bears similarities with the well-known openMI initiative. OpenDA makes use of a set of interfaces that describe the interaction between models, observations and data assimilation algorithms. It focuses on flexible applications in portable systems for modeling geophysical processes. It provides a generic interfacing protocol that allows combination of the implemented data assimilation techniques with, in principle, any time-stepping model describing a process (atmospheric processes, 3D circulation, 2D water flow, rainfall-runoff, unsaturated flow, groundwater flow, etc.). Presently, openDA features filtering techniques and calibration techniques. The presentation will give an overview of openDA and the results of some of its practical applications.

  8. OpenSpace: An Open-Source Framework for Data Visualization and Contextualization

    NASA Astrophysics Data System (ADS)

    Bock, A.; Pembroke, A. D.; Mays, M. L.; Emmart, C. B.; Ynnerman, A.

    2015-12-01

    We present an open-source software development effort called OpenSpace that is tailored for the dissemination of space-related data visualization. In the current stages of the project, we have focussed on the public dissemination of space missions (Rosetta and New Horizons) as well as the support of space weather forecasting. The presented work will focus on the latter of these foci and elaborate on the efforts that have gone into developing a system that allows the user to assess the accuracy and validity of ENLIL ensemble simulations. It becomes possible to compare the results of ENLIL CME simulations with STEREO and SOHO images using an optical flow algorithm. This allows the user to compare velocities in the volumetric rendering of ENLIL data with the movement of CMEs through the field-of-views of various instruments onboard the space craft. By allowing the user access to these comparisons, new information about the time evolution of CMEs through the interplanetary medium is possible. Additionally, contextualizing this information in three-dimensional rendering scene, allows the analyst and the public to disseminate this data. This dissemination is further improved by the ability to connect multiple instances of the software and, thus, reach a broader audience. In a second step, we plan to combine the two foci of the project to enable the visualization of the SWAP instrument onboard New Horizons in context with a far-reaching ENLIL simulation, thus providing additional information about the solar wind dynamics of the outer solar system. The initial work regarding this plan will be presented.

  9. Free and Open Source Software for land degradation vulnerability assessment

    NASA Astrophysics Data System (ADS)

    Imbrenda, Vito; Calamita, Giuseppe; Coluzzi, Rosa; D'Emilio, Mariagrazia; Lanfredi, Maria Teresa; Perrone, Angela; Ragosta, Maria; Simoniello, Tiziana

    2013-04-01

    the vulnerability to anthropic factors mainly connected with agricultural and grazing management. To achieve the final ESAs Index depicting the overall vulnerability to degradation of the investigated area we applied the geometric mean to cross normalized indices related to each examined component. In this context QGIS was used to display data and to perform basic GIS calculations, whereas GRASS was used for map-algebra operations and image processing. Finally R was used for computing statistical analysis (Principal Component Analysis) aimed to determine the relative importance of each adopted indicator. Our results show that GRASS, QGIS and R software are suitable to map land degradation vulnerability and identify highly vulnerable areas in which rehabilitation/recovery interventions are urgent. In addition they allow us to put into evidence the most important drivers of degradation thus supplying basic information for the setting up of intervention strategies. Ultimately, Free Open Source Software deliver a fair chance for geoscientific investigations thanks to their high interoperability and flexibility enabling to preserve the accuracy of the data and to reduce processing time. Moreover, the presence of several communities that steadily support users allows for achieving high quality results, making free open source software a valuable and easy alternative to conventional commercial software.

  10. Transforming High School Classrooms with Free/Open Source Software: "It's Time for an Open Source Software Revolution"

    ERIC Educational Resources Information Center

    Pfaffman, Jay

    2008-01-01

    Free/Open Source Software (FOSS) applications meet many of the software needs of high school science classrooms. In spite of the availability and quality of FOSS tools, they remain unknown to many teachers and utilized by fewer still. In a world where most software has restrictions on copying and use, FOSS is an anomaly, free to use and to…

  11. Open Source Clinical NLP - More than Any Single System.

    PubMed

    Masanz, James; Pakhomov, Serguei V; Xu, Hua; Wu, Stephen T; Chute, Christopher G; Liu, Hongfang

    2014-01-01

    The number of Natural Language Processing (NLP) tools and systems for processing clinical free-text has grown as interest and processing capability have surged. Unfortunately any two systems typically cannot simply interoperate, even when both are built upon a framework designed to facilitate the creation of pluggable components. We present two ongoing activities promoting open source clinical NLP. The Open Health Natural Language Processing (OHNLP) Consortium was originally founded to foster a collaborative community around clinical NLP, releasing UIMA-based open source software. OHNLP's mission currently includes maintaining a catalog of clinical NLP software and providing interfaces to simplify the interaction of NLP systems. Meanwhile, Apache cTAKES aims to integrate best-of-breed annotators, providing a world-class NLP system for accessing clinical information within free-text. These two activities are complementary. OHNLP promotes open source clinical NLP activities in the research community and Apache cTAKES bridges research to the health information technology (HIT) practice.

  12. How Open Source Can Still Save the World

    NASA Astrophysics Data System (ADS)

    Behlendorf, Brian

    Many of the worlds’ major problems - economic distress, natural disaster responses, broken health care systems, education crises, and more - are not fundamentally information technology issues. However, in every case mentioned and more, there exist opportunities for Open Source software to uniquely change the way we can address these problems. At times this is about addressing a need for which no sufficient commercial market exists. For others, it is in the way Open Source licenses free the recipient from obligations to the creators, creating a relationship of mutual empowerment rather than one of dependency. For yet others, it is in the way the open collaborative processes that form around Open Source software provide a neutral ground for otherwise competitive parties to find a greatest common set of mutual needs to address together rather than in parallel. Several examples of such software exist today and are gaining traction. Governments, NGOs, and businesses are beginning to recognize the potential and are organizing to meet it. How far can this be taken?

  13. Aerostat-Lofted Instrument Platform and Sampling Method for Determination of Emissions from Open Area Sources

    EPA Science Inventory

    Sampling emissions from open area sources, particularly sources of open burning, is difficult due to fast dilution of emissions and safety concerns for personnel. Representative emission samples can be difficult to obtain with flaming and explosive sources since personnel safety ...

  14. openBIS ELN-LIMS: an open-source database for academic laboratories

    PubMed Central

    Barillari, Caterina; Ottoz, Diana S. M.; Fuentes-Serna, Juan Mariano; Ramakrishnan, Chandrasekhar; Rinn, Bernd; Rudolf, Fabian

    2016-01-01

    Summary: The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched. Availability and implementation: The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch. The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS (Ottoz et al., 2014). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available. Contact: brinn@ethz.ch or fabian.rudolf@bsse.ethz.ch PMID:26508761

  15. Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

    NASA Astrophysics Data System (ADS)

    Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

    2013-12-01

    Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third

  16. Using RSS feeds to track open source radiology informatics projects

    NASA Astrophysics Data System (ADS)

    Nagy, Paul; Daly, Mark; Warnock, Michael; Siddiqui, Khan; Siegel, Eliot

    2005-04-01

    There are over 40 open source projects in the field of radiology informatics. Because these are organized and written by volunteers, the development speed varies greatly from one project to the next. To keep track of updates, users must constantly check in on each project's Web page. Many projects remain dormant for years, and ad hoc checking becomes both an inefficient and unreliable means of determining when new versions are available. The result is that most end users track only a few projects and are unaware when others that may be more germane to their interests leapfrog in development. RSS feeds provide a machine readable XML format to track software project updates. Currently only 8 of the 40 projects provide RSS feeds for automatic propagation of news updates. We have a built a news aggregation engine around open source projects in radiology informatics.

  17. OPERA: Open-source Pipeline for Espadons Reduction and Analysis

    NASA Astrophysics Data System (ADS)

    Teeple, Douglas

    2014-11-01

    OPERA (Open-source Pipeline for Espadons Reduction and Analysis) is an open-source collaborative software reduction pipeline for ESPaDOnS data. ESPaDOnS is a bench-mounted high-resolution echelle spectrograph and spectro-polarimeter designed to obtain a complete optical spectrum (from 370 to 1,050 nm) in a single exposure with a mode-dependent resolving power between 68,000 and 81,000. OPERA is fully automated, calibrates on two-dimensional images and reduces data to produce one-dimensional intensity and polarimetric spectra. Spectra are extracted using an optimal extraction algorithm. Though designed for CFHT ESPaDOnS data, the pipeline is extensible to other echelle spectrographs.

  18. Long distance education for croatian nurses with open source software.

    PubMed

    Radenovic, Aleksandar; Kalauz, Sonja

    2006-01-01

    Croatian Nursing Informatics Association (CNIA) has been established as result of continuing work on promoting nursing informatics in Croatia. Main goals of CNIA are promoting nursing informatics and education of nurses about nursing informatics and using information technology in nursing process. CNIA in start of work is developed three courses from nursing informatics all designed with support of long distance education with open source software. Courses are: A - 'From Data to Wisdom', B - 'Introduction to Nursing Informatics' and C - 'Nursing Informatics I'. Courses A and B are obligatory for C course. Technology used to implement these online courses is based on the open source Learning Management System (LMS), Claroline, free online collaborative learning platform. Courses are divided in two modules/days. First module/day participants have classical approach to education and second day with E-learning from home. These courses represent first courses from nursing informatics' and first long distance education for nurses also. PMID:17102315

  19. Open source data analysis and visualization software for optical engineering

    NASA Astrophysics Data System (ADS)

    Smith, Greg A.; Lewis, Benjamin J.; Palmer, Michael; Kim, Dae Wook; Loeff, Adrian R.; Burge, James H.

    2012-10-01

    SAGUARO is open-source software developed to simplify data assimilation, analysis, and visualization by providing a single framework for disparate data sources from raw hardware measurements to optical simulation output. Developed with a user-friendly graphical interface in the MATLABTM environment, SAGUARO is intended to be easy for the enduser in search of useful optical information as well as the developer wanting to add new modules and functionalities. We present here the flexibility of the SAGUARO software and discuss how it can be applied to the wider optical engineering community.

  20. Open Source Software For Patient Data Management In Critical Care.

    PubMed

    Massaut, Jacques; Charretk, Nicolas; Gayraud, Olivia; Van Den Bergh, Rafael; Charles, Adelin; Edema, Nathalie

    2015-01-01

    We have previously developed a Patient Data Management System for Intensive Care based on Open Source Software. The aim of this work was to adapt this software to use in Emergency Departments in low resource environments. The new software includes facilities for utilization of the South African Triage Scale and prediction of mortality based on independent predictive factors derived from data from the Tabarre Emergency Trauma Center in Port au Prince, Haiti.

  1. GISCube, an Open Source Web-based GIS Application

    NASA Astrophysics Data System (ADS)

    Boustani, M.; Mattmann, C. A.; Ramirez, P.

    2014-12-01

    There are many Earth science projects and data systems being developed at the Jet Propulsion Laboratory, California Institute of Technology (JPL) that require the use of Geographic Information Systems (GIS). Three in particular are: (1) the JPL Airborne Snow Observatory (ASO) that measures the amount of water being generated from snow melt in mountains; (2) the Regional Climate Model Evaluation System (RCMES) that compares climate model outputs with remote sensing datasets in the context of model evaluation and the Intergovernmental Panel on Climate Change and for the U.S. National Climate Assessment and; (3) the JPL Snow Server that produces a snow and ice climatology for the Western US and Alaska, for the U.S. National Climate Assessment. Each of these three examples and all other earth science projects are strongly in need of having GIS and geoprocessing capabilities to process, visualize, manage and store GeoSpatial data. Beside some open source GIS libraries and some software like ArcGIS there are comparatively few open source, web-based and easy to use application that are capable of doing GIS processing and visualization. To address this, we present GISCube, an open source web-based GIS application that can store, visualize and process GIS and GeoSpatial data. GISCube is powered by Geothon, an open source python GIS cookbook. Geothon has a variety of Geoprocessing tools such data conversion, processing, spatial analysis and data management tools. GISCube has the capability of supporting a variety of well known GIS data formats in both vector and raster formats, and the system is being expanded to support NASA's and scientific data formats such as netCDF and HDF files. In this talk, we demonstrate how Earth science and other projects can benefit by using GISCube and Geothon, its current goals and our future work in the area.

  2. Crux: rapid open source protein tandem mass spectrometry analysis.

    PubMed

    McIlwain, Sean; Tamura, Kaipo; Kertesz-Farkas, Attila; Grant, Charles E; Diament, Benjamin; Frewen, Barbara; Howbert, J Jeffry; Hoopmann, Michael R; Käll, Lukas; Eng, Jimmy K; MacCoss, Michael J; Noble, William Stafford

    2014-10-01

    Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit ( http://cruxtoolkit.sourceforge.net ) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

  3. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  4. Harvesting, Integrating and Distributing Large Open Geospatial Datasets Using Free and Open-Source Software

    NASA Astrophysics Data System (ADS)

    Oliveira, Ricardo; Moreno, Rafael

    2016-06-01

    Federal, State and Local government agencies in the USA are investing heavily on the dissemination of Open Data sets produced by each of them. The main driver behind this thrust is to increase agencies' transparency and accountability, as well as to improve citizens' awareness. However, not all Open Data sets are easy to access and integrate with other Open Data sets available even from the same agency. The City and County of Denver Open Data Portal distributes several types of geospatial datasets, one of them is the city parcels information containing 224,256 records. Although this data layer contains many pieces of information it is incomplete for some custom purposes. Open-Source Software were used to first collect data from diverse City of Denver Open Data sets, then upload them to a repository in the Cloud where they were processed using a PostgreSQL installation on the Cloud and Python scripts. Our method was able to extract non-spatial information from a `not-ready-to-download' source that could then be combined with the initial data set to enhance its potential use.

  5. Going open source: some lessons learned from the development of OpenRecLink.

    PubMed

    Camargo Jr, Kenneth Rochel de; Coeli, Claudia Medina

    2015-02-01

    Record linkage is the process of identifying and merging records across different databases belonging to the same entity. The health sector is one of the pioneering areas of record linkage techniques applications. In 1998 we began the development of a software package, called RecLink that implemented probabilistic record linkage techniques. In this article we report the development of a new, open-source version of that program, now named OpenRecLink. The aim of this article is to present the main characteristics of the new version and some of the lessons learned during its development. The new version is a total rewrite of the program, based on three goals: (1) to migrate to a free and open source software (FOSS) platform; (2) to implement a multiplatform version; (3) to implement the support for internationalization. We describe the tools that we adopted, the process of development and some of the problems encountered. PMID:25760160

  6. Opening Up to Open Source: Looking at How Moodle Was Adopted in Higher Education

    ERIC Educational Resources Information Center

    Costello, Eamon

    2013-01-01

    The virtual learning environment (VLE) has grown to become a piece of complex infrastructure that is now deemed critical to higher educational provision. This paper looks at Moodle and its adoption in higher education. Moodle's origins, as an open source VLE, are investigated and its growth examined in the context of how higher educational…

  7. A Dozen Years after Open Source's 1998 Birth, It's Time for "OpenTechComm"

    ERIC Educational Resources Information Center

    Still, Brian

    2010-01-01

    2008 marked the 10-year Anniversary of the Open Source movement, which has had a substantial impact on not only software production and adoption, but also on the sharing and distribution of information. Technical communication as a discipline has taken some advantage of the movement or its derivative software, but this article argues not as much…

  8. Nowcasting influenza outbreaks using open-source media report.

    SciTech Connect

    Ray, Jaideep; Brownstein, John S.

    2013-02-01

    We construct and verify a statistical method to nowcast influenza activity from a time-series of the frequency of reports concerning influenza related topics. Such reports are published electronically by both public health organizations as well as newspapers/media sources, and thus can be harvested easily via web crawlers. Since media reports are timely, whereas reports from public health organization are delayed by at least two weeks, using timely, open-source data to compensate for the lag in %E2%80%9Cofficial%E2%80%9D reports can be useful. We use morbidity data from networks of sentinel physicians (both the Center of Disease Control's ILINet and France's Sentinelles network) as the gold standard of influenza-like illness (ILI) activity. The time-series of media reports is obtained from HealthMap (http://healthmap.org). We find that the time-series of media reports shows some correlation ( 0.5) with ILI activity; further, this can be leveraged into an autoregressive moving average model with exogenous inputs (ARMAX model) to nowcast ILI activity. We find that the ARMAX models have more predictive skill compared to autoregressive (AR) models fitted to ILI data i.e., it is possible to exploit the information content in the open-source data. We also find that when the open-source data are non-informative, the ARMAX models reproduce the performance of AR models. The statistical models are tested on data from the 2009 swine-flu outbreak as well as the mild 2011-2012 influenza season in the U.S.A.

  9. Building an Open Source Framework for Integrated Catchment Modeling

    NASA Astrophysics Data System (ADS)

    Jagers, B.; Meijers, E.; Villars, M.

    2015-12-01

    In order to develop effective strategies and associated policies for environmental management, we need to understand the dynamics of the natural system as a whole and the human role therein. This understanding is gained by comparing our mental model of the world with observations from the field. However, to properly understand the system we should look at dynamics of water, sediments, water quality, and ecology throughout the whole system from catchment to coast both at the surface and in the subsurface. Numerical models are indispensable in helping us understand the interactions of the overall system, but we need to be able to update and adjust them to improve our understanding and test our hypotheses. To support researchers around the world with this challenging task we started a few years ago with the development of a new open source modeling environment DeltaShell that integrates distributed hydrological models with 1D, 2D, and 3D hydraulic models including generic components for the tracking of sediment, water quality, and ecological quantities throughout the hydrological cycle composed of the aforementioned components. The open source approach combined with a modular approach based on open standards, which allow for easy adjustment and expansion as demands and knowledge grow, provides an ideal starting point for addressing challenging integrated environmental questions.

  10. OpenDrift - an open source framework for ocean trajectory modeling

    NASA Astrophysics Data System (ADS)

    Dagestad, Knut-Frode; Breivik, Øyvind; Ådlandsvik, Bjørn

    2016-04-01

    We will present a new, open source tool for modeling the trajectories and fate of particles or substances (Lagrangian Elements) drifting in the ocean, or even in the atmosphere. The software is named OpenDrift, and has been developed at Norwegian Meteorological Institute in cooperation with Institute of Marine Research. OpenDrift is a generic framework written in Python, and is openly available at https://github.com/knutfrode/opendrift/. The framework is modular with respect to three aspects: (1) obtaining input data, (2) the transport/morphological processes, and (3) exporting of results to file. Modularity is achieved through well defined interfaces between components, and use of a consistent vocabulary (CF conventions) for naming of variables. Modular input implies that it is not necessary to preprocess input data (e.g. currents, wind and waves from Eulerian models) to a particular file format. Instead "reader modules" can be written/used to obtain data directly from any original source, including files or through web based protocols (e.g. OPeNDAP/Thredds). Modularity of processes implies that a model developer may focus on the geophysical processes relevant for the application of interest, without needing to consider technical tasks such as reading, reprojecting, and colocating input data, rotation and scaling of vectors and model output. We will show a few example applications of using OpenDrift for predicting drifters, oil spills, and search and rescue objects.

  11. Adding tools to the open source toolbox: The Internet

    NASA Technical Reports Server (NTRS)

    Porth, Tricia

    1994-01-01

    The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

  12. A new chapter in environmental sensing: The Open-Source Published Environmental Sensing (OPENS) laboratory

    NASA Astrophysics Data System (ADS)

    Selker, J. S.; Roques, C.; Higgins, C. W.; Good, S. P.; Hut, R.; Selker, A.

    2015-12-01

    The confluence of 3-Dimensional printing, low-cost solid-state-sensors, low-cost, low-power digital controllers (e.g., Arduinos); and open-source publishing (e.g., Github) is poised to transform environmental sensing. The Open-Source Published Environmental Sensing (OPENS) laboratory has launched and is available for all to use. OPENS combines cutting edge technologies and makes them available to the global environmental sensing community. OPENS includes a Maker lab space where people may collaborate in person or virtually via on-line forum for the publication and discussion of environmental sensing technology (Corvallis, Oregon, USA, please feel free to request a free reservation for space and equipment use). The physical lab houses a test-bed for sensors, as well as a complete classical machine shop, 3-D printers, electronics development benches, and workstations for code development. OPENS will provide a web-based formal publishing framework wherein global students and scientists can peer-review publish (with DOI) novel and evolutionary advancements in environmental sensor systems. This curated and peer-reviewed digital collection will include complete sets of "printable" parts and operating computer code for sensing systems. The physical lab will include all of the machines required to produce these sensing systems. These tools can be addressed in person or virtually, creating a truly global venue for advancement in monitoring earth's environment and agricultural systems. In this talk we will present an example of the process of design and publication the design and data from the OPENS-Permeameter. The publication includes 3-D printing code, Arduino (or other control/logging platform) operational code; sample data sets, and a full discussion of the design set in the scientific context of previous related devices. Editors for the peer-review process are currently sought - contact John.Selker@Oregonstate.edu or Clement.Roques@Oregonstate.edu.

  13. Models for Deploying Open Source and Commercial Software to Support Earth Science Data Processing and Distribution

    NASA Astrophysics Data System (ADS)

    Yetman, G.; Downs, R. R.

    2011-12-01

    Software deployment is needed to process and distribute scientific data throughout the data lifecycle. Developing software in-house can take software development teams away from other software development projects and can require efforts to maintain the software over time. Adopting and reusing software and system modules that have been previously developed by others can reduce in-house software development and maintenance costs and can contribute to the quality of the system being developed. A variety of models are available for reusing and deploying software and systems that have been developed by others. These deployment models include open source software, vendor-supported open source software, commercial software, and combinations of these approaches. Deployment in Earth science data processing and distribution has demonstrated the advantages and drawbacks of each model. Deploying open source software offers advantages for developing and maintaining scientific data processing systems and applications. By joining an open source community that is developing a particular system module or application, a scientific data processing team can contribute to aspects of the software development without having to commit to developing the software alone. Communities of interested developers can share the work while focusing on activities that utilize in-house expertise and addresses internal requirements. Maintenance is also shared by members of the community. Deploying vendor-supported open source software offers similar advantages to open source software. However, by procuring the services of a vendor, the in-house team can rely on the vendor to provide, install, and maintain the software over time. Vendor-supported open source software may be ideal for teams that recognize the value of an open source software component or application and would like to contribute to the effort, but do not have the time or expertise to contribute extensively. Vendor-supported software may

  14. Conceptual Architecture of Building Energy Management Open Source Software (BEMOSS)

    SciTech Connect

    Khamphanchai, Warodom; Saha, Avijit; Rathinavel, Kruthika; Kuzlu, Murat; Pipattanasomporn, Manisa; Rahman, Saifur; Akyol, Bora A.; Haack, Jereme N.

    2014-12-01

    The objective of this paper is to present a conceptual architecture of a Building Energy Management Open Source Software (BEMOSS) platform. The proposed BEMOSS platform is expected to improve sensing and control of equipment in small- and medium-sized buildings, reduce energy consumption and help implement demand response (DR). It aims to offer: scalability, robustness, plug and play, open protocol, interoperability, cost-effectiveness, as well as local and remote monitoring. In this paper, four essential layers of BEMOSS software architecture -- namely User Interface, Application and Data Management, Operating System and Framework, and Connectivity layers -- are presented. A laboratory test bed to demonstrate the functionality of BEMOSS located at the Advanced Research Institute of Virginia Tech is also briefly described.

  15. The Pixhawk Open-Source Computer Vision Framework for Mavs

    NASA Astrophysics Data System (ADS)

    Meier, L.; Tanskanen, P.; Fraundorfer, F.; Pollefeys, M.

    2011-09-01

    Unmanned aerial vehicles (UAV) and micro air vehicles (MAV) are already intensively used in geodetic applications. State of the art autonomous systems are however geared towards the application area in safe and obstacle-free altitudes greater than 30 meters. Applications at lower altitudes still require a human pilot. A new application field will be the reconstruction of structures and buildings, including the facades and roofs, with semi-autonomous MAVs. Ongoing research in the MAV robotics field is focusing on enabling this system class to operate at lower altitudes in proximity to nearby obstacles and humans. PIXHAWK is an open source and open hardware toolkit for this purpose. The quadrotor design is optimized for onboard computer vision and can connect up to four cameras to its onboard computer. The validity of the system design is shown with a fully autonomous capture flight along a building.

  16. FreeSASA: An open source C library for solvent accessible surface area calculations

    PubMed Central

    Mitternacht, Simon

    2016-01-01

    Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards’ and Shrake and Rupley’s approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality. PMID:26973785

  17. FreeSASA: An open source C library for solvent accessible surface area calculations.

    PubMed

    Mitternacht, Simon

    2016-01-01

    Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards' and Shrake and Rupley's approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

  18. A Stigmergy Approach for Open Source Software Developer Community Simulation

    SciTech Connect

    Cui, Xiaohui; Beaver, Justin M; Potok, Thomas E; Pullum, Laura L; Treadwell, Jim N

    2009-01-01

    The stigmergy collaboration approach provides a hypothesized explanation about how online groups work together. In this research, we presented a stigmergy approach for building an agent based open source software (OSS) developer community collaboration simulation. We used group of actors who collaborate on OSS projects as our frame of reference and investigated how the choices actors make in contribution their work on the projects determinate the global status of the whole OSS projects. In our simulation, the forum posts and project codes served as the digital pheromone and the modified Pierre-Paul Grasse pheromone model is used for computing developer agent behaviors selection probability.

  19. An open-source java platform for automated reaction mapping.

    PubMed

    Crabtree, John D; Mehta, Dinesh P; Kouri, Tina M

    2010-09-27

    This article presents software applications that have been built upon a modular, open-source, reaction mapping library that can be used in both cheminformatics and bioinformatics research. We first describe the theoretical underpinnings and modular architecture of the core software library. We then describe two applications that have been built upon that core. The first is a generic reaction viewer and mapper, and the second classifies reactions according to rules that can be modified by end users with little or no programming skills.

  20. Open-source, Rapid Reporting of Dementia Evaluations.

    PubMed

    Graves, Rasinio S; Mahnken, Jonathan D; Swerdlow, Russell H; Burns, Jeffrey M; Price, Cathy; Amstein, Brad; Hunt, Suzanne L; Brown, Lexi; Adagarla, Bhargav; Vidoni, Eric D

    2015-01-01

    The National Institutes of Health Alzheimer's Disease Center consortium requires member institutions to build and maintain a longitudinally characterized cohort with a uniform standard data set. Increasingly, centers are employing electronic data capture to acquire data at annual evaluations. In this paper, the University of Kansas Alzheimer's Disease Center reports on an open-source system of electronic data collection and reporting to improve efficiency. This Center capitalizes on the speed, flexibility and accessibility of the system to enhance the evaluation process while rapidly transferring data to the National Alzheimer's Coordinating Center. This framework holds promise for other consortia that regularly use and manage large, standardized datasets. PMID:26779306

  1. Implementing Open Source Platform for Education Quality Enhancement in Primary Education: Indonesia Experience

    ERIC Educational Resources Information Center

    Kisworo, Marsudi Wahyu

    2016-01-01

    Information and Communication Technology (ICT)-supported learning using free and open source platform draws little attention as open source initiatives were focused in secondary or tertiary educations. This study investigates possibilities of ICT-supported learning using open source platform for primary educations. The data of this study is taken…

  2. Understanding How the "Open" of Open Source Software (OSS) Will Improve Global Health Security.

    PubMed

    Hahn, Erin; Blazes, David; Lewis, Sheri

    2016-01-01

    Improving global health security will require bold action in all corners of the world, particularly in developing settings, where poverty often contributes to an increase in emerging infectious diseases. In order to mitigate the impact of emerging pandemic threats, enhanced disease surveillance is needed to improve early detection and rapid response to outbreaks. However, the technology to facilitate this surveillance is often unattainable because of high costs, software and hardware maintenance needs, limited technical competence among public health officials, and internet connectivity challenges experienced in the field. One potential solution is to leverage open source software, a concept that is unfortunately often misunderstood. This article describes the principles and characteristics of open source software and how it may be applied to solve global health security challenges. PMID:26889576

  3. Inexpensive Open-Source Data Logging in the Field

    NASA Astrophysics Data System (ADS)

    Wickert, A. D.

    2013-12-01

    I present a general-purpose open-source field-capable data logger, which provides a mechanism to develop dense networks of inexpensive environmental sensors. This data logger was developed as a low-power variant of the Arduino open-source development system, and is named the ALog ("Arduino Logger") BottleLogger (it is slim enough to fit inside a Nalgene water bottle) version 1.0. It features an integrated high-precision real-time clock, SD card slot for high-volume data storage, and integrated power switching. The ALog can interface with sensors via six analog/digital pins, two digital pins, and one digital interrupt pin that can read event-based inputs, such as those from a tipping-bucket rain gauge. We have successfully tested the ALog BottleLogger with ultrasonic rangefinders (for water stage and snow accumulation and melt), temperature sensors, tipping-bucket rain gauges, soil moisture and water potential sensors, resistance-based tools to measure frost heave, and cameras that it triggers based on events. The source code for the ALog, including functions to interface with a a range of commercially-available sensors, is provided as an Arduino C++ library with example implementations. All schematics, circuit board layouts, and source code files are open-source and freely available under GNU GPL v3.0 and Creative Commons Attribution-ShareAlike 3.0 Unported licenses. Through this work, we hope to foster a community-driven movement to collect field environmental data on a budget that permits citizen-scientists and researchers from low-income countries to collect the same high-quality data as researchers in wealthy countries. These data can provide information about global change to managers, governments, scientists, and interested citizens worldwide. Watertight box with ALog BottleLogger data logger on the left and battery pack with 3 D cells on the right. Data can be collected for 3-5 years on one set of batteries.

  4. openPSTD: The open source pseudospectral time-domain method for acoustic propagation

    NASA Astrophysics Data System (ADS)

    Hornikx, Maarten; Krijnen, Thomas; van Harten, Louis

    2016-06-01

    An open source implementation of the Fourier pseudospectral time-domain (PSTD) method for computing the propagation of sound is presented, which is geared towards applications in the built environment. Being a wave-based method, PSTD captures phenomena like diffraction, but maintains efficiency in processing time and memory usage as it allows to spatially sample close to the Nyquist criterion, thus keeping both the required spatial and temporal resolution coarse. In the implementation it has been opted to model the physical geometry as a composition of rectangular two-dimensional subdomains, hence initially restricting the implementation to orthogonal and two-dimensional situations. The strategy of using subdomains divides the problem domain into local subsets, which enables the simulation software to be built according to Object-Oriented Programming best practices and allows room for further computational parallelization. The software is built using the open source components, Blender, Numpy and Python, and has been published under an open source license itself as well. For accelerating the software, an option has been included to accelerate the calculations by a partial implementation of the code on the Graphical Processing Unit (GPU), which increases the throughput by up to fifteen times. The details of the implementation are reported, as well as the accuracy of the code.

  5. Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)

    NASA Astrophysics Data System (ADS)

    Namias, R.; Donnelly Kehoe, P.; D'Amato, J. P.; Nagel, J.

    2015-12-01

    The removal of non-brain regions in neuroimaging is a critical task to perform a favorable preprocessing. The skull-stripping depends on different factors including the noise level in the image, the anatomy of the subject being scanned and the acquisition sequence. For these and other reasons, an ideal brain extraction method should be fast, accurate, user friendly, open-source and knowledge based (to allow for the interaction with the algorithm in case the expected outcome is not being obtained), producing stable results and making it possible to automate the process for large datasets. There are already a large number of validated tools to perform this task but none of them meets the desired characteristics. In this paper we introduced an open source brain extraction tool (OSBET), composed of four steps using simple well-known operations such as: optimal thresholding, binary morphology, labeling and geometrical analysis that aims to assemble all the desired features. We present an experiment comparing OSBET with other six state-of-the-art techniques against a publicly available dataset consisting of 40 T1-weighted 3D scans and their corresponding manually segmented images. OSBET gave both: a short duration with an excellent accuracy, getting the best Dice Coefficient metric. Further validation should be performed, for instance, in unhealthy population, to generalize its usage for clinical purposes.

  6. Building integrated business environments: analysing open-source ESB

    NASA Astrophysics Data System (ADS)

    Martínez-Carreras, M. A.; García Jimenez, F. J.; Gómez Skarmeta, A. F.

    2015-05-01

    Integration and interoperability are two concepts that have gained significant prominence in the business field, providing tools which enable enterprise application integration (EAI). In this sense, enterprise service bus (ESB) has played a crucial role as the underpinning technology for creating integrated environments in which companies may connect all their legacy-applications. However, the potential of these technologies remains unknown and some important features are not used to develop suitable business environments. The aim of this paper is to describe and detail the elements for building the next generation of integrated business environments (IBE) and to analyse the features of ESBs as the core of this infrastructure. For this purpose, we evaluate how well-known open-source ESB products fulfil these needs. Moreover, we introduce a scenario in which the collaborative system 'Alfresco' is integrated in the business infrastructure. Finally, we provide a comparison of the different open-source ESBs available for IBE requirements. According to this study, Fuse ESB provides the best results, considering features such as support for a wide variety of standards and specifications, documentation and implementation, security, advanced business trends, ease of integration and performance.

  7. 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. PMID:26668933

  8. Open source projects in software engineering education: a mapping study

    NASA Astrophysics Data System (ADS)

    Nascimento, Debora M. C.; Almeida Bittencourt, Roberto; Chavez, Christina

    2015-01-01

    Context: It is common practice in academia to have students work with "toy" projects in software engineering (SE) courses. One way to make such courses more realistic and reduce the gap between academic courses and industry needs is getting students involved in open source projects (OSP) with faculty supervision. Objective: This study aims to summarize the literature on how OSP have been used to facilitate students' learning of SE. Method: A systematic mapping study was undertaken by identifying, filtering and classifying primary studies using a predefined strategy. Results: 72 papers were selected and classified. The main results were: (a) most studies focused on comprehensive SE courses, although some dealt with specific areas; (b) the most prevalent approach was the traditional project method; (c) studies' general goals were: learning SE concepts and principles by using OSP, learning open source software or both; (d) most studies tried out ideas in regular courses within the curriculum; (e) in general, students had to work with predefined projects; (f) there was a balance between approaches where instructors had either inside control or no control on the activities performed by students; (g) when learning was assessed, software artefacts, reports and presentations were the main instruments used by teachers, while surveys were widely used for students' self-assessment; (h) most studies were published in the last seven years. Conclusions: The resulting map gives an overview of the existing initiatives in this context and shows gaps where further research can be pursued.

  9. Open Source Quartz Crystal Microbalance with dissipation monitoring

    NASA Astrophysics Data System (ADS)

    Mista, C.; Zalazar, M.; Peñalva, A.; Martina, M.; Reta, J. M.

    2016-04-01

    The dissipation factor and subsequently the characterization of the viscoelasticity of deposition films have become crucial for the study of biomolecular adsorption. Most of the commercial quartz crystal microbalance (QCM) systems offer this feature, but it has not been incorporated in open source systems. This article describes the design, construction, and simulation of an open source QCM module for measuring dissipation factor. The module includes two blocks: switch and envelope detector. The switch rapidly disrupts the excitation of the crystal, and connects the output to the envelope detector which demodulates the amplitude of the signal. Damped sinusoidal exponential signals with different time constant were used for simulating viscosity interfaces. The incorporation of few elements facilitated a double-faced PCB design with reduced dimensions. The results from simulation show that the system has a good performance in the range of the biomolecular processes; greater relative error are observed for time constant lower than 1 us. In conclusion, a dissipation module has been developed for calculate dissipation factor using QCM, which is compact and shows great performance for use in biomolecular adsorption.

  10. Open Source Software Reuse in the Airborne Cloud Computing Environment

    NASA Astrophysics Data System (ADS)

    Khudikyan, S. E.; Hart, A. F.; Hardman, S.; Freeborn, D.; Davoodi, F.; Resneck, G.; Mattmann, C. A.; Crichton, D. J.

    2012-12-01

    Earth science airborne missions play an important role in helping humans understand our climate. A challenge for airborne campaigns in contrast to larger NASA missions is that their relatively modest budgets do not permit the ground-up development of data management tools. These smaller missions generally consist of scientists whose primary focus is on the algorithmic and scientific aspects of the mission, which often leaves data management software and systems to be addressed as an afterthought. The Airborne Cloud Computing Environment (ACCE), developed by the Jet Propulsion Laboratory (JPL) to support Earth Science Airborne Program, is a reusable, multi-mission data system environment for NASA airborne missions. ACCE provides missions with a cloud-enabled platform for managing their data. The platform consists of a comprehensive set of robust data management capabilities that cover everything from data ingestion and archiving, to algorithmic processing, and to data delivery. Missions interact with this system programmatically as well as via browser-based user interfaces. The core components of ACCE are largely based on Apache Object Oriented Data Technology (OODT), an open source information integration framework at the Apache Software Foundation (ASF). Apache OODT is designed around a component-based architecture that allows for selective combination of components to create highly configurable data management systems. The diverse and growing community that currently contributes to Apache OODT fosters on-going growth and maturation of the software. ACCE's key objective is to reduce cost and risks associated with developing data management systems for airborne missions. Software reuse plays a prominent role in mitigating these problems. By providing a reusable platform based on open source software, ACCE enables airborne missions to allocate more resources to their scientific goals, thereby opening the doors to increased scientific discovery.

  11. Comparative Analysis Study of Open Source GIS in Malaysia

    NASA Astrophysics Data System (ADS)

    Rasid, Muhammad Zamir Abdul; Kamis, Naddia; Khuizham Abd Halim, Mohd

    2014-06-01

    Open source origin might appear like a major prospective change which is qualified to deliver in various industries and also competing means in developing countries. The leading purpose of this research study is to basically discover the degree of adopting Open Source Software (OSS) that is connected with Geographic Information System (GIS) application within Malaysia. It was derived based on inadequate awareness with regards to the origin ideas or even on account of techie deficiencies in the open origin instruments. This particular research has been carried out based on two significant stages; the first stage involved a survey questionnaire: to evaluate the awareness and acceptance level based on the comparison feedback regarding OSS and commercial GIS. This particular survey was conducted among three groups of candidates: government servant, university students and lecturers, as well as individual. The approaches of measuring awareness in this research were based on a comprehending signal plus a notion signal for each survey questions. These kinds of signs had been designed throughout the analysis in order to supply a measurable and also a descriptive signal to produce the final result. The second stage involved an interview session with a major organization that carries out available origin internet GIS; the Federal Department of Town and Country Planning Peninsular Malaysia (JPBD). The impact of this preliminary study was to understand the particular viewpoint of different groups of people on the available origin, and also their insufficient awareness with regards to origin ideas as well as likelihood may be significant root of adopting level connected with available origin options.

  12. Apache Open Climate Workbench: Building Open Source Climate Science Tools and Community at the Apache Software Foundation

    NASA Astrophysics Data System (ADS)

    Joyce, M.; Ramirez, P.; Boustani, M.; Mattmann, C. A.; Khudikyan, S.; McGibbney, L. J.; Whitehall, K. D.

    2014-12-01

    Apache Open Climate Workbench (OCW; https://climate.apache.org/) is a Top-Level Project at the Apache Software Foundation that aims to provide a suite of tools for performing climate science evaluations using model outputs from a multitude of different sources (ESGF, CORDEX, U.S. NCA, NARCCAP) with remote sensing data from NASA, NOAA, and other agencies. Apache OCW is the second NASA project to become a Top-Level Project at the Apache Software Foundation. It grew out of the Jet Propulsion Laboratory's (JPL) Regional Climate Model Evaluation System (RCMES) project, a collaboration between JPL and the University of California, Los Angeles' Joint Institute for Regional Earth System Science and Engineering (JIFRESSE). Apache OCW provides scientists and developers with tools for data manipulation, metrics for dataset comparisons, and a visualization suite. In addition to a powerful low-level API, Apache OCW also supports a web application for quick, browser-controlled evaluations, a command line application for local evaluations, and a virtual machine for isolated experimentation with minimal setup. This talk will look at the difficulties and successes of moving a closed community research project out into the wild world of open source. We'll explore the growing pains Apache OCW went through to become a Top-Level Project at the Apache Software Foundation as well as the benefits gained by opening up development to the broader climate and computer science communities.

  13. Choosing Open Source ERP Systems: What Reasons Are There For Doing So?

    NASA Astrophysics Data System (ADS)

    Johansson, Björn; Sudzina, Frantisek

    Enterprise resource planning (ERP) systems attract a high attention and open source software does it as well. The question is then if, and if so, when do open source ERP systems take off. The paper describes the status of open source ERP systems. Based on literature review of ERP system selection criteria based on Web of Science articles, it discusses reported reasons for choosing open source or proprietary ERP systems. Last but not least, the article presents some conclusions that could act as input for future research. The paper aims at building up a foundation for the basic question: What are the reasons for an organization to adopt open source ERP systems.

  14. Combining Open-Source Packages for Planetary Exploration

    NASA Astrophysics Data System (ADS)

    Schmidt, Albrecht; Grieger, Björn; Völk, Stefan

    2015-04-01

    The science planning of the ESA Rosetta mission has presented challenges which were addressed with combining various open-source software packages, such as the SPICE toolkit, the Python language and the Web graphics library three.js. The challenge was to compute certain parameters from a pool of trajectories and (possible) attitudes to describe the behaviour of the spacecraft. To be able to do this declaratively and efficiently, a C library was implemented that allows to interface the SPICE toolkit for geometrical computations from the Python language and process as much data as possible during one subroutine call. To minimise the lines of code one has to write special care was taken to ensure that the bindings were idiomatic and thus integrate well into the Python language and ecosystem. When done well, this very much simplifies the structure of the code and facilitates the testing for correctness by automatic test suites and visual inspections. For rapid visualisation and confirmation of correctness of results, the geometries were visualised with the three.js library, a popular Javascript library for displaying three-dimensional graphics in a Web browser. Programmatically, this was achieved by generating data files from SPICE sources that were included into templated HTML and displayed by a browser, thus made easily accessible to interested parties at large. As feedback came and new ideas were to be explored, the authors benefited greatly from the design of the Python-to-SPICE library which allowed the expression of algorithms to be concise and easier to communicate. In summary, by combining several well-established open-source tools, we were able to put together a flexible computation and visualisation environment that helped communicate and build confidence in planning ideas.

  15. GRASS GIS: The first Open Source Temporal GIS

    NASA Astrophysics Data System (ADS)

    Gebbert, Sören; Leppelt, Thomas

    2015-04-01

    GRASS GIS is a full featured, general purpose Open Source geographic information system (GIS) with raster, 3D raster and vector processing support[1]. Recently, time was introduced as a new dimension that transformed GRASS GIS into the first Open Source temporal GIS with comprehensive spatio-temporal analysis, processing and visualization capabilities[2]. New spatio-temporal data types were introduced in GRASS GIS version 7, to manage raster, 3D raster and vector time series. These new data types are called space time datasets. They are designed to efficiently handle hundreds of thousands of time stamped raster, 3D raster and vector map layers of any size. Time stamps can be defined as time intervals or time instances in Gregorian calendar time or relative time. Space time datasets are simplifying the processing and analysis of large time series in GRASS GIS, since these new data types are used as input and output parameter in temporal modules. The handling of space time datasets is therefore equal to the handling of raster, 3D raster and vector map layers in GRASS GIS. A new dedicated Python library, the GRASS GIS Temporal Framework, was designed to implement the spatio-temporal data types and their management. The framework provides the functionality to efficiently handle hundreds of thousands of time stamped map layers and their spatio-temporal topological relations. The framework supports reasoning based on the temporal granularity of space time datasets as well as their temporal topology. It was designed in conjunction with the PyGRASS [3] library to support parallel processing of large datasets, that has a long tradition in GRASS GIS [4,5]. We will present a subset of more than 40 temporal modules that were implemented based on the GRASS GIS Temporal Framework, PyGRASS and the GRASS GIS Python scripting library. These modules provide a comprehensive temporal GIS tool set. The functionality range from space time dataset and time stamped map layer management

  16. The Case for Open Source: Open Source Has Made Significant Leaps in Recent Years. What Does It Have to Offer Education?

    ERIC Educational Resources Information Center

    Guhlin, Miguel

    2007-01-01

    Open source has continued to evolve and in the past three years the development of a graphical user interface has made it increasingly accessible and viable for end users without special training. Open source relies to a great extent on the free software movement. In this context, the term free refers not to cost, but to the freedom users have to…

  17. An Extensible Open-Source Compiler Infrastructure for Testing

    SciTech Connect

    Quinlan, D; Ur, S; Vuduc, R

    2005-12-09

    Testing forms a critical part of the development process for large-scale software, and there is growing need for automated tools that can read, represent, analyze, and transform the application's source code to help carry out testing tasks. However, the support required to compile applications written in common general purpose languages is generally inaccessible to the testing research community. In this paper, we report on an extensible, open-source compiler infrastructure called ROSE, which is currently in development at Lawrence Livermore National Laboratory. ROSE specifically targets developers who wish to build source-based tools that implement customized analyses and optimizations for large-scale C, C++, and Fortran90 scientific computing applications (on the order of a million lines of code or more). However, much of this infrastructure can also be used to address problems in testing, and ROSE is by design broadly accessible to those without a formal compiler background. This paper details the interactions between testing of applications and the ways in which compiler technology can aid in the understanding of those applications. We emphasize the particular aspects of ROSE, such as support for the general analysis of whole programs, that are particularly well-suited to the testing research community and the scale of the problems that community solves.

  18. Flood hazard mapping using open source hydrological tools

    NASA Astrophysics Data System (ADS)

    Tollenaar, Daniel; Wensveen, Lex; Winsemius, Hessel; Schellekens, Jaap

    2014-05-01

    Commonly, flood hazard maps are produced by building detailed hydrological and hydraulic models. These models are forced and parameterized by locally available, high resolution and preferably high quality data. The models use a high spatio-temporal resolution, resulting in large computational effort. Also, many hydraulic packages that solve 1D (canal) and 2D (overland) shallow water equations, are not freeware nor open source. In this contribution, we evaluate whether simplified open source data and models can be used for a rapid flood hazard assessment and to highlight areas where more detail may be required. The validity of this approach is tested by using four combinations of open-source tools: (1) a global hydrological model (PCR-GLOBWB, Van Beek and Bierkens, 2009) with a static inundation routine (GLOFRIS, Winsemius et al. 2013); (2) a global hydrological model with a dynamic inundation model (Subgrid, Stelling, 2012); (3) a local hydrological model (WFLOW) with a static inundation routine; (4) and a local hydrological model with a dynamic inundation model. The applicability of tools is assessed on (1) accuracy to reproduce the phenomenon, (2) time for model setup and (3) computational time. The performance is tested in a case study in the Rio Mamoré, one of the tributaries of the Amazone River (230,000 km2). References: Stelling, G.S.: Quadtree flood simulations with sub-grid digital elevation models, Proceedings of the ICE - Water Management, Volume 165, Issue 10, 01 November 2012 , pages 567 -580 Winsemius, H. C., Van Beek, L. P. H., Jongman, B., Ward, P. J., and Bouwman, A.: A framework for global river flood risk assessments, Hydrol. Earth Syst. Sci. Discuss., 9, 9611-9659, doi:10.5194/hessd-9-9611-2012, 2012 Van Beek, L. P. H. and Bierkens, M. F. P.: The global hydrological model PCR-GLOBWB: conceptualization, parameterization and verification, Dept. of Physical Geography, Utrecht University, Utrecht, available at: http

  19. OpenDA Open Source Generic Data Assimilation Environment and its Application in Process Models

    NASA Astrophysics Data System (ADS)

    El Serafy, Ghada; Verlaan, Martin; Hummel, Stef; Weerts, Albrecht; Dhondia, Juzer

    2010-05-01

    Data Assimilation techniques are essential elements in state-of-the-art development of models and their optimization with data in the field of groundwater, surface water and soil systems. They are essential tools in calibration of complex modelling systems and improvement of model forecasts. The OpenDA is a new and generic open source data assimilation environment for application to a choice of physical process models, applied to case dependent domains. OpenDA was introduced recently when the developers of Costa, an open-source TU Delft project [http://www.costapse.org; Van Velzen and Verlaan; 2007] and those of the DATools from the former WL|Delft Hydraulics [El Serafy et al 2007; Weerts et al. 2009] decided to join forces. OpenDA makes use of a set of interfaces that describe the interaction between models, observations and data assimilation algorithms. It focuses on flexible applications in portable systems for modelling geophysical processes. It provides a generic interfacing protocol that allows combination of the implemented data assimilation techniques with, in principle, any time-stepping model duscribing a process(atmospheric processes, 3D circulation, 2D water level, sea surface temperature, soil systems, groundwater etc.). Presently, OpenDA features filtering techniques and calibration techniques. The presentation will give an overview of the OpenDA and the results of some of its practical applications. Application of data assimilation in portable operational forecasting systems—the DATools assimilation environment, El Serafy G.Y., H. Gerritsen, S. Hummel, A. H. Weerts, A.E. Mynett and M. Tanaka (2007), Journal of Ocean Dynamics, DOI 10.1007/s10236-007-0124-3, pp.485-499. COSTA a problem solving environment for data assimilation applied for hydrodynamical modelling, Van Velzen and Verlaan (2007), Meteorologische Zeitschrift, Volume 16, Number 6, December 2007 , pp. 777-793(17). Application of generic data assimilation tools (DATools) for flood

  20. Open source cardiology electronic health record development for DIGICARDIAC implementation

    NASA Astrophysics Data System (ADS)

    Dugarte, Nelson; Medina, Rubén.; Huiracocha, Lourdes; Rojas, Rubén.

    2015-12-01

    This article presents the development of a Cardiology Electronic Health Record (CEHR) system. Software consists of a structured algorithm designed under Health Level-7 (HL7) international standards. Novelty of the system is the integration of high resolution ECG (HRECG) signal acquisition and processing tools, patient information management tools and telecardiology tools. Acquisition tools are for management and control of the DIGICARDIAC electrocardiograph functions. Processing tools allow management of HRECG signal analysis searching for indicative patterns of cardiovascular pathologies. Telecardiology tools incorporation allows system communication with other health care centers decreasing access time to the patient information. CEHR system was completely developed using open source software. Preliminary results of process validation showed the system efficiency.

  1. Open Source GIS Connectors to NASA GES DISC Satellite Data

    NASA Technical Reports Server (NTRS)

    Kempler, Steve; Pham, Long; Yang, Wenli

    2014-01-01

    The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) houses a suite of high spatiotemporal resolution GIS data including satellite-derived and modeled precipitation, air quality, and land surface parameter data. The data are valuable to various GIS research and applications at regional, continental, and global scales. On the other hand, many GIS users, especially those from the ArcGIS community, have difficulties in obtaining, importing, and using our data due to factors such as the variety of data products, the complexity of satellite remote sensing data, and the data encoding formats. We introduce a simple open source ArcGIS data connector that significantly simplifies the access and use of GES DISC data in ArcGIS.

  2. Open-source products for a lighting experiment device.

    PubMed

    Gildea, Kevin M; Milburn, Nelda

    2014-12-01

    The capabilities of open-source software and microcontrollers were used to construct a device for controlled lighting experiments. The device was designed to ascertain whether individuals with certain color vision deficiencies were able to discriminate between the red and white lights in fielded systems on the basis of luminous intensity. The device provided the ability to control the timing and duration of light-emitting diode (LED) and incandescent light stimulus presentations, to present the experimental sequence and verbal instructions automatically, to adjust LED and incandescent luminous intensity, and to display LED and incandescent lights with various spectral emissions. The lighting device could easily be adapted for experiments involving flashing or timed presentations of colored lights, or the components could be expanded to study areas such as threshold light perception and visual alerting systems.

  3. Introducing djatoka: a reuse friendly, open source JPEG image server

    SciTech Connect

    Chute, Ryan M; Van De Sompel, Herbert

    2008-01-01

    The ISO-standardized JPEG 2000 image format has started to attract significant attention. Support for the format is emerging in major consumer applications, and the cultural heritage community seriously considers it a viable format for digital preservation. So far, only commercial image servers with JPEG 2000 support have been available. They come with significant license fees and typically provide the customers with limited extensibility capabilities. Here, we introduce djatoka, an open source JPEG 2000 image server with an attractive basic feature set, and extensibility under control of the community of implementers. We describe djatoka, and point at demonstrations that feature digitized images of marvelous historical manuscripts from the collections of the British Library and the University of Ghent. We also caIl upon the community to engage in further development of djatoka.

  4. IP address management : augmenting Sandia's capabilities through open source tools.

    SciTech Connect

    Nayar, R. Daniel

    2005-08-01

    Internet Protocol (IP) address management is an increasingly growing concern at Sandia National Laboratories (SNL) and the networking community as a whole. The current state of the available IP addresses indicates that they are nearly exhausted. Currently SNL doesn't have the justification to obtain more IP address space from Internet Assigned Numbers Authority (IANA). There must exist a local entity to manage and allocate IP assignments efficiently. Ongoing efforts at Sandia have been in the form of a multifunctional database application notably known as Network Information System (NWIS). NWIS is a database responsible for a multitude of network administrative services including IP address management. This study will explore the feasibility of augmenting NWIS's IP management capabilities utilizing open source tools. Modifications of existing capabilities to better allocate available IP address space are studied.

  5. Open-Source Software in Computational Research: A Case Study

    DOE PAGES

    Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; Gel, Aytekin; Pannala, Sreekanth

    2008-01-01

    A case study of open-source (OS) development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized inmore » the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.« less

  6. Performance testing open source products for the TMT event service

    NASA Astrophysics Data System (ADS)

    Gillies, K.; Bhate, Yogesh

    2014-07-01

    The software system for TMT is a distributed system with many components on many computers. Each component integrates with the overall system using a set of software services. The Event Service is a publish-subscribe message system that allows the distribution of demands and other events. The performance requirements for the Event Service are demanding with a goal of over 60 thousand events/second. This service is critical to the success of the TMT software architecture; therefore, a project was started to survey the open source and commercial market for viable software products. A trade study led to the selection of five products for thorough testing using a specially constructed computer/network configuration and test suite. The best performing product was chosen as the basis of a prototype Event Service implementation. This paper describes the process and performance tests conducted by Persistent Systems that led to the selection of the product for the prototype Event Service.

  7. An open source mobile platform for psychophysiological self tracking.

    PubMed

    Gaggioli, Andrea; Cipresso, Pietro; Serino, Silvia; Pioggia, Giovanni; Tartarisco, Gennaro; Baldus, Giovanni; Corda, Daniele; Riva, Giuseppe

    2012-01-01

    Self tracking is a recent trend in e-health that refers to the collection, elaboration and visualization of personal health data through ubiquitous computing tools such as mobile devices and wearable sensors. Here, we describe the design of a mobile self-tracking platform that has been specifically designed for clinical and research applications in the field of mental health. The smartphone-based application allows collecting a) self-reported feelings and activities from pre-programmed questionnaires; b) electrocardiographic (ECG) data from a wireless sensor platform worn by the user; c) movement activity information obtained from a tri-axis accelerometer embedded in the wearable platform. Physiological signals are further processed by the application and stored on the smartphone's memory. The mobile data collection platform is free and released under an open source licence to allow wider adoption by the research community (download at: http://sourceforge.net/projects/psychlog/).

  8. Development of parallel DEM for the open source code MFIX

    SciTech Connect

    Gopalakrishnan, Pradeep; Tafti, Danesh

    2013-02-01

    The paper presents the development of a parallel Discrete Element Method (DEM) solver for the open source code, Multiphase Flow with Interphase eXchange (MFIX) based on the domain decomposition method. The performance of the code was evaluated by simulating a bubbling fluidized bed with 2.5 million particles. The DEM solver shows strong scalability up to 256 processors with an efficiency of 81%. Further, to analyze weak scaling, the static height of the fluidized bed was increased to hold 5 and 10 million particles. The results show that global communication cost increases with problem size while the computational cost remains constant. Further, the effects of static bed height on the bubble hydrodynamics and mixing characteristics are analyzed.

  9. Management of Astronomical Software Projects with Open Source Tools

    NASA Astrophysics Data System (ADS)

    Briegel, F.; Bertram, T.; Berwein, J.; Kittmann, F.

    2010-12-01

    In this paper we will offer an innovative approach to managing the software development process with free open source tools, for building and automated testing, a system to automate the compile/test cycle on a variety of platforms to validate code changes, using virtualization to compile in parallel on various operating system platforms, version control and change management, enhanced wiki and issue tracking system for online documentation and reporting and groupware tools as they are: blog, discussion and calendar. Initially starting with the Linc-Nirvana instrument a new project and configuration management tool for developing astronomical software was looked for. After evaluation of various systems of this kind, we are satisfied with the selection we are using now. Following the lead of Linc-Nirvana most of the other software projects at the MPIA are using it now.

  10. Dentocase - open-source education management system in dentistry.

    PubMed

    Peroz, I; Seidel, O; Böning, K; Bösel, C; Schütte, U

    2004-04-01

    Since 2001, an interdisciplinary project on multimedia education in medicine has been sponsored by the Federal Ministry of Education and Research at the Charité. One part of the project is on dentistry. In the light of the results of a survey of dental students, an Internet-based education management system was created using open-source back-end systems. It supports four didactic levels for editing documentation of patient treatments. Each level corresponds to the learning abilities of the students. The patient documentation is organized to simulate the working methods of a physician or dentist. The system was tested for the first time by students in the summer semester of 2003 and has been used since the winter semester of 2003 as part of the curriculum. PMID:15516095

  11. Open Source Dataturbine (OSDT) Android Sensorpod in Environmental Observing Systems

    NASA Astrophysics Data System (ADS)

    Fountain, T. R.; Shin, P.; Tilak, S.; Trinh, T.; Smith, J.; Kram, S.

    2014-12-01

    The OSDT Android SensorPod is a custom-designed mobile computing platform for assembling wireless sensor networks for environmental monitoring applications. Funded by an award from the Gordon and Betty Moore Foundation, the OSDT SensorPod represents a significant technological advance in the application of mobile and cloud computing technologies to near-real-time applications in environmental science, natural resources management, and disaster response and recovery. It provides a modular architecture based on open standards and open-source software that allows system developers to align their projects with industry best practices and technology trends, while avoiding commercial vendor lock-in to expensive proprietary software and hardware systems. The integration of mobile and cloud-computing infrastructure represents a disruptive technology in the field of environmental science, since basic assumptions about technology requirements are now open to revision, e.g., the roles of special purpose data loggers and dedicated site infrastructure. The OSDT Android SensorPod was designed with these considerations in mind, and the resulting system exhibits the following characteristics - it is flexible, efficient and robust. The system was developed and tested in the three science applications: 1) a fresh water limnology deployment in Wisconsin, 2) a near coastal marine science deployment at the UCSD Scripps Pier, and 3) a terrestrial ecological deployment in the mountains of Taiwan. As part of a public education and outreach effort, a Facebook page with daily ocean pH measurements from the UCSD Scripps pier was developed. Wireless sensor networks and the virtualization of data and network services is the future of environmental science infrastructure. The OSDT Android SensorPod was designed and developed to harness these new technology developments for environmental monitoring applications.

  12. An open-source wireless sensor stack: from Arduino to SDI-12 to Water One Flow

    NASA Astrophysics Data System (ADS)

    Hicks, S.; Damiano, S. G.; Smith, K. M.; Olexy, J.; Horsburgh, J. S.; Mayorga, E.; Aufdenkampe, A. K.

    2013-12-01

    Implementing a large-scale streaming environmental sensor network has previously been limited by the high cost of the datalogging and data communication infrastructure. The Christina River Basin Critical Zone Observatory (CRB-CZO) is overcoming the obstacles to large near-real-time data collection networks by using Arduino, an open source electronics platform, in combination with XBee ZigBee wireless radio modules. These extremely low-cost and easy-to-use open source electronics are at the heart of the new DIY movement and have provided solutions to countless projects by over half a million users worldwide. However, their use in environmental sensing is in its infancy. At present a primary limitation to widespread deployment of open-source electronics for environmental sensing is the lack of a simple, open-source software stack to manage streaming data from heterogeneous sensor networks. Here we present a functioning prototype software stack that receives sensor data over a self-meshing ZigBee wireless network from over a hundred sensors, stores the data locally and serves it on demand as a CUAHSI Water One Flow (WOF) web service. We highlight a few new, innovative components, including: (1) a versatile open data logger design based the Arduino electronics platform and ZigBee radios; (2) a software library implementing SDI-12 communication protocol between any Arduino platform and SDI12-enabled sensors without the need for additional hardware (https://github.com/StroudCenter/Arduino-SDI-12); and (3) 'midStream', a light-weight set of Python code that receives streaming sensor data, appends it with metadata on the fly by querying a relational database structured on an early version of the Observations Data Model version 2.0 (ODM2), and uses the WOFpy library to serve the data as WaterML via SOAP and REST web services.

  13. Assessing the Impact of Security Behavior on the Awareness of Open-Source Intelligence: A Quantitative Study of IT Knowledge Workers

    ERIC Educational Resources Information Center

    Daniels, Daniel B., III

    2014-01-01

    There is a lack of literature linking end-user behavior to the availability of open-source intelligence (OSINT). Most OSINT literature has been focused on the use and assessment of open-source intelligence, not the proliferation of personally or organizationally identifiable information (PII/OII). Additionally, information security studies have…

  14. JSim, an open-source modeling system for data analysis.

    PubMed

    Butterworth, Erik; Jardine, Bartholomew E; Raymond, Gary M; Neal, Maxwell L; Bassingthwaighte, James B

    2013-01-01

    JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it

  15. JSim, an open-source modeling system for data analysis.

    PubMed

    Butterworth, Erik; Jardine, Bartholomew E; Raymond, Gary M; Neal, Maxwell L; Bassingthwaighte, James B

    2013-01-01

    JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it

  16. JSim, an open-source modeling system for data analysis

    PubMed Central

    Bassingthwaighte, James B.

    2013-01-01

    JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it

  17. When Free Isn't Free: The Realities of Running Open Source in School

    ERIC Educational Resources Information Center

    Derringer, Pam

    2009-01-01

    Despite the last few years' growth in awareness of open-source software in schools and the potential savings it represents, its widespread adoption is still hampered. Randy Orwin, technology director of the Bainbridge Island School District in Washington State and a strong open-source advocate, cautions that installing an open-source…

  18. HOS-ocean: Open-source solver for nonlinear waves in open ocean based on High-Order Spectral method

    NASA Astrophysics Data System (ADS)

    Ducrozet, Guillaume; Bonnefoy, Félicien; Le Touzé, David; Ferrant, Pierre

    2016-06-01

    HOS-ocean is an efficient High-Order Spectral code developed to solve the deterministic propagation of nonlinear wavefields in open ocean. HOS-ocean is released as open-source, developed and distributed under the terms of GNU General Public License (GPLv3). Along with the source code, a documentation under wiki format is available which makes easy the compilation and execution of the source files. The code has been shown to be accurate and efficient.

  19. A low-cost, open-source, wireless electrophysiology system.

    PubMed

    Ghomashchi, A; Zheng, Z; Majaj, N; Trumpis, M; Kiorpes, L; Viventi, J

    2014-01-01

    Many experiments in neuroscience require or would benefit tremendously from a wireless neural recording system. However, commercially available wireless systems are expensive, have moderate to high noise and are often not customizable. Academic wireless systems present impressive capabilities, but are not available for other labs to use. To overcome these limitations, we have developed an ultra-low noise 8 channel wireless electrophysiological data acquisition system using standard, commercially available components. The system is capable of recording many types of neurological signals, including EEG, ECoG, LFP and unit activity. With a diameter of just 25 mm and height of 9 mm, including a CR2032 Lithium coin cell battery, it is designed to fit into a small recording chamber while minimizing the overall implant height (Fig. 1 and 3). Using widely available parts we were able to keep the material cost of our system under $100 dollars. The complete design, including schematic, PCB layout, bill of materials and source code, will be released through an open source license, allowing other labs to modify the design to fit their needs. We have also developed a driver to acquire data using the BCI2000 software system. Feedback from the community will allow us to improve the design and create a more useful neuroscience research tool. PMID:25570656

  20. VSEARCH: a versatile open source tool for metagenomics

    PubMed Central

    Flouri, Tomáš; Nichols, Ben; Quince, Christopher; Mahé, Frédéric

    2016-01-01

    Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par

  1. OpenStereo: Open Source, Cross-Platform Software for Structural Geology Analysis

    NASA Astrophysics Data System (ADS)

    Grohmann, C. H.; Campanha, G. A.

    2010-12-01

    Free and open source software (FOSS) are increasingly seen as synonyms of innovation and progress. Freedom to run, copy, distribute, study, change and improve the software (through access to the source code) assure a high level of positive feedback between users and developers, which results in stable, secure and constantly updated systems. Several software packages for structural geology analysis are available to the user, with commercial licenses or that can be downloaded at no cost from the Internet. Some provide basic tools of stereographic projections such as plotting poles, great circles, density contouring, eigenvector analysis, data rotation etc, while others perform more specific tasks, such as paleostress or geotechnical/rock stability analysis. This variety also means a wide range of data formating for input, Graphical User Interface (GUI) design and graphic export format. The majority of packages is built for MS-Windows and even though there are packages for the UNIX-based MacOS, there aren't native packages for *nix (UNIX, Linux, BSD etc) Operating Systems (OS), forcing the users to run these programs with emulators or virtual machines. Those limitations lead us to develop OpenStereo, an open source, cross-platform software for stereographic projections and structural geology. The software is written in Python, a high-level, cross-platform programming language and the GUI is designed with wxPython, which provide a consistent look regardless the OS. Numeric operations (like matrix and linear algebra) are performed with the Numpy module and all graphic capabilities are provided by the Matplolib library, including on-screen plotting and graphic exporting to common desktop formats (emf, eps, ps, pdf, png, svg). Data input is done with simple ASCII text files, with values of dip direction and dip/plunge separated by spaces, tabs or commas. The user can open multiple file at the same time (or the same file more than once), and overlay different elements of

  2. Using "Moodle[TM]" (Open Source Software) with Grades 3-6

    ERIC Educational Resources Information Center

    Menges, Beth

    2009-01-01

    "Moodle[TM]," an acronym for Modular Object-Oriented Dynamic Learning Environment, is an open source software package that teachers can use to produce Internet-based courses and Web sites. "Open source" basically means that it is copyrighted, but it can be used at no cost as long as the user agrees to provide the source to others. "Moodle[TM]" can…

  3. A generic open-source software framework supporting scenario simulations in bioterrorist crises.

    PubMed

    Falenski, Alexander; Filter, Matthias; Thöns, Christian; Weiser, Armin A; Wigger, Jan-Frederik; Davis, Matthew; Douglas, Judith V; Edlund, Stefan; Hu, Kun; Kaufman, James H; Appel, Bernd; Käsbohrer, Annemarie

    2013-09-01

    Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of the open-source Spatiotemporal Epidemiological Modeler (STEM) simulation and modeling software for agro- or bioterrorist crisis scenarios. STEM, originally designed to enable community-driven public health disease models and simulations, was extended with new features that enable integration of proprietary data as well as visualization of agent spread along supply and production chains. STEM now provides a fully developed open-source software infrastructure supporting critical modeling tasks such as ad hoc model generation, parameter estimation, simulation of scenario evolution, estimation of effects of mitigation or management measures, and documentation. This open-source software resource can be used free of charge. Additionally, STEM provides critical features like built-in worldwide data on administrative boundaries, transportation networks, or environmental conditions (eg, rainfall, temperature, elevation, vegetation). Users can easily combine their own confidential data with built-in public data to create customized models of desired resolution. STEM also supports collaborative and joint efforts in crisis situations by extended import and export functionalities. In this article we demonstrate specifically those new software features implemented to accomplish STEM application in agro- or bioterrorist crisis scenarios. PMID:23971799

  4. Open Source Seismic Software in NOAA's Next Generation Tsunami Warning System

    NASA Astrophysics Data System (ADS)

    Hellman, S. B.; Baker, B. I.; Hagerty, M. T.; Leifer, J. M.; Lisowski, S.; Thies, D. A.; Donnelly, B. K.; Griffith, F. P.

    2014-12-01

    The Tsunami Information technology Modernization (TIM) is a project spearheaded by National Oceanic and Atmospheric Administration to update the United States' Tsunami Warning System software currently employed at the Pacific Tsunami Warning Center (Eva Beach, Hawaii) and the National Tsunami Warning Center (Palmer, Alaska). This entirely open source software project will integrate various seismic processing utilities with the National Weather Service Weather Forecast Office's core software, AWIPS2. For the real-time and near real-time seismic processing aspect of this project, NOAA has elected to integrate the open source portions of GFZ's SeisComP 3 (SC3) processing system into AWIPS2. To provide for better tsunami threat assessments we are developing open source tools for magnitude estimations (e.g., moment magnitude, energy magnitude, surface wave magnitude), detection of slow earthquakes with the Theta discriminant, moment tensor inversions (e.g. W-phase and teleseismic body waves), finite fault inversions, and array processing. With our reliance on common data formats such as QuakeML and seismic community standard messaging systems, all new facilities introduced into AWIPS2 and SC3 will be available as stand-alone tools or could be easily integrated into other real time seismic monitoring systems such as Earthworm, Antelope, etc. Additionally, we have developed a template based design paradigm so that the developer or scientist can efficiently create upgrades, replacements, and/or new metrics to the seismic data processing with only a cursory knowledge of the underlying SC3.

  5. A generic open-source software framework supporting scenario simulations in bioterrorist crises.

    PubMed

    Falenski, Alexander; Filter, Matthias; Thöns, Christian; Weiser, Armin A; Wigger, Jan-Frederik; Davis, Matthew; Douglas, Judith V; Edlund, Stefan; Hu, Kun; Kaufman, James H; Appel, Bernd; Käsbohrer, Annemarie

    2013-09-01

    Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of the open-source Spatiotemporal Epidemiological Modeler (STEM) simulation and modeling software for agro- or bioterrorist crisis scenarios. STEM, originally designed to enable community-driven public health disease models and simulations, was extended with new features that enable integration of proprietary data as well as visualization of agent spread along supply and production chains. STEM now provides a fully developed open-source software infrastructure supporting critical modeling tasks such as ad hoc model generation, parameter estimation, simulation of scenario evolution, estimation of effects of mitigation or management measures, and documentation. This open-source software resource can be used free of charge. Additionally, STEM provides critical features like built-in worldwide data on administrative boundaries, transportation networks, or environmental conditions (eg, rainfall, temperature, elevation, vegetation). Users can easily combine their own confidential data with built-in public data to create customized models of desired resolution. STEM also supports collaborative and joint efforts in crisis situations by extended import and export functionalities. In this article we demonstrate specifically those new software features implemented to accomplish STEM application in agro- or bioterrorist crisis scenarios.

  6. Open Knee: Open Source Modeling & Simulation to Enable Scientific Discovery and Clinical Care in Knee Biomechanics

    PubMed Central

    Erdemir, Ahmet

    2016-01-01

    Virtual representations of the knee joint can provide clinicians, scientists, and engineers the tools to explore mechanical function of the knee and its tissue structures in health and disease. Modeling and simulation approaches such as finite element analysis also provide the possibility to understand the influence of surgical procedures and implants on joint stresses and tissue deformations. A large number of knee joint models are described in the biomechanics literature. However, freely accessible, customizable, and easy-to-use models are scarce. Availability of such models can accelerate clinical translation of simulations, where labor intensive reproduction of model development steps can be avoided. The interested parties can immediately utilize readily available models for scientific discovery and for clinical care. Motivated by this gap, this study aims to describe an open source and freely available finite element representation of the tibiofemoral joint, namely Open Knee, which includes detailed anatomical representation of the joint's major tissue structures, their nonlinear mechanical properties and interactions. Three use cases illustrate customization potential of the model, its predictive capacity, and its scientific and clinical utility: prediction of joint movements during passive flexion, examining the role of meniscectomy on contact mechanics and joint movements, and understanding anterior cruciate ligament mechanics. A summary of scientific and clinically directed studies conducted by other investigators are also provided. The utilization of this open source model by groups other than its developers emphasizes the premise of model sharing as an accelerator of simulation-based medicine. Finally, the imminent need to develop next generation knee models are noted. These are anticipated to incorporate individualized anatomy and tissue properties supported by specimen-specific joint mechanics data for evaluation, all acquired in vitro from varying age

  7. Biosecurity and Open-Source Biology: The Promise and Peril of Distributed Synthetic Biological Technologies.

    PubMed

    Evans, Nicholas G; Selgelid, Michael J

    2015-08-01

    In this article, we raise ethical concerns about the potential misuse of open-source biology (OSB): biological research and development that progresses through an organisational model of radical openness, deskilling, and innovation. We compare this organisational structure to that of the open-source software model, and detail salient ethical implications of this model. We demonstrate that OSB, in virtue of its commitment to openness, may be resistant to governance attempts.

  8. Implementation of an OAIS Repository Using Free, Open Source Software

    NASA Astrophysics Data System (ADS)

    Flathers, E.; Gessler, P. E.; Seamon, E.

    2015-12-01

    The Northwest Knowledge Network (NKN) is a regional data repository located at the University of Idaho that focuses on the collection, curation, and distribution of research data. To support our home institution and others in the region, we offer services to researchers at all stages of the data lifecycle—from grant application and data management planning to data distribution and archive. In this role, we recognize the need to work closely with other data management efforts at partner institutions and agencies, as well as with larger aggregation efforts such as our state geospatial data clearinghouses, data.gov, DataONE, and others. In the past, one of our challenges with monolithic, prepackaged data management solutions is that customization can be difficult to implement and maintain, especially as new versions of the software are released that are incompatible with our local codebase. Our solution is to break the monolith up into its constituent parts, which offers us several advantages. First, any customizations that we make are likely to fall into areas that can be accessed through Application Program Interfaces (API) that are likely to remain stable over time, so our code stays compatible. Second, as components become obsolete or insufficient to meet new demands that arise, we can replace the individual components with minimal effect on the rest of the infrastructure, causing less disruption to operations. Other advantages include increased system reliability, staggered rollout of new features, enhanced compatibility with legacy systems, reduced dependence on a single software company as a point of failure, and the separation of development into manageable tasks. In this presentation, we describe our application of the Service Oriented Architecture (SOA) design paradigm to assemble a data repository that conforms to the Open Archival Information System (OAIS) Reference Model primarily using a collection of free and open-source software. We detail the design

  9. An Open Source modular platform for hydrological model implementation

    NASA Astrophysics Data System (ADS)

    Kolberg, Sjur; Bruland, Oddbjørn

    2010-05-01

    An implementation framework for setup and evaluation of spatio-temporal models is developed, forming a highly modularized distributed model system. The ENKI framework allows building space-time models for hydrological or other environmental purposes, from a suite of separately compiled subroutine modules. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines in a fixed framework. The open-source license and modular design of ENKI will also facilitate rapid dissemination of new methods to institutions engaged in operational hydropower forecasting or other water resource management. Written in C++, ENKI uses a plug-in structure to build a complete model from separately compiled subroutine implementations. These modules contain very little code apart from the core process simulation, and are compiled as dynamic-link libraries (dll). A narrow interface allows the main executable to recognise the number and type of the different variables in each routine. The framework then exposes these variables to the user within the proper context, ensuring that time series exist for input variables, initialisation for states, GIS data sets for static map data, manually or automatically calibrated values for parameters etc. ENKI is designed to meet three different levels of involvement in model construction: • Model application: Running and evaluating a given model. Regional calibration against arbitrary data using a rich suite of objective functions, including likelihood and Bayesian estimation. Uncertainty analysis directed towards input or parameter uncertainty. o Need not: Know the model's composition of subroutines, or the internal variables in the model, or the creation of method modules. • Model analysis: Link together different process methods, including parallel setup of alternative methods for solving the same task. Investigate the effect of different spatial discretization schemes. o Need not

  10. HELIOS: A new open-source radiative transfer code

    NASA Astrophysics Data System (ADS)

    Malik, Matej; Grosheintz, Luc; Lukas Grimm, Simon; Mendonça, João; Kitzmann, Daniel; Heng, Kevin

    2015-12-01

    I present the new open-source code HELIOS, developed to accurately describe radiative transfer in a wide variety of irradiated atmospheres. We employ a one-dimensional multi-wavelength two-stream approach with scattering. Written in Cuda C++, HELIOS uses the GPU’s potential of massive parallelization and is able to compute the TP-profile of an atmosphere in radiative equilibrium and the subsequent emission spectrum in a few minutes on a single computer (for 60 layers and 1000 wavelength bins).The required molecular opacities are obtained with the recently published code HELIOS-K [1], which calculates the line shapes from an input line list and resamples the numerous line-by-line data into a manageable k-distribution format. Based on simple equilibrium chemistry theory [2] we combine the k-distribution functions of the molecules H2O, CO2, CO & CH4 to generate a k-table, which we then employ in HELIOS.I present our results of the following: (i) Various numerical tests, e.g. isothermal vs. non-isothermal treatment of layers. (ii) Comparison of iteratively determined TP-profiles with their analytical parametric prescriptions [3] and of the corresponding spectra. (iii) Benchmarks of TP-profiles & spectra for various elemental abundances. (iv) Benchmarks of averaged TP-profiles & spectra for the exoplanets GJ1214b, HD189733b & HD209458b. (v) Comparison with secondary eclipse data for HD189733b, XO-1b & Corot-2b.HELIOS is being developed, together with the dynamical core THOR and the chemistry solver VULCAN, in the group of Kevin Heng at the University of Bern as part of the Exoclimes Simulation Platform (ESP) [4], which is an open-source project aimed to provide community tools to model exoplanetary atmospheres.-----------------------------[1] Grimm & Heng 2015, ArXiv, 1503.03806[2] Heng, Lyons & Tsai, Arxiv, 1506.05501Heng & Lyons, ArXiv, 1507.01944[3] e.g. Heng, Mendonca & Lee, 2014, ApJS, 215, 4H[4] exoclime.net

  11. Common characteristics of open source software development and applicability for drug discovery: a systematic review

    PubMed Central

    2011-01-01

    Background Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery. Methods A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project. Results Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined. Conclusions We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents. PMID:21955914

  12. OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data

    PubMed Central

    2010-01-01

    Background Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform. Results This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported. Conclusions OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). There are no license constraints regarding extensions. They can be published using open source as well as proprietary licenses. OpenChrom is available free of charge at http://www.openchrom.net. PMID:20673335

  13. Evaluation of Open-Source Hard Real Time Software Packages

    NASA Technical Reports Server (NTRS)

    Mattei, Nicholas S.

    2004-01-01

    replacing this somewhat costly implementation is the focus of one of the SA group s current research projects. The explosion of open source software in the last ten years has led to the development of a multitude of software solutions which were once only produced by major corporations. The benefits of these open projects include faster release and bug patching cycles as well as inexpensive if not free software solutions. The main packages for hard real time solutions under Linux are Real Time Application Interface (RTAI) and two varieties of Real Time Linux (RTL), RTLFree and RTLPro. During my time here at NASA I have been testing various hard real time solutions operating as layers on the Linux Operating System. All testing is being run on an Intel SBC 2590 which is a common embedded hardware platform. The test plan was provided to me by the Software Assurance group at the start of my internship and my job has been to test the systems by developing and executing the test cases on the hardware. These tests are constructed so that the Software Assurance group can get hard test data for a comparison between the open source and proprietary implementations of hard real time solutions.

  14. MetaTrans: an open-source pipeline for metatranscriptomics

    PubMed Central

    Martinez, Xavier; Pozuelo, Marta; Pascal, Victoria; Campos, David; Gut, Ivo; Gut, Marta; Azpiroz, Fernando; Guarner, Francisco; Manichanh, Chaysavanh

    2016-01-01

    To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples. Compared to an existing web application server, MetaTrans shows more efficiency in terms of runtime (around 2 hours per million of transcripts) and presents adapted tools to compare gene expression levels. It has been tested with a human gut microbiome database but also proposes an option to use a general database in order to analyze other ecosystems. For the installation and use of the pipeline, we provide a detailed guide at the following website (www.metatrans.org). PMID:27211518

  15. Cloud based, Open Source Software Application for Mitigating Herbicide Drift

    NASA Astrophysics Data System (ADS)

    Saraswat, D.; Scott, B.

    2014-12-01

    The spread of herbicide resistant weeds has resulted in the need for clearly marked fields. In response to this need, the University of Arkansas Cooperative Extension Service launched a program named Flag the Technology in 2011. This program uses color-coded flags as a visual alert of the herbicide trait technology within a farm field. The flag based program also serves to help avoid herbicide misapplication and prevent herbicide drift damage between fields with differing crop technologies. This program has been endorsed by Southern Weed Science Society of America and is attracting interest from across the USA, Canada, and Australia. However, flags have risk of misplacement or disappearance due to mischief or severe windstorms/thunderstorms, respectively. This presentation will discuss the design and development of a cloud-based, free application utilizing open-source technologies, called Flag the Technology Cloud (FTTCloud), for allowing agricultural stakeholders to color code their farm fields for indicating herbicide resistant technologies. The developed software utilizes modern web development practices, widely used design technologies, and basic geographic information system (GIS) based interactive interfaces for representing, color-coding, searching, and visualizing fields. This program has also been made compatible for a wider usability on different size devices- smartphones, tablets, desktops and laptops.

  16. Open-Source Software for Modeling of Nanoelectronic Devices

    NASA Technical Reports Server (NTRS)

    Oyafuso, Fabiano; Hua, Hook; Tisdale, Edwin; Hart, Don

    2004-01-01

    The Nanoelectronic Modeling 3-D (NEMO 3-D) computer program has been upgraded to open-source status through elimination of license-restricted components. The present version functions equivalently to the version reported in "Software for Numerical Modeling of Nanoelectronic Devices" (NPO-30520), NASA Tech Briefs, Vol. 27, No. 11 (November 2003), page 37. To recapitulate: NEMO 3-D performs numerical modeling of the electronic transport and structural properties of a semiconductor device that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantum-mechanical behavior of the device resolved to the atomistic level of granularity. NEMO 3-D solves the applicable quantum matrix equation on a Beowulf-class cluster computer by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. A prior upgrade of NEMO 3-D incorporated a capability for a strain treatment, parameterized for bulk material properties of GaAs and InAs, for two tight-binding submodels. NEMO 3-D has been demonstrated in atomistic analyses of effects of disorder in alloys and, in particular, in bulk In(x)Ga(1-x)As and in In(0.6)Ga(0.4)As quantum dots.

  17. An Open Source Software Tool for Hydrologic Climate Change Assessment

    NASA Astrophysics Data System (ADS)

    Park, Dong Kwan; Shin, Mun-Ju; Kim, Young-Oh

    2015-04-01

    With the Intergovernmental Panel on Climate Change (IPCC) publishing Climate Change Assessment Reports containing updated forecasts and scenarios regularly, it is necessary to also periodically perform hydrologic assessments studies on these scenarios. The practical users including scientists and government people need to use handy tools that operate from climate input data of historical observations and climate change scenarios to rainfall-runoff simulation and assessment periodically. We propose HydroCAT (Hydrologic Climate change Assessment Tool), which is a flexible software tool designed to simplify and streamline hydrologic climate change assessment studies with the incorporation of: taking climate input values from general circulation models using the latest climate change scenarios; simulation of downscaled values using statistical downscaling methods; calibration and simulation of well-know multiple lumped conceptual hydrologic models; assessment of results using statistical methods. This package is designed in an open source, R-based, software package that includes an operating framework to support wide data frameworks, variety of hydrologic models, and climate change scenarios. The use of the software is demonstrated in a case study of the Geum River basin in Republic of Korea.

  18. An Open Source Embedding Code for the Condensed Phase

    NASA Astrophysics Data System (ADS)

    Genova, Alessandro; Ceresoli, Davide; Krishtal, Alisa; Andreussi, Oliviero; Distasio, Robert; Pavanello, Michele

    Work from our group as well as others has shown that for many systems such as molecular aggregates, liquids, and complex layered materials, subsystem Density-Functional Theory (DFT) is capable of immensely reducing the computational cost while providing a better and more intuitive insight into the underlying physics. We developed a massively parallel implementation of Subsystem DFT for the condensed phase into the open-source Quantum ESPRESSO software package. In this talk, we will discuss how we: (1) implemented such a flexible parallel framework aiming at the optimal load balancing; (2) simplified the solution of the electronic structure problem by allowing a fragment specific sampling of the first Brillouin Zone; (3) achieve enormous speedups by solving the electronic structure of each fragment in a unit cell smaller than the supersystem simulation cell, effectively introducing a fragment specific basis set, with no deterioration of the fully periodic simulation. As of March 14, 2016, the code has been released and is available to the public.

  19. 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.

  20. Open-Source Photometric System for Enzymatic Nitrate Quantification.

    PubMed

    Wittbrodt, B T; Squires, D A; Walbeck, J; Campbell, E; Campbell, W H; Pearce, J M

    2015-01-01

    Nitrate, the most oxidized form of nitrogen, is regulated to protect people and animals from harmful levels as there is a large over abundance due to anthropogenic factors. Widespread field testing for nitrate could begin to address the nitrate pollution problem, however, the Cadmium Reduction Method, the leading certified method to detect and quantify nitrate, demands the use of a toxic heavy metal. An alternative, the recently proposed Environmental Protection Agency Nitrate Reductase Nitrate-Nitrogen Analysis Method, eliminates this problem but requires an expensive proprietary spectrophotometer. The development of an inexpensive portable, handheld photometer will greatly expedite field nitrate analysis to combat pollution. To accomplish this goal, a methodology for the design, development, and technical validation of an improved open-source water testing platform capable of performing Nitrate Reductase Nitrate-Nitrogen Analysis Method. This approach is evaluated for its potential to i) eliminate the need for toxic chemicals in water testing for nitrate and nitrite, ii) reduce the cost of equipment to perform this method for measurement for water quality, and iii) make the method easier to carryout in the field. The device is able to perform as well as commercial proprietary systems for less than 15% of the cost for materials. This allows for greater access to the technology and the new, safer nitrate testing technique. PMID:26244342

  1. Agile Methods for Open Source Safety-Critical Software

    PubMed Central

    Enquobahrie, Andinet; Ibanez, Luis; Cheng, Patrick; Yaniv, Ziv; Cleary, Kevin; Kokoori, Shylaja; Muffih, Benjamin; Heidenreich, John

    2011-01-01

    The introduction of software technology in a life-dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety-critical software development. Agile methods are flexible enough to encourage the right amount of ceremony; therefore if safety-critical systems require greater emphasis on activities like formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code-level quality than classic software engineering process models. We present our experiences on the image-guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested they are not suitable for safety-critical systems almost a decade ago, we present our experiences as a case study for renewing the discussion. PMID:21799545

  2. MetaTrans: an open-source pipeline for metatranscriptomics.

    PubMed

    Martinez, Xavier; Pozuelo, Marta; Pascal, Victoria; Campos, David; Gut, Ivo; Gut, Marta; Azpiroz, Fernando; Guarner, Francisco; Manichanh, Chaysavanh

    2016-05-23

    To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples. Compared to an existing web application server, MetaTrans shows more efficiency in terms of runtime (around 2 hours per million of transcripts) and presents adapted tools to compare gene expression levels. It has been tested with a human gut microbiome database but also proposes an option to use a general database in order to analyze other ecosystems. For the installation and use of the pipeline, we provide a detailed guide at the following website (www.metatrans.org).

  3. Application of Open Source Technologies for Oceanographic Data Analysis

    NASA Astrophysics Data System (ADS)

    Huang, T.; Gangl, M.; Quach, N. T.; Wilson, B. D.; Chang, G.; Armstrong, E. M.; Chin, T. M.; Greguska, F.

    2015-12-01

    NEXUS is a data-intensive analysis solution developed with a new approach for handling science data that enables large-scale data analysis by leveraging open source technologies such as Apache Cassandra, Apache Spark, Apache Solr, and Webification. NEXUS has been selected to provide on-the-fly time-series and histogram generation for the Soil Moisture Active Passive (SMAP) mission for Level 2 and Level 3 Active, Passive, and Active Passive products. It also provides an on-the-fly data subsetting capability. NEXUS is designed to scale horizontally, enabling it to handle massive amounts of data in parallel. It takes a new approach on managing time and geo-referenced array data by dividing data artifacts into chunks and stores them in an industry-standard, horizontally scaled NoSQL database. This approach enables the development of scalable data analysis services that can infuse and leverage the elastic computing infrastructure of the Cloud. It is equipped with a high-performance geospatial and indexed data search solution, coupled with a high-performance data Webification solution free from file I/O bottlenecks, as well as a high-performance, in-memory data analysis engine. In this talk, we will focus on the recently funded AIST 2014 project by using NEXUS as the core for oceanographic anomaly detection service and web portal. We call it, OceanXtremes

  4. Assesing Ecohydrological Impacts of Forest Disturbance using Open Source Software

    NASA Astrophysics Data System (ADS)

    Lovette, J. P.; Chang, T.; Treglia, M.; Gan, T.; Duncan, J.

    2014-12-01

    In the past 30 years, land management protocols, climate change, and land use have radically changed the frequency and magnitudes of disturbance regimes. Landscape scale disturbances can change a forest structure, resulting in impacts on adjacent watersheds that may affect water amount/quality for human and natural resource use. Our project quantifies hydrologic changes from of a suite of disturbance events resulting in vegetation cover shifts at watersheds across the continental United States. These disturbance events include: wildfire, insect/disease, deforestation(logging), hurricanes, ice storms, and human land use. Our major question is: Can the effects of disturbance on ecohydrology be generalized across regions, time scales, and spatial scales? Using a workflow of open source tools, and utilizing publicly available data, this work could be extended and leveraged by other researchers. Spatial data on disturbance include the MODIS Global Disturbance Index (NTSG), Landsat 7 Global Forest Change (Hansen dataset), and the Degree of Human Modification (Theobald dataset). Ecohydrologic response data includes USGS NWIS, USFS-LTER climDB/hydroDB, and the CUAHSI HIS.

  5. Open-Source Photometric System for Enzymatic Nitrate Quantification.

    PubMed

    Wittbrodt, B T; Squires, D A; Walbeck, J; Campbell, E; Campbell, W H; Pearce, J M

    2015-01-01

    Nitrate, the most oxidized form of nitrogen, is regulated to protect people and animals from harmful levels as there is a large over abundance due to anthropogenic factors. Widespread field testing for nitrate could begin to address the nitrate pollution problem, however, the Cadmium Reduction Method, the leading certified method to detect and quantify nitrate, demands the use of a toxic heavy metal. An alternative, the recently proposed Environmental Protection Agency Nitrate Reductase Nitrate-Nitrogen Analysis Method, eliminates this problem but requires an expensive proprietary spectrophotometer. The development of an inexpensive portable, handheld photometer will greatly expedite field nitrate analysis to combat pollution. To accomplish this goal, a methodology for the design, development, and technical validation of an improved open-source water testing platform capable of performing Nitrate Reductase Nitrate-Nitrogen Analysis Method. This approach is evaluated for its potential to i) eliminate the need for toxic chemicals in water testing for nitrate and nitrite, ii) reduce the cost of equipment to perform this method for measurement for water quality, and iii) make the method easier to carryout in the field. The device is able to perform as well as commercial proprietary systems for less than 15% of the cost for materials. This allows for greater access to the technology and the new, safer nitrate testing technique.

  6. 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.

  7. Hydrognomon - open source software for the analysis of hydrological data

    NASA Astrophysics Data System (ADS)

    Kozanis, Stefanos; Christofides, Antonios; Mamassis, Nikos; Efstratiadis, Andreas; Koutsoyiannis, Demetris

    2010-05-01

    Hydrognomon is a software tool for the processing of hydrological data. It is an open source application running on standard Microsoft Windows platforms, and it is part of the openmeteo.org framework. Data are imported through standard text files, spreadsheets or by typing. Standard hydrological data processing techniques include time step aggregation and regularization, interpolation, regression analysis and infilling of missing values, consistency tests, data filtering, graphical and tabular visualisation of time series, etc. It supports several time steps, from the finest minute scales up to decades; specific cases of irregular time steps and offsets are also supported. The program also includes common hydrological applications, such as evapotranspiration modelling, stage-discharge analysis, homogeneity tests, areal integration of point data series, processing of hydrometric data, as well as lumped hydrological modelling with automatic calibration facilities. Here the emphasis is given on the statistical module of Hydrognomon, which provides tools for data exploration, fitting of distribution functions, statistical prediction, Monte-Carlo simulation, determination of confidence limits, analysis of extremes, and construction of ombrian (intensity-duration-frequency) curves. Hydrognomon is available for download from http://www.hydrognomon.org/.

  8. BRISC-an open source pulmonary nodule image retrieval framework.

    PubMed

    Lam, Michael O; Disney, Tim; Raicu, Daniela S; Furst, Jacob; Channin, David S

    2007-11-01

    We have created a content-based image retrieval framework for computed tomography images of pulmonary nodules. When presented with a nodule image, the system retrieves images of similar nodules from a collection prepared by the Lung Image Database Consortium (LIDC). The system (1) extracts images of individual nodules from the LIDC collection based on LIDC expert annotations, (2) stores the extracted data in a flat XML database, (3) calculates a set of quantitative descriptors for each nodule that provide a high-level characterization of its texture, and (4) uses various measures to determine the similarity of two nodules and perform queries on a selected query nodule. Using our framework, we compared three feature extraction methods: Haralick co-occurrence, Gabor filters, and Markov random fields. Gabor and Markov descriptors perform better at retrieving similar nodules than do Haralick co-occurrence techniques, with best retrieval precisions in excess of 88%. Because the software we have developed and the reference images are both open source and publicly available they may be incorporated into both commercial and academic imaging workstations and extended by others in their research.

  9. Open-Source Photometric System for Enzymatic Nitrate Quantification

    PubMed Central

    Wittbrodt, B. T.; Squires, D. A.; Walbeck, J.; Campbell, E.; Campbell, W. H.; Pearce, J. M.

    2015-01-01

    Nitrate, the most oxidized form of nitrogen, is regulated to protect people and animals from harmful levels as there is a large over abundance due to anthropogenic factors. Widespread field testing for nitrate could begin to address the nitrate pollution problem, however, the Cadmium Reduction Method, the leading certified method to detect and quantify nitrate, demands the use of a toxic heavy metal. An alternative, the recently proposed Environmental Protection Agency Nitrate Reductase Nitrate-Nitrogen Analysis Method, eliminates this problem but requires an expensive proprietary spectrophotometer. The development of an inexpensive portable, handheld photometer will greatly expedite field nitrate analysis to combat pollution. To accomplish this goal, a methodology for the design, development, and technical validation of an improved open-source water testing platform capable of performing Nitrate Reductase Nitrate-Nitrogen Analysis Method. This approach is evaluated for its potential to i) eliminate the need for toxic chemicals in water testing for nitrate and nitrite, ii) reduce the cost of equipment to perform this method for measurement for water quality, and iii) make the method easier to carryout in the field. The device is able to perform as well as commercial proprietary systems for less than 15% of the cost for materials. This allows for greater access to the technology and the new, safer nitrate testing technique. PMID:26244342

  10. Agile Methods for Open Source Safety-Critical Software.

    PubMed

    Gary, Kevin; Enquobahrie, Andinet; Ibanez, Luis; Cheng, Patrick; Yaniv, Ziv; Cleary, Kevin; Kokoori, Shylaja; Muffih, Benjamin; Heidenreich, John

    2011-08-01

    The introduction of software technology in a life-dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety-critical software development. Agile methods are flexible enough to encourage the rightamount of ceremony; therefore if safety-critical systems require greater emphasis on activities like formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code-level quality than classic software engineering process models. We present our experiences on the image-guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested they are not suitable for safety-critical systems almost a decade ago, we present our experiences as a case study for renewing the discussion.

  11. Special population planner 4 : an open source release.

    SciTech Connect

    Kuiper, J.; Metz, W.; Tanzman, E.

    2008-01-01

    Emergencies like Hurricane Katrina and the recent California wildfires underscore the critical need to meet the complex challenge of planning for individuals with special needs and for institutionalized special populations. People with special needs and special populations often have difficulty responding to emergencies or taking protective actions, and emergency responders may be unaware of their existence and situations during a crisis. Special Population Planner (SPP) is an ArcGIS-based emergency planning system released as an open source product. SPP provides for easy production of maps, reports, and analyses to develop and revise emergency response plans. It includes tools to manage a voluntary registry of data for people with special needs, integrated links to plans and documents, tools for response planning and analysis, preformatted reports and maps, and data on locations of special populations, facility and resource characteristics, and contacts. The system can be readily adapted for new settings without programming and is broadly applicable. Full documentation and a demonstration database are included in the release.

  12. Agile Methods for Open Source Safety-Critical Software.

    PubMed

    Gary, Kevin; Enquobahrie, Andinet; Ibanez, Luis; Cheng, Patrick; Yaniv, Ziv; Cleary, Kevin; Kokoori, Shylaja; Muffih, Benjamin; Heidenreich, John

    2011-08-01

    The introduction of software technology in a life-dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety-critical software development. Agile methods are flexible enough to encourage the rightamount of ceremony; therefore if safety-critical systems require greater emphasis on activities like formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code-level quality than classic software engineering process models. We present our experiences on the image-guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested they are not suitable for safety-critical systems almost a decade ago, we present our experiences as a case study for renewing the discussion. PMID:21799545

  13. La Cura, An Open Source Cure for Cancer.

    PubMed

    Iaconesi, Salvatore

    2013-09-01

    When I was diagnosed with brain cancer, I opened up my medical records to the Web, asking for help. The response was incredible: a global source of crowd-generated information about how to cure my own cancer. This work explores the many issues involved in handling such a peculiar form of information (including privacy, preserving the complexity of the human being, the reliability of responses, and more) and the outcomes of the overall process. "[Critique] does not aim to make possible metaphysics which becomes, in the end, science; its aim is to look as more as possible beyond and beside at the infinite work of freedom." -M. Foucault, "What is Illuminism" "Maybe today the most important objective is not to understand what we are, but to refuse it. We must imagine and build what we could be, to drop that political double bind which is constituted by the simultaneous individualization and totalitarianization of the structures of modern powers. The conclusion might be that the political, ethical, social and philosophical issue today is not to liberate individuals from the State and its institutions, but to free ourselves from the State and from the individualization which is bound to the State. We must promote new ways for subjectivity through the refusal of that kind of individuality which has been imposed to us for so many centuries." -M. Foucault, "Why Study Power: The Question of the Subject" (1).

  14. Tessera: Open source software for accelerated data science

    SciTech Connect

    Sego, Landon H.; Hafen, Ryan P.; Director, Hannah M.; LaMothe, Ryan R.

    2014-06-30

    Extracting useful, actionable information from data can be a formidable challenge for the safeguards, nonproliferation, and arms control verification communities. Data scientists are often on the “front-lines” of making sense of complex and large datasets. They require flexible tools that make it easy to rapidly reformat large datasets, interactively explore and visualize data, develop statistical algorithms, and validate their approaches—and they need to perform these activities with minimal lines of code. Existing commercial software solutions often lack extensibility and the flexibility required to address the nuances of the demanding and dynamic environments where data scientists work. To address this need, Pacific Northwest National Laboratory developed Tessera, an open source software suite designed to enable data scientists to interactively perform their craft at the terabyte scale. Tessera automatically manages the complicated tasks of distributed storage and computation, empowering data scientists to do what they do best: tackling critical research and mission objectives by deriving insight from data. We illustrate the use of Tessera with an example analysis of computer network data.

  15. Wndchrm – an open source utility for biological image analysis

    PubMed Central

    Shamir, Lior; Orlov, Nikita; Eckley, D Mark; Macura, Tomasz; Johnston, Josiah; Goldberg, Ilya G

    2008-01-01

    Background Biological imaging is an emerging field, covering a wide range of applications in biological and clinical research. However, while machinery for automated experimenting and data acquisition has been developing rapidly in the past years, automated image analysis often introduces a bottleneck in high content screening. Methods Wndchrm is an open source utility for biological image analysis. The software works by first extracting image content descriptors from the raw image, image transforms, and compound image transforms. Then, the most informative features are selected, and the feature vector of each image is used for classification and similarity measurement. Results Wndchrm has been tested using several publicly available biological datasets, and provided results which are favorably comparable to the performance of task-specific algorithms developed for these datasets. The simple user interface allows researchers who are not knowledgeable in computer vision methods and have no background in computer programming to apply image analysis to their data. Conclusion We suggest that wndchrm can be effectively used for a wide range of biological image analysis tasks. Using wndchrm can allow scientists to perform automated biological image analysis while avoiding the costly challenge of implementing computer vision and pattern recognition algorithms. PMID:18611266

  16. Functionality pattern matching as an efficient complementary structure/reaction search tool: an open-source approach.

    PubMed

    Haider, Norbert

    2010-08-01

    An open-source software package for creating and operating web-based structure and/or reaction databases is presented. Besides standard search capabilities (text, structure/substructure/similarity), the system offers a fast additional search option, entirely based on binary pattern matching, which uses automatically assigned functional group descriptors.

  17. Open Source and Open Standard based decision support system: the example of lake Verbano floods management.

    NASA Astrophysics Data System (ADS)

    Cannata, Massimiliano; Antonovic, Milan; Pozzoni, Maurizio; Graf, Andrea

    2015-04-01

    The Locarno area (Switzerland, Canton Ticino) is exposed to lacual floods with a return period of about 7-8 years. The risk is of particular concern because the area is located in a floodplain that registered in the last decades a great increase in settlement and values of the real estates. Moreover small differences in lake altitude may produce a significant increase in flooded area due to the very low average slope of the terrain. While fatalities are not generally registered, several important economic costs are associated, e.g.: damages to real estates, interruption of activities, evacuation and relocation and environmental damages. While important events were registered in 1978, 1993, 2000, 2002 and 2014 the local stakeholder invested time and money in the set-up of an up-to-date decision support system that allows for the reduction of risks. Thanks to impressive technological advances the visionary concept of the Digital Earth (Gore 1992, 1998) is being realizing: geospatial coverages and monitoring systems data are increasingly available on the Web, and more importantly, in a standard format. As a result, today is possible to develop innovative decision support systems (Molinari et al. 2013) which mesh-up several information sources and offers special features for risk scenarios evaluation. In agreement with the exposed view, the authors have recently developed a new Web system whose design is based on the Service Oriented Architecture pattern. Open source software (e.g.: Geoserver, PostGIS, OpenLayers) has been used throughout the whole system and geospatial Open Standards (e.g.: SOS, WMS, WFS) are the pillars it rely on. SITGAP 2.0, implemented in collaboration with the Civil protection of Locarno e Vallemaggia, combines a number of data sources such as the Federal Register of Buildings and Dwellings, the Cantonal Register of residents, the Cadastral Surveying, the Cantonal Hydro-meteorological monitoring observations, the Meteoswiss weather forecasts, and

  18. Cloud computing geospatial application for water resources based on free and open source software and open standards - a prototype

    NASA Astrophysics Data System (ADS)

    Delipetrev, Blagoj

    2016-04-01

    Presently, most of the existing software is desktop-based, designed to work on a single computer, which represents a major limitation in many ways, starting from limited computer processing, storage power, accessibility, availability, etc. The only feasible solution lies in the web and cloud. This abstract presents research and development of a cloud computing geospatial application for water resources based on free and open source software and open standards using hybrid deployment model of public - private cloud, running on two separate virtual machines (VMs). The first one (VM1) is running on Amazon web services (AWS) and the second one (VM2) is running on a Xen cloud platform. The presented cloud application is developed using free and open source software, open standards and prototype code. The cloud application presents a framework how to develop specialized cloud geospatial application that needs only a web browser to be used. This cloud application is the ultimate collaboration geospatial platform because multiple users across the globe with internet connection and browser can jointly model geospatial objects, enter attribute data and information, execute algorithms, and visualize results. The presented cloud application is: available all the time, accessible from everywhere, it is scalable, works in a distributed computer environment, it creates a real-time multiuser collaboration platform, the programing languages code and components are interoperable, and it is flexible in including additional components. The cloud geospatial application is implemented as a specialized water resources application with three web services for 1) data infrastructure (DI), 2) support for water resources modelling (WRM), 3) user management. The web services are running on two VMs that are communicating over the internet providing services to users. The application was tested on the Zletovica river basin case study with concurrent multiple users. The application is a state

  19. EHDViz: clinical dashboard development using open-source technologies

    PubMed Central

    Badgeley, Marcus A; Shameer, Khader; Glicksberg, Benjamin S; Tomlinson, Max S; Levin, Matthew A; McCormick, Patrick J; Kasarskis, Andrew; Reich, David L; Dudley, Joel T

    2016-01-01

    -driven precision medicine. As an open-source visualisation framework capable of integrating health assessment, EHDViz aims to be a valuable toolkit for rapid design, development and implementation of scalable clinical data visualisation dashboards. PMID:27013597

  20. moocRP: Enabling Open Learning Analytics with an Open Source Platform for Data Distribution, Analysis, and Visualization

    ERIC Educational Resources Information Center

    Pardos, Zachary A.; Whyte, Anthony; Kao, Kevin

    2016-01-01

    In this paper, we address issues of transparency, modularity, and privacy with the introduction of an open source, web-based data repository and analysis tool tailored to the Massive Open Online Course community. The tool integrates data request/authorization and distribution workflow features as well as provides a simple analytics module upload…

  1. The open source, object- and process oriented simulation system OpenGeoSys - concepts, development, community

    NASA Astrophysics Data System (ADS)

    Bauer, S.; Li, D.; Beyer, C.; Wang, W.; Bilke, L.; Graupner, B.

    2011-12-01

    Many geoscientific problems, such as underground waste disposal, nuclear waste disposal, CO2 sequestration, geothermal energy, etc., require for prediction of ongoing processes as well as risk and safety assessment a numerical simulation system. The governing processes are thermal heat transfer (T), hydraulic flow in multi-phase systems (H), mechanical deformation (M) and geochemical reactions (C), which interact in a complex way (THMC). The development of suitable simulation systems requires a large amount of effort for code development, verification and applications. OpenGeoSys (OGS) is an open source scientific initiative for the simulation of these THMC processes in porous media. A flexible numerical framework based on the Finite Element Method is provided and applied to the governing process equations. Due to the object- and process-oriented character of the code, functionality enhancement and code coupling with external simulators can be performed reasonably effectively. This structure also allows for a distributed development, with developers at different locations contributing to the common code. The code is platform independent, accessible via internet for development and application, and checked by an automated benchmarking system regularly.

  2. Collaboration using open standards and open source software (examples of DIAS/CEOS Water Portal)

    NASA Astrophysics Data System (ADS)

    Miura, S.; Sekioka, S.; Kuroiwa, K.; Kudo, Y.

    2015-12-01

    The DIAS/CEOS Water Portal is a part of the DIAS (Data Integration and Analysis System, http://www.editoria.u-tokyo.ac.jp/projects/dias/?locale=en_US) systems for data distribution for users including, but not limited to, scientists, decision makers and officers like river administrators. One of the functions of this portal is to enable one-stop search and access variable water related data archived multiple data centers located all over the world. This portal itself does not store data. Instead, according to requests made by users on the web page, it retrieves data from distributed data centers on-the-fly and lets them download and see rendered images/plots. Our system mainly relies on the open source software GI-cat (http://essi-lab.eu/do/view/GIcat) and open standards such as OGC-CSW, Opensearch and OPeNDAP protocol to enable the above functions. Details on how it works will be introduced during the presentation. Although some data centers have unique meta data format and/or data search protocols, our portal's brokering function enables users to search across various data centers at one time. And this portal is also connected to other data brokering systems, including GEOSS DAB (Discovery and Access Broker). As a result, users can search over thousands of datasets, millions of files at one time. Users can access the DIAS/CEOS Water Portal system at http://waterportal.ceos.org/.

  3. Towards the Implementation of an openEHR-based Open Source EHR Platform (a vision paper).

    PubMed

    Pazos Gutiérrez, Pablo

    2015-01-01

    Healthcare Information Systems are a big business. Currently there is an explosion of EHR/EMR products available on the market, and the best tools are really expensive. Many developing countries and healthcare providers cannot access such tools, and for those who can, there is not a clear strategy for the evolution, scaling, and cost of these electronic health products. The lack of standard-based implementations conduct to the creation of isolated information silos that cannot be exploited (i.e. shared between providers to promote a holistic view of each patient's medical history). This paper exposes the main elements behind a Standard-based Open Source EHR Platform that is future-proof and allows to evolve and scale with minimal cost. The proposed EHR Architecture is based on openEHR specifications, adding elements emerged from research and development experiences, leading to a design that can be implemented in any modern technology. Different implementations will be interoperable by design. This Platform will leverage contexts of scarce resources, reusing clinical knowledge, a common set of software components and services.

  4. A flexible open-source toolkit for lava flow simulations

    NASA Astrophysics Data System (ADS)

    Mossoux, Sophie; Feltz, Adelin; Poppe, Sam; Canters, Frank; Kervyn, Matthieu

    2014-05-01

    Lava flow hazard modeling is a useful tool for scientists and stakeholders confronted with imminent or long term hazard from basaltic volcanoes. It can improve their understanding of the spatial distribution of volcanic hazard, influence their land use decisions and improve the city evacuation during a volcanic crisis. Although a range of empirical, stochastic and physically-based lava flow models exists, these models are rarely available or require a large amount of physical constraints. We present a GIS toolkit which models lava flow propagation from one or multiple eruptive vents, defined interactively on a Digital Elevation Model (DEM). It combines existing probabilistic (VORIS) and deterministic (FLOWGO) models in order to improve the simulation of lava flow spatial spread and terminal length. Not only is this toolkit open-source, running in Python, which allows users to adapt the code to their needs, but it also allows users to combine the models included in different ways. The lava flow paths are determined based on the probabilistic steepest slope (VORIS model - Felpeto et al., 2001) which can be constrained in order to favour concentrated or dispersed flow fields. Moreover, the toolkit allows including a corrective factor in order for the lava to overcome small topographical obstacles or pits. The lava flow terminal length can be constrained using a fixed length value, a Gaussian probability density function or can be calculated based on the thermo-rheological properties of the open-channel lava flow (FLOWGO model - Harris and Rowland, 2001). These slope-constrained properties allow estimating the velocity of the flow and its heat losses. The lava flow stops when its velocity is zero or the lava temperature reaches the solidus. Recent lava flows of Karthala volcano (Comoros islands) are here used to demonstrate the quality of lava flow simulations with the toolkit, using a quantitative assessment of the match of the simulation with the real lava flows. The

  5. Development of AN Open-Source Automatic Deformation Monitoring System for Geodetical and Geotechnical Measurements

    NASA Astrophysics Data System (ADS)

    Engel, P.; Schweimler, B.

    2016-04-01

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

  6. Development of a web application for water resources based on open source software

    NASA Astrophysics Data System (ADS)

    Delipetrev, Blagoj; Jonoski, Andreja; Solomatine, Dimitri P.

    2014-01-01

    This article presents research and development of a prototype web application for water resources using latest advancements in Information and Communication Technologies (ICT), open source software and web GIS. The web application has three web services for: (1) managing, presenting and storing of geospatial data, (2) support of water resources modeling and (3) water resources optimization. The web application is developed using several programming languages (PhP, Ajax, JavaScript, Java), libraries (OpenLayers, JQuery) and open source software components (GeoServer, PostgreSQL, PostGIS). The presented web application has several main advantages: it is available all the time, it is accessible from everywhere, it creates a real time multi-user collaboration platform, the programing languages code and components are interoperable and designed to work in a distributed computer environment, it is flexible for adding additional components and services and, it is scalable depending on the workload. The application was successfully tested on a case study with concurrent multi-users access.

  7. An open-source chemical kinetics network: VULCAN

    NASA Astrophysics Data System (ADS)

    Tsai, Shang-Min; Lyons, James; Heng, Kevin

    2015-12-01

    I will present VULCAN, an open-source 1D chemical kinetics code suited for the temperature and pressure range relevant to observable exoplanet atmospheres. The chemical network is based on a set of reduced rate coefficients for C-H-O systems. Most of the rate coefficients are based on the NIST online database, and validated by comparing withthermodynamic equilibrium codes (TEA, STANJAN). The difference between the experimental rates and those from the thermodynamical data is carefully examined and discussed. For the numerical method, a simple, quick, semi-implicit Euler integrator is adopted to solve the stiff chemical reactions, within an operator-splitting scheme for computational efficiency.Several test runs of VULCAN are shown in a hierarchical way: pure H, H+O, H+O+C, including controlled experiments performed with a simple analytical temperature-pressure profiles, so that different parameters, such as the stellar irradiation, atmospheric opacities and albedo can be individually explored to understand how these properties affect the temperaturestructure and hence the chemical abundances. I will also revisit the "transport-induced-quenching” effects, and discuss the limitation of this approximation and its impact on observations. Finally, I will discuss the effects of C/O ratio and compare with published work in the literature.VULCAN is written in Python and is part of the publicly-available set of community tools we call the Exoclimes Simulation Platform (ESP; www.exoclime.org). I am a Ph.D student of Kevin Heng at the University of Bern, Switzerland.

  8. Acquire: an open-source comprehensive cancer biobanking system

    PubMed Central

    Dowst, Heidi; Pew, Benjamin; Watkins, Chris; McOwiti, Apollo; Barney, Jonathan; Qu, Shijing; Becnel, Lauren B.

    2015-01-01

    Motivation: The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable mutations. To this end, many human cancer biobanks are integrating more tightly with genomic sequencing facilities and with those creating and maintaining patient-derived xenografts (PDX) and cell lines to provide renewable resources for translational research. Results: To support the complex data management needs and workflows of several such biobanks, we developed Acquire. It is a robust, secure, web-based, database-backed open-source system that supports all major needs of a modern cancer biobank. Its modules allow for i) up-to-the-minute ‘scoreboard’ and graphical reporting of collections; ii) end user roles and permissions; iii) specimen inventory through caTissue Suite; iv) shipping forms for distribution of specimens to pathology, genomic analysis and PDX/cell line creation facilities; v) robust ad hoc querying; vi) molecular and cellular quality control metrics to track specimens’ progress and quality; vii) public researcher request; viii) resource allocation committee distribution request review and oversight and ix) linkage to available derivatives of specimen. Availability and Implementation: Acquire implements standard controlled vocabularies, ontologies and objects from the NCI, CDISC and others. Here we describe the functionality of the system, its technological stack and the processes it supports. A test version Acquire is available at https://tcrbacquire-stg.research.bcm.edu; software is available in https://github.com/BCM-DLDCC/Acquire; and UML models, data and workflow diagrams, behavioral specifications and other documents are available at https://github.com/BCM-DLDCC/Acquire/tree/master/supplementaryMaterials. Contact: becnel@bcm.edu PMID:25573920

  9. The OpenPicoAmp: an open-source planar lipid bilayer amplifier for hands-on learning of neuroscience.

    PubMed

    Shlyonsky, Vadim; Dupuis, Freddy; Gall, David

    2014-01-01

    Understanding the electrical biophysical properties of the cell membrane can be difficult for neuroscience students as it relies solely on lectures of theoretical models without practical hands on experiments. To address this issue, we developed an open-source lipid bilayer amplifier, the OpenPicoAmp, which is appropriate for use in introductory courses in biophysics or neurosciences at the undergraduate level, dealing with the electrical properties of the cell membrane. The amplifier is designed using the common lithographic printed circuit board fabrication process and off-the-shelf electronic components. In addition, we propose a specific design for experimental chambers allowing the insertion of a commercially available polytetrafluoroethylene film. We provide a complete documentation allowing to build the amplifier and the experimental chamber. The students hand-out giving step-by step instructions to perform a recording is also included. Our experimental setup can be used in basic experiments in which students monitor the bilayer formation by capacitance measurement and record unitary currents produced by ionic channels like gramicidin A dimers. Used in combination with a low-cost data acquisition board this system provides a complete solution for hands-on lessons, therefore improving the effectiveness in teaching basic neurosciences or biophysics. PMID:25251830

  10. The OpenPicoAmp: An Open-Source Planar Lipid Bilayer Amplifier for Hands-On Learning of Neuroscience

    PubMed Central

    Shlyonsky, Vadim; Dupuis, Freddy; Gall, David

    2014-01-01

    Understanding the electrical biophysical properties of the cell membrane can be difficult for neuroscience students as it relies solely on lectures of theoretical models without practical hands on experiments. To address this issue, we developed an open-source lipid bilayer amplifier, the OpenPicoAmp, which is appropriate for use in introductory courses in biophysics or neurosciences at the undergraduate level, dealing with the electrical properties of the cell membrane. The amplifier is designed using the common lithographic printed circuit board fabrication process and off-the-shelf electronic components. In addition, we propose a specific design for experimental chambers allowing the insertion of a commercially available polytetrafluoroethylene film. We provide a complete documentation allowing to build the amplifier and the experimental chamber. The students hand-out giving step-by step instructions to perform a recording is also included. Our experimental setup can be used in basic experiments in which students monitor the bilayer formation by capacitance measurement and record unitary currents produced by ionic channels like gramicidin A dimers. Used in combination with a low-cost data acquisition board this system provides a complete solution for hands-on lessons, therefore improving the effectiveness in teaching basic neurosciences or biophysics. PMID:25251830

  11. The OpenPicoAmp: an open-source planar lipid bilayer amplifier for hands-on learning of neuroscience.

    PubMed

    Shlyonsky, Vadim; Dupuis, Freddy; Gall, David

    2014-01-01

    Understanding the electrical biophysical properties of the cell membrane can be difficult for neuroscience students as it relies solely on lectures of theoretical models without practical hands on experiments. To address this issue, we developed an open-source lipid bilayer amplifier, the OpenPicoAmp, which is appropriate for use in introductory courses in biophysics or neurosciences at the undergraduate level, dealing with the electrical properties of the cell membrane. The amplifier is designed using the common lithographic printed circuit board fabrication process and off-the-shelf electronic components. In addition, we propose a specific design for experimental chambers allowing the insertion of a commercially available polytetrafluoroethylene film. We provide a complete documentation allowing to build the amplifier and the experimental chamber. The students hand-out giving step-by step instructions to perform a recording is also included. Our experimental setup can be used in basic experiments in which students monitor the bilayer formation by capacitance measurement and record unitary currents produced by ionic channels like gramicidin A dimers. Used in combination with a low-cost data acquisition board this system provides a complete solution for hands-on lessons, therefore improving the effectiveness in teaching basic neurosciences or biophysics.

  12. Looking toward the Future: A Case Study of Open Source Software in the Humanities

    ERIC Educational Resources Information Center

    Quamen, Harvey

    2006-01-01

    In this article Harvey Quamen examines how the philosophy of open source software might be of particular benefit to humanities scholars in the near future--particularly for academic journals with limited financial resources. To this end he provides a case study in which he describes his use of open source technology (MySQL database software and…

  13. You Can Deliver the Goods Better, Faster Cheaper with Open Source Databases

    ERIC Educational Resources Information Center

    Banerjee, Kyle

    2005-01-01

    Most people don't realize how easy it is to improve library services with open source databases. Despite the fact that they are distributed free of charge, open source databases are powerful and stable enough for critical applications. With a little knowledge of HTML and some basic technical skills, you can quickly create databases to register…

  14. 76 FR 75875 - Defense Federal Acquisition Regulation Supplement; Open Source Software Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-05

    ... Software Public Meeting AGENCY: Defense Acquisition Regulations System, Department of Defense (DoD). ACTION... regarding the use of open source software in DoD contracts. DATES: Public Meeting: January 12, 2012, from 10... for the discussions in the meeting. Please cite ``Public Meeting, DFARS--Open Source Software'' in...

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

    ERIC Educational Resources Information Center

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

    2003-01-01

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

  16. An Evaluation of Open Source Learning Management Systems According to Learners Tools

    ERIC Educational Resources Information Center

    Uzunboylu, Huseyin; Ozdamli, Fezile; Ozcinar, Zehra

    2006-01-01

    Learning Management System (LMS) is the main element of internet-based education. In parallel to this, studies in this area are increasing. The aim of this research is to evaluate the current existing Open Source Learning Management Systems in the market. For this, seventy-two Open Source Learning Management Systems have been subjected to a…

  17. The Implications of Incumbent Intellectual Property Strategies for Open Source Software Success and Commercialization

    ERIC Educational Resources Information Center

    Wen, Wen

    2012-01-01

    While open source software (OSS) emphasizes open access to the source code and avoids the use of formal appropriability mechanisms, there has been little understanding of how the existence and exercise of formal intellectual property rights (IPR) such as patents influence the direction of OSS innovation. This dissertation seeks to bridge this gap…

  18. Build, Buy, Open Source, or Web 2.0?: Making an Informed Decision for Your Library

    ERIC Educational Resources Information Center

    Fagan, Jody Condit; Keach, Jennifer A.

    2010-01-01

    When improving a web presence, today's libraries have a choice: using a free Web 2.0 application, opting for open source, buying a product, or building a web application. This article discusses how to make an informed decision for one's library. The authors stress that deciding whether to use a free Web 2.0 application, to choose open source, to…

  19. Perceptions of Open Source versus Commercial Software: Is Higher Education Still on the Fence?

    ERIC Educational Resources Information Center

    van Rooij, Shahron Williams

    2007-01-01

    This exploratory study investigated the perceptions of technology and academic decision-makers about open source benefits and risks versus commercial software applications. The study also explored reactions to a concept for outsourcing campus-wide deployment and maintenance of open source. Data collected from telephone interviews were analyzed,…

  20. Government Technology Acquisition Policy: The Case of Proprietary versus Open Source Software

    ERIC Educational Resources Information Center

    Hemphill, Thomas A.

    2005-01-01

    This article begins by explaining the concepts of proprietary and open source software technology, which are now competing in the marketplace. A review of recent individual and cooperative technology development and public policy advocacy efforts, by both proponents of open source software and advocates of proprietary software, subsequently…

  1. Open-Source Learning Management Systems: A Predictive Model for Higher Education

    ERIC Educational Resources Information Center

    van Rooij, S. Williams

    2012-01-01

    The present study investigated the role of pedagogical, technical, and institutional profile factors in an institution of higher education's decision to select an open-source learning management system (LMS). Drawing on the results of previous research that measured patterns of deployment of open-source software (OSS) in US higher education and…

  2. An Evaluation of Open Source Learning Management Systems According to Administration Tools and Curriculum Design

    ERIC Educational Resources Information Center

    Ozdamli, Fezile

    2007-01-01

    Distance education is becoming more important in the universities and schools. The aim of this research is to evaluate the current existing Open Source Learning Management Systems according to Administration tool and Curriculum Design. For this, seventy two Open Source Learning Management Systems have been subjected to a general evaluation. After…

  3. Evaluating Open Source Software for Use in Library Initiatives: A Case Study Involving Electronic Publishing

    ERIC Educational Resources Information Center

    Samuels, Ruth Gallegos; Griffy, Henry

    2012-01-01

    This article discusses best practices for evaluating open source software for use in library projects, based on the authors' experience evaluating electronic publishing solutions. First, it presents a brief review of the literature, emphasizing the need to evaluate open source solutions carefully in order to minimize Total Cost of Ownership. Next,…

  4. Implementing an Open Source Learning Management System: A Critical Analysis of Change Strategies

    ERIC Educational Resources Information Center

    Uys, Philip M.

    2010-01-01

    This paper analyses the change and innovation strategies that Charles Sturt University (CSU) used from 2007 to 2009 during the implementation and mainstreaming of an open source learning management system (LMS), Sakai, named locally as "CSU Interact". CSU was in January 2008 the first Australian University to implement an open source learning…

  5. Prazosin addition to fluvoxamine: A preclinical study and open clinical trial in OCD.

    PubMed

    Feenstra, Matthijs G P; Klompmakers, André; Figee, Martijn; Fluitman, Sjoerd; Vulink, Nienke; Westenberg, Herman G M; Denys, Damiaan

    2016-02-01

    The efficacy of selective serotonin reuptake inhibitors (SRIs) in psychiatric disorders may be "augmented" through the addition of atypical antipsychotic drugs. A synergistic increase in dopamine (DA) release in the prefrontal cortex has been suggested to underlie this augmentation effect, though the mechanism of action is not clear yet. We used in vivo microdialysis in rats to study DA release following the administration of combinations of fluvoxamine (10 mg/kg) and quetiapine (10 mg/kg) with various monoamine-related drugs. The results confirmed that the selective 5-HT1A antagonist WAY-100635 (0.05 mg/kg) partially blocked the fluvoxamine-quetiapine synergistic effect (maximum DA increase dropped from 325% to 214%). A novel finding is that the α1-adrenergic blocker prazosin (1 mg/kg), combined with fluvoxamine, partially mimicked the effect of augmentation (maximum DA increase 205%; area-under-the-curve 163%). As this suggested that prazosin augmentation might be tested in a clinical study, we performed an open clinical trial of prazosin 20 mg addition to SRI in therapy-resistant patients with obsessive-compulsive disorder applying for neurosurgery. A small, non-significant reduction in Yale Brown Obsessive Compulsive Scale (Y-BOCS) scores was observed in 10 patients and one patient was classified as a responder with a reduction in Y-BOCS scores of more than 25%. We suggest that future clinical studies augmenting SRIs with an α1-adrenergic blocker in less treatment resistant cases should be considered. The clinical trial "Prazosin in combination with a serotonin reuptake inhibitor for patients with Obsessive Compulsive disorder: an open label study" was registered at 24/05/2011 under trial number ISRCTN61562706: http://www.controlled-trials.com/ISRCTN61562706. PMID:26712326

  6. Application of polar orbiter products in weather forecasting using open source tools and open standards

    NASA Astrophysics Data System (ADS)

    Plieger, Maarten; de Vreede, Ernst

    2015-04-01

    EUMETSAT disseminates data for a number of polar satellites. At KNMI these data are not fully used for operational weather forecasting mainly because of the irregular coverage and lack of tools for handling these different types of data and products. For weather forecasting there is a lot of interest in the application of products from these polar orbiters. One of the key aspects is the high-resolution of these products, which can complement the information provided by numerical weather forecasts. Another advantage over geostationary satellites is the high coverage at higher latitudes and lack of parallax. Products like the VIIRS day-night band offer many possibilities for this application. This presentation will describe a project that aims to make available a number of products from polar satellites to the forecasting operation. The goal of the project is to enable easy and timely access to polar orbiter products and enable combined presentations of satellite imagery with model data. The system will be able to generate RGB composites (“false colour images”) for operational use. The system will be built using open source components and open standards. Pytroll components are used for data handling, reprojection and derived product generation. For interactive presentation of imagery the browser based ADAGUC WMS viewer component is used. Image generation is done by ADAGUC server components, which provide OGC WMS services. Polar satellite products are stored as true color RGBA data in the NetCDF file format, the satellite swaths are stored as regular grids with their own custom geographical projection. The ADAGUC WMS system is able to reproject, render and combine these data in a webbrowser interactively. Results and lessons learned will be presented at the conference.

  7. An Earthquake Information Service with Free and Open Source Tools

    NASA Astrophysics Data System (ADS)

    Jüngling, Sebastian; Schroeder, Matthias; Lühr, Birger-Gottfried; Woith, Heiko; Wächter, Joachim

    2016-04-01

    At the GFZ German Research Centre for Geosciences in Potsdam, the working group Earthquakes and Volcano Physics examines the spatiotemporal behavior of earthquakes. In this context also the hazards of volcanic eruptions and tsunamis are explored. The aim is to collect related event parameters after the occurrence of extreme events and make them available for science and public as quick as possible. However, the overall objective of this research is to reduce geological risks that emanate from such natural hazards. In order to meet the stated objectives and to get a quick overview about the seismicity of a particular region and to compare the situation to historical and current events, a comprehensive visualization is necessary. Based on the web-accessible data from the famous GFZ GEOFON network a user-friendly interactive web mapping application could be realized. Further, this web service tool integrates historical and current earthquake information from the USGS earthquake database NEIC, and more historical events from various other catalogues like Pacheco, International Seismological Centre (ISC) and others. This compilation of data sources is unique in Earth sciences. Additionally, information about historical and current occurrences of volcanic eruptions and tsunamis are retrievable too. Another special feature in the application is the limitation of time spans via a time shifting tool. Users can interactively vary the visualization by moving the time slider. In addition, the events can be narrowed down based on the magnitude, the wave height of tsunamis or the volcanic explosion index. Furthermore, the use of the latest JavaScript libraries makes it possible to display the application on all screen sizes and devices. With this application, information on current and historical earthquakes and other extreme events can be obtained based on the spatio-temporal context, such as the concomitant visualization of seismicity of a particular region.

  8. Chromium Renderserver: Scalable and Open Source Remote RenderingInfrastructure

    SciTech Connect

    Paul, Brian; Ahern, Sean; Bethel, E. Wes; Brugger, Eric; Cook,Rich; Daniel, Jamison; Lewis, Ken; Owen, Jens; Southard, Dale

    2007-12-01

    Chromium Renderserver (CRRS) is software infrastructure thatprovides the ability for one or more users to run and view image outputfrom unmodified, interactive OpenGL and X11 applications on a remote,parallel computational platform equipped with graphics hardwareaccelerators via industry-standard Layer 7 network protocolsand clientviewers. The new contributions of this work include a solution to theproblem of synchronizing X11 and OpenGL command streams, remote deliveryof parallel hardware-accelerated rendering, and a performance analysis ofseveral different optimizations that are generally applicable to avariety of rendering architectures. CRRSis fully operational, Open Sourcesoftware.

  9. OpenMebius: An Open Source Software for Isotopically Nonstationary 13C-Based Metabolic Flux Analysis

    PubMed Central

    Furusawa, Chikara

    2014-01-01

    The in vivo measurement of metabolic flux by 13C-based metabolic flux analysis (13C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a 13C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas 13C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary 13C metabolic flux analysis (INST-13C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-13C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-13C-MFA. Confidence intervals determined by INST-13C-MFA were less than those determined by conventional methods, indicating the potential of INST-13C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-13C-MFA. PMID:25006579

  10. OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.

    PubMed

    Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio; Shimizu, Hiroshi

    2014-01-01

    The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas (13)C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary (13)C metabolic flux analysis (INST-(13)C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-(13)C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA. Confidence intervals determined by INST-(13)C-MFA were less than those determined by conventional methods, indicating the potential of INST-(13)C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-(13)C-MFA.

  11. Ancient Secrets of Open-Source Geoscience Software Management (Invited)

    NASA Astrophysics Data System (ADS)

    Zender, C. S.

    2009-12-01

    Geoscience research often involves complex models and data analysis designed to test increasingly sophisticated theories. Re-use and improvement of existing models and tools can be more efficient than their re-invention, and this re-use can accelerate knowledge generation and discovery. Open Source Software (OSS) is designed and intended to be re-used, extended, and improved. Hence Earth and Space Science Models (ESSMs) intended for community use are commonly distributed with OSS or OSS-like licenses. Why is it that, despite their permissive licenses, only a relatively small fraction of ESSMs receive community adoption, improvement, and extension? One reason is that developing community geoscience software remains a difficult and perilous exercise for the practicing researcher. This presentation will intercompare the rationale and results of different software management approaches taken in my dozen years as a developer and maintainer of, and participant in, four distinct ESSMs with 10 to 10,000 users. The primary lesson learned is that geoscience research is similar to the wider OSS universe in that most participants are motivated by the desire for greater professional recognition and attribution best summarized as "mindshare". ESSM adoption often hinges on whether the tension between users and developers for mindshare manifests as cooperation or competition. ESSM project management, therefore, should promote (but not require) recognition of all contributors. More practical model management practices include mailing lists, highly visible documentation, consistent APIs, regression tests, and periodic releases to improve features and fix bugs and builds. However, most ESSMs originate as working incarnations of short-term (~three year) research projects and, as such, lack permanent institutional support. Adhering to best software practices to transition these ESSMs from personal to community models often requires sacrificing research time. Recently, funding agencies

  12. THOR: an open-source exo-GCM

    NASA Astrophysics Data System (ADS)

    Grosheintz, Luc; Mendonça, João; Käppeli, Roger; Lukas Grimm, Simon; Mishra, Siddhartha; Heng, Kevin

    2015-12-01

    implicit GCM. By ESS3, I hope to present results for the advection equation.THOR is part of the Exoclimes Simulation Platform (ESP), a set of open-source community codes for simulating and understanding the atmospheres of exoplanets. The ESP also includes tools for radiative transfer and retrieval (HELIOS), an opacity calculator (HELIOS-K), and a chemical kinetics solver (VULCAN). We expect to publicly release an initial version of THOR in 2016 on www.exoclime.org.

  13. Open Source assimilation tool for distributed hydrological model

    NASA Astrophysics Data System (ADS)

    Richard, Julien; Giangola-Murzyn, Agathe; Tchiguirinskaia, Ioulia; Schertzer, Daniel

    2013-04-01

    An advanced GIS data assimilation interface is a requisite to obtain a distributed hydrological model that is both transportable from catchment to catchment and is easily adaptable to data resolution. This tool is achieved for the cartographic data as well as the linked information data. In the case of the Multi-Hydro-Version2 model (A. Giangola-Murzyn et al. 2012), several types of information are distributed on a regular grid. The grid cell size has to be chosen by the user and each cell has to be filled up with information. In order to be the most realistic as possible, the Multi-Hydro model takes into account several data. For that, the assimilation tool (MH-AssimTool) has to be able to import all these different information. The needed flexibility of the studied area and grid size requires that the GIS interface must be easy to take in hand and also practical. The solution of a main window for the geographical visualisation and hierarchical menus coupled with checkboxes was chosen. For example, the geographical information, like the topography or the land use can be visualized in the main window. For the other data, like the soil conductivity, the geology or the initial moisture, the information is demanded through several pop-up windows. Once the needed information imported, MH-AssimTool prepares automatically the data. For the topography data conversion, if the resolution is too small, an interpolation is done during the processing. As a result, all the converted data is in a good resolution for the modelling. As Multi-Hydro, MH-AssimTool is open source. It's coded in Visual Basic language coupled with a GIS library. The interface is built in such a way then it can be used by a non specialist. We will illustrate the efficiency of the tool with some case studies of peri-urban catchments of widely different sizes and characteristics. We will also explain some parts of the coding of the interface.

  14. Open science: Investigating precipitation cycles in dynamically downscaled data using openly available radar data and open source software

    NASA Astrophysics Data System (ADS)

    Collis, Scott; helmus, Jonathan; Kotamarthi, Rao; Wang, Jiali; Feng, Yan; Ghate, Virendra

    2016-04-01

    In order to assess infrastructure resilience to climate change in urban centers, climate model output is needed at spatial resolutions required for urban planning. This is most commonly achieved using either empirical or dynamic downscaling at present. The utility of these downscaling methods for assessments depends on having estimates of biases in the models estimate climate variables and their extremes, surface temperature and precipitation as an example, developed using historical data sets. Since precipitation is a multi-scale stochastic process direct comparison with observations is challenging and even modern data sets work at scales too coarse to capture extreme events. Gauge data requires a direct hit by a storm to see the highest rain rates, often leading to an underestimation in the 1-100 year rainfall. This is exacerbated by phenomena such as training that can cause very high gradients in accumulation. This presentation details a long-term (multi-year) study of precipitation derived from open data from the NOAA Next-Generation Radar (NEXRAD) network. Two locations are studied; Portland, Maine, location for a pilot study conducted by the US Department of Homeland Security's on regional resilience to climate change and the Southern Great Plains of Oklahoma, home to the Department of Energy's ARM program. Both are located within 40km of a NEXRAD radar allowing retrievals of rainfall rates on the order of one kilometer using the Python-ARM Radar Toolkit (Py-ART). Both the diurnal and season cycle of precipitation is studied and compared to WRF dynamically downscaled precipitation rates. This project makes heavy use of open source community tools such as project Jupyter and the Scientific Python ecosystem to manage and process 10's of TB of data on midrange cluster infrastructure. Both the meteorological aspects and the data infrastructure and architecture will be discussed.

  15. Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

    PubMed

    Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

    2015-02-01

    Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages.

  16. Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

    PubMed

    Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

    2015-02-01

    Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. PMID:25483886

  17. What's mine is yours-open source as a new paradigm for sustainable healthcare education.

    PubMed

    Ellaway, Rachel; Martin, Ross D

    2008-01-01

    Free and open access to information, and increasingly digital content and tools, is one of the defining characteristics of the Internet and as such it presents a challenge to traditional models of development and provision of educational materials and activities. Open source is a particular way of giving access to materials and processes in that the source material is available alongside the finished artifact, thereby allowing subsequent adaptation and redevelopment by anyone wishing to undertake the work. Open source is now being developed as a concept that can be applied in settings outside software development (Kelty 2005), and it is increasingly being linked to moral and ethical agendas about the nature of society itself (Lessig 2005). The open source movement also raises issues regarding authority challenging the role of the expert voice. The imperative of open source and associated economic and social factors all point to an opportunity-rich area for both reflection and development. This paper explores the open source phenomena and it will consider ways in which open source principles and ideas can benefit and extend the provision of a wide range of healthcare education services and activities. PMID:18464143

  18. An Earthquake Information Service with Free and Open Source Tools

    NASA Astrophysics Data System (ADS)

    Schroeder, M.; Stender, V.; Jüngling, S.

    2015-12-01

    At the GFZ German Research Centre for Geosciences in Potsdam, the working group Earthquakes and Volcano Physics examines the spatiotemporal behavior of earthquakes. In this context also the hazards of volcanic eruptions and tsunamis are explored. The aim is to collect related information after the occurrence of such extreme event and make them available for science and partly to the public as quickly as possible. However, the overall objective of this research is to reduce the geological risks that emanate from such natural hazards. In order to meet the stated objectives and to get a quick overview about the seismicity of a particular region and to compare the situation to historical events, a comprehensive visualization was desired. Based on the web-accessible data from the famous GFZ GEOFON network a user-friendly web mapping application was realized. Further, this web service integrates historical and current earthquake information from the USGS earthquake database, and more historical events from various other catalogues like Pacheco, International Seismological Centre (ISC) and more. This compilation of sources is unique in Earth sciences. Additionally, information about historical and current occurrences of volcanic eruptions and tsunamis are also retrievable. Another special feature in the application is the containment of times via a time shifting tool. Users can interactively vary the visualization by moving the time slider. Furthermore, the application was realized by using the newest JavaScript libraries which enables the application to run in all sizes of displays and devices. Our contribution will present the making of, the architecture behind, and few examples of the look and feel of this application.

  19. An Open-Source Approach for Catchment's Physiographic Characterization

    NASA Astrophysics Data System (ADS)

    Di Leo, M.; Di Stefano, M.

    2013-12-01

    A water catchment's hydrologic response is intimately linked to its morphological shape, which is a signature on the landscape of the particular climate conditions that generated the hydrographic basin over time. Furthermore, geomorphologic structures influence hydrologic regimes and land cover (vegetation). For these reasons, a basin's characterization is a fundamental element in hydrological studies. Physiographic descriptors have been extracted manually for long time, but currently Geographic Information System (GIS) tools ease such task by offering a powerful instrument for hydrologists to save time and improve accuracy of result. Here we present a program combining the flexibility of the Python programming language with the reliability of GRASS GIS, which automatically performing the catchment's physiographic characterization. GRASS (Geographic Resource Analysis Support System) is a Free and Open Source GIS, that today can look back on 30 years of successful development in geospatial data management and analysis, image processing, graphics and maps production, spatial modeling and visualization. The recent development of new hydrologic tools, coupled with the tremendous boost in the existing flow routing algorithms, reduced the computational time and made GRASS a complete toolset for hydrological analysis even for large datasets. The tool presented here is a module called r.basin, based on GRASS' traditional nomenclature, where the "r" stands for "raster", and it is available for GRASS version 6.x and more recently for GRASS 7. As input it uses a Digital Elevation Model and the coordinates of the outlet, and, powered by the recently developed r.stream.* hydrological tools, it performs the flow calculation, delimits the basin's boundaries and extracts the drainage network, returning the flow direction and accumulation, the distance to outlet and the hill slopes length maps. Based on those maps, it calculates hydrologically meaningful shape factors and

  20. DiameterJ: A Validated Open Source Nanofiber Diameter Measurement Tool

    PubMed Central

    Hotaling, Nathan A.; Bharti, Kapil; Kriel, Haydn; Simon, Carl G.

    2015-01-01

    Despite the growing use of nanofiber scaffolds for tissue engineering applications, there is not a validated, readily available, free solution for rapid, automated analysis of nanofiber diameter from scanning electron microscope (SEM) micrographs. Thus, the goal of this study was to create a user friendly ImageJ/FIJI plugin that would analyze SEM micrographs of nanofibers to determine nanofiber diameter on a desktop computer within 60 seconds. Additional design goals included 1) compatibility with a variety of existing segmentation algorithms, and 2) an open source code to enable further improvement of the plugin. Using existing algorithms for centerline determination, Euclidean distance transforms and a novel pixel transformation technique, a plugin called “DiameterJ” was created for ImageJ/FIJI. The plugin was validated using 1) digital synthetic images of white lines on a black background and 2) SEM images of nominally monodispersed steel wires of known diameters. DiameterJ analyzed SEM micrographs in 20 seconds, produced diameters not statistically different from known values, was over 10-times closer to known diameter values than other open source software, provided hundreds of times the sampling of manual measurement, and was hundreds of times faster than manual assessment of nanofiber diameter. DiameterJ enables users to rapidly and thoroughly determine the structural features of nanofiber scaffolds and could potentially allow new insights to be formed into fiber diameter distribution and cell response. PMID:26043061

  1. Energy Spectral Behaviors of Communication Networks of Open-Source Communities.

    PubMed

    Yang, Jianmei; Yang, Huijie; Liao, Hao; Wang, Jiangtao; Zeng, Jinqun

    2015-01-01

    Large-scale online collaborative production activities in open-source communities must be accompanied by large-scale communication activities. Nowadays, the production activities of open-source communities, especially their communication activities, have been more and more concerned. Take CodePlex C # community for example, this paper constructs the complex network models of 12 periods of communication structures of the community based on real data; then discusses the basic concepts of quantum mapping of complex networks, and points out that the purpose of the mapping is to study the structures of complex networks according to the idea of quantum mechanism in studying the structures of large molecules; finally, according to this idea, analyzes and compares the fractal features of the spectra in different quantum mappings of the networks, and concludes that there are multiple self-similarity and criticality in the communication structures of the community. In addition, this paper discusses the insights and application conditions of different quantum mappings in revealing the characteristics of the structures. The proposed quantum mapping method can also be applied to the structural studies of other large-scale organizations. PMID:26047331

  2. Energy Spectral Behaviors of Communication Networks of Open-Source Communities.

    PubMed

    Yang, Jianmei; Yang, Huijie; Liao, Hao; Wang, Jiangtao; Zeng, Jinqun

    2015-01-01

    Large-scale online collaborative production activities in open-source communities must be accompanied by large-scale communication activities. Nowadays, the production activities of open-source communities, especially their communication activities, have been more and more concerned. Take CodePlex C # community for example, this paper constructs the complex network models of 12 periods of communication structures of the community based on real data; then discusses the basic concepts of quantum mapping of complex networks, and points out that the purpose of the mapping is to study the structures of complex networks according to the idea of quantum mechanism in studying the structures of large molecules; finally, according to this idea, analyzes and compares the fractal features of the spectra in different quantum mappings of the networks, and concludes that there are multiple self-similarity and criticality in the communication structures of the community. In addition, this paper discusses the insights and application conditions of different quantum mappings in revealing the characteristics of the structures. The proposed quantum mapping method can also be applied to the structural studies of other large-scale organizations.

  3. 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

  4. DiameterJ: A validated open source nanofiber diameter measurement tool.

    PubMed

    Hotaling, Nathan A; Bharti, Kapil; Kriel, Haydn; Simon, Carl G

    2015-08-01

    Despite the growing use of nanofiber scaffolds for tissue engineering applications, there is not a validated, readily available, free solution for rapid, automated analysis of nanofiber diameter from scanning electron microscope (SEM) micrographs. Thus, the goal of this study was to create a user friendly ImageJ/FIJI plugin that would analyze SEM micrographs of nanofibers to determine nanofiber diameter on a desktop computer within 60 s. Additional design goals included 1) compatibility with a variety of existing segmentation algorithms, and 2) an open source code to enable further improvement of the plugin. Using existing algorithms for centerline determination, Euclidean distance transforms and a novel pixel transformation technique, a plugin called "DiameterJ" was created for ImageJ/FIJI. The plugin was validated using 1) digital synthetic images of white lines on a black background and 2) SEM images of nominally monodispersed steel wires of known diameters. DiameterJ analyzed SEM micrographs in 20 s, produced diameters not statistically different from known values, was over 10-times closer to known diameter values than other open source software, provided hundreds of times the sampling of manual measurement, and was hundreds of times faster than manual assessment of nanofiber diameter. DiameterJ enables users to rapidly and thoroughly determine the structural features of nanofiber scaffolds and could potentially allow new insights to be formed into fiber diameter distribution and cell response.

  5. Energy Spectral Behaviors of Communication Networks of Open-Source Communities

    PubMed Central

    Yang, Jianmei; Yang, Huijie; Liao, Hao; Wang, Jiangtao; Zeng, Jinqun

    2015-01-01

    Large-scale online collaborative production activities in open-source communities must be accompanied by large-scale communication activities. Nowadays, the production activities of open-source communities, especially their communication activities, have been more and more concerned. Take CodePlex C # community for example, this paper constructs the complex network models of 12 periods of communication structures of the community based on real data; then discusses the basic concepts of quantum mapping of complex networks, and points out that the purpose of the mapping is to study the structures of complex networks according to the idea of quantum mechanism in studying the structures of large molecules; finally, according to this idea, analyzes and compares the fractal features of the spectra in different quantum mappings of the networks, and concludes that there are multiple self-similarity and criticality in the communication structures of the community. In addition, this paper discusses the insights and application conditions of different quantum mappings in revealing the characteristics of the structures. The proposed quantum mapping method can also be applied to the structural studies of other large-scale organizations. PMID:26047331

  6. DiameterJ: A validated open source nanofiber diameter measurement tool.

    PubMed

    Hotaling, Nathan A; Bharti, Kapil; Kriel, Haydn; Simon, Carl G

    2015-08-01

    Despite the growing use of nanofiber scaffolds for tissue engineering applications, there is not a validated, readily available, free solution for rapid, automated analysis of nanofiber diameter from scanning electron microscope (SEM) micrographs. Thus, the goal of this study was to create a user friendly ImageJ/FIJI plugin that would analyze SEM micrographs of nanofibers to determine nanofiber diameter on a desktop computer within 60 s. Additional design goals included 1) compatibility with a variety of existing segmentation algorithms, and 2) an open source code to enable further improvement of the plugin. Using existing algorithms for centerline determination, Euclidean distance transforms and a novel pixel transformation technique, a plugin called "DiameterJ" was created for ImageJ/FIJI. The plugin was validated using 1) digital synthetic images of white lines on a black background and 2) SEM images of nominally monodispersed steel wires of known diameters. DiameterJ analyzed SEM micrographs in 20 s, produced diameters not statistically different from known values, was over 10-times closer to known diameter values than other open source software, provided hundreds of times the sampling of manual measurement, and was hundreds of times faster than manual assessment of nanofiber diameter. DiameterJ enables users to rapidly and thoroughly determine the structural features of nanofiber scaffolds and could potentially allow new insights to be formed into fiber diameter distribution and cell response. PMID:26043061

  7. KNIME for Open-Source Bioimage Analysis: A Tutorial.

    PubMed

    Dietz, Christian; Berthold, Michael R

    2016-01-01

    The open analytics platform KNIME is a modular environment that enables easy visual assembly and interactive execution of workflows. KNIME is already widely used in various areas of research, for instance in cheminformatics or classical data analysis. In this tutorial the KNIME Image Processing Extension is introduced, which adds the capabilities to process and analyse huge amounts of images. In combination with other KNIME extensions, KNIME Image Processing opens up new possibilities for inter-domain analysis of image data in an understandable and reproducible way. PMID:27207367

  8. KNIME for Open-Source Bioimage Analysis: A Tutorial.

    PubMed

    Dietz, Christian; Berthold, Michael R

    2016-01-01

    The open analytics platform KNIME is a modular environment that enables easy visual assembly and interactive execution of workflows. KNIME is already widely used in various areas of research, for instance in cheminformatics or classical data analysis. In this tutorial the KNIME Image Processing Extension is introduced, which adds the capabilities to process and analyse huge amounts of images. In combination with other KNIME extensions, KNIME Image Processing opens up new possibilities for inter-domain analysis of image data in an understandable and reproducible way.

  9. Sketching Up New Geographies: Open Sourcing and Curriculum Development

    ERIC Educational Resources Information Center

    Boyd, William; Ellis, David

    2013-01-01

    The functionality of web 2.0 technologies has caused academics to rethink their development of teaching and learning methods and approaches. The editable, open access nature of web 2.0 encourages the innovative collaboration of ideas, the creation of equitable visual and tactile learning environments, and opportunity for academics to develop…

  10. Open source software integrated into data services of Japanese planetary explorations

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  11. wradlib - an Open Source Library for Weather Radar Data Processing

    NASA Astrophysics Data System (ADS)

    Pfaff, Thomas; Heistermann, Maik; Jacobi, Stephan

    2014-05-01

    Even though weather radar holds great promise for the hydrological sciences, offering precipitation estimates with unrivaled spatial and temporal resolution, there are still problems impeding its widespread use, among which are: almost every radar data set comes with a different data format with public reading software being available only rarely. standard products as issued by the meteorological services often do not serve the needs of original research, having either too many or too few corrections applied. Especially when new correction methods are to be developed, researchers are often forced to start from scratch having to implement many corrections in addition to those they are actually interested in. many algorithms published in the literature cannot be recreated using the corresponding article only. Public codes, providing insight into the actual implementation and how an approach deals with possible exceptions are rare. the radial scanning setup of weather radar measurements produces additional challenges, when it comes to visualization or georeferencing of this type of data. Based on these experiences, and in the hope to spare others at least some of these tedious tasks, wradlib offers the results of the author's own efforts and a growing number of community-supplied methods. wradlib is designed as a Python library of functions and classes to assist users in their analysis of weather radar data. It provides solutions for all tasks along a typical processing chain leading from raw reflectivity data to corrected, georeferenced and possibly gauge adjusted quantitative precipitation estimates. There are modules for data input/output, data transformation including Z/R transformation, clutter identification, attenuation correction, dual polarization and differential phase processing, interpolation, georeferencing, compositing, gauge adjustment, verification and visualization. The interpreted nature of the Python programming language makes wradlib an ideal tool

  12. Evidence for an Additional Heat Source in the Warm Ionized Medium of Galaxies.

    PubMed

    Reynolds; Haffner; Tufte

    1999-11-01

    Spatial variations of the [S ii]/Halpha and [N ii]/Halpha line intensity ratios observed in the gaseous halo of the Milky Way and other galaxies are inconsistent with pure photoionization models. They appear to require a supplemental heating mechanism that increases the electron temperature at low densities, ne. This would imply that in addition to photoionization, which has a heating rate per unit volume proportional to n2e, there is another source of heat with a rate per unit volume proportional to a lower power of ne. One possible mechanism is the dissipation of interstellar plasma turbulence, which, according to Minter & Spangler, heats the ionized interstellar medium in the Milky Way at a rate of approximately 1x10-25ne ergs cm-3 s-1. If such a source were present, it would dominate over photoionization heating in regions where ne less, similar0.1 cm-3, producing the observed increases in the [S ii]/Halpha and [N ii]/Halpha intensity ratios at large distances from the galactic midplane as well as accounting for the constancy of [S ii]/[N ii], which is not explained by pure photoionization. Other supplemental heating sources, such as magnetic reconnection, cosmic rays, or photoelectric emission from small grains, could also account for these observations, provided they supply approximately 10-5 ergs s-1 per square centimeter of the Galactic disk to the warm ionized medium.

  13. Sticks AND Carrots: Encouraging Open Science at its source

    PubMed Central

    Leonelli, Sabina; Spichtinger, Daniel; Prainsack, Barbara

    2015-01-01

    The Open Science (OS) movement has been seen as an important facilitator for public participation in science. This has been underpinned by the assumption that widespread and free access to research outputs leads to (i) better and more efficient science, (ii) economic growth, in particular for small and medium-sized enterprises wishing to capitalise on research findings and (iii) increased transparency of knowledge production and its outcomes. The latter in particular could function as a catalyst for public participation and engagement. Whether OS is likely to help realise these benefits, however, will depend on the emergence of systemic incentives for scientists to utilise OS in a meaningful manner. While some areas, the environmental sciences have a long tradition of open ethos, citizen inclusion and global collaborations, such activities need to be more systematically supported and promoted by funders and learned societies in order to improve scientific research and public participation. PMID:26435842

  14. Open-Source 3-D Platform for Low-Cost Scientific Instrument Ecosystem.

    PubMed

    Zhang, C; Wijnen, B; Pearce, J M

    2016-08-01

    The combination of open-source software and hardware provides technically feasible methods to create low-cost, highly customized scientific research equipment. Open-source 3-D printers have proven useful for fabricating scientific tools. Here the capabilities of an open-source 3-D printer are expanded to become a highly flexible scientific platform. An automated low-cost 3-D motion control platform is presented that has the capacity to perform scientific applications, including (1) 3-D printing of scientific hardware; (2) laboratory auto-stirring, measuring, and probing; (3) automated fluid handling; and (4) shaking and mixing. The open-source 3-D platform not only facilities routine research while radically reducing the cost, but also inspires the creation of a diverse array of custom instruments that can be shared and replicated digitally throughout the world to drive down the cost of research and education further. PMID:26763293

  15. Human terrain exploitation suite: applying visual analytics to open source information.

    NASA Astrophysics Data System (ADS)

    Hanratty, Timothy; Richardson, John; Mittrick, Mark; Dumer, John; Heilman, Eric; Roy, Heather; Kase, Sue

    2014-05-01

    This paper presents the concept development and demonstration of the Human Terrain Exploitation Suite (HTES) under development at the U.S. Army Research Laboratory's Tactical Information Fusion Branch. The HTES is an amalgamation of four complementary visual analytic capabilities that target the exploitation of open source information. Open source information, specifically news feeds, blogs and other social media, provide a unique opportunity to collect and examine salient topics and trends. Analysis of open source information provides valuable insights into determining opinions, values, cultural nuances and other socio-political aspects within a military area of interest. The early results of the HTES field study indicate that the tools greatly increased the analysts' ability to exploit open source information, but improvement through greater cross-tool integration and correlation of their results is necessary for further advances.

  16. Open-Source 3-D Platform for Low-Cost Scientific Instrument Ecosystem.

    PubMed

    Zhang, C; Wijnen, B; Pearce, J M

    2016-08-01

    The combination of open-source software and hardware provides technically feasible methods to create low-cost, highly customized scientific research equipment. Open-source 3-D printers have proven useful for fabricating scientific tools. Here the capabilities of an open-source 3-D printer are expanded to become a highly flexible scientific platform. An automated low-cost 3-D motion control platform is presented that has the capacity to perform scientific applications, including (1) 3-D printing of scientific hardware; (2) laboratory auto-stirring, measuring, and probing; (3) automated fluid handling; and (4) shaking and mixing. The open-source 3-D platform not only facilities routine research while radically reducing the cost, but also inspires the creation of a diverse array of custom instruments that can be shared and replicated digitally throughout the world to drive down the cost of research and education further.

  17. Accelerated Source-Encoding Full-Waveform Inversion with Additional Constraints

    NASA Astrophysics Data System (ADS)

    Boehm, C.; Fichtner, A.; Ulbrich, M.

    2014-12-01

    We present a flexible framework of Newton-type methods for constrained full-waveform inversion in the time domain. Our main goal is (1) to incorporate additional prior knowledge by using general constraints on the model parameters and (2) to reduce the computational costs of solving the inverse problem by tailoring source-encoding strategies to Newton-type methods.In particular, we apply the Moreau-Yosida regularization to handle the constraints and use a continuation strategy to adjust the regularization parameter. Furthermore, we propose a semismooth Newton method with a trust-region globalization that relies on second-order adjoints to compute the Newton system with a matrix-free preconditioned conjugate gradient solver. The costs of conventional FWI approaches scale proportionally with the number of seismic sources. Here, source-encoding strategies that trigger different sources simultaneously have been proven to be a successful tool to trade a small loss of information for huge savings of computational time to solve the inverse problem. This is particularly interesting for our setting as one iteration of Newton's methods using the full Hessian is considerably more expensive than quasi-Newton methods like L-BFGS. To this end, we discuss a sample average approximation model that is accelerated by using inexact Hessian information based on mini-batches of the samples. Furthermore, we compare its performance with stochastic descent schemes. Here, the classical stochastic gradient method is accelerated by an L-BFGS preconditioner and moreover, the stability of this stochastic preconditioner is enhanced by using the Hessian instead of only gradient information.Numerical results are presented for problems in geophysical exploration on reservoir-scale.

  18. SIMPEG: An open source framework for simulation and gradient based parameter estimation in geophysical applications

    NASA Astrophysics Data System (ADS)

    Cockett, Rowan; Kang, Seogi; Heagy, Lindsey J.; Pidlisecky, Adam; Oldenburg, Douglas W.

    2015-12-01

    Inverse modeling is a powerful tool for extracting information about the subsurface from geophysical data. Geophysical inverse problems are inherently multidisciplinary, requiring elements from the relevant physics, numerical simulation, and optimization, as well as knowledge of the geologic setting, and a comprehension of the interplay between all of these elements. The development and advancement of inversion methodologies can be enabled by a framework that supports experimentation, is flexible and extensible, and allows the knowledge generated to be captured and shared. The goal of this paper is to propose a framework that supports many different types of geophysical forward simulations and deterministic inverse problems. Additionally, we provide an open source implementation of this framework in Python called SIMPEG (Simulation and Parameter Estimation in Geophysics,

  19. Design of a high order Campbelling mode measurement system using open source hardware

    NASA Astrophysics Data System (ADS)

    Izarra, G. de; Elter, Zs.; Jammes, C.

    2016-12-01

    This paper reviews a new real-time measurement instrument dedicated for online neutron monitoring with fission chambers in nuclear reactors. The instrument implements the higher order Campbelling methods and self-monitoring capabilities on an open source development board. The board includes an CPU/FPGA System on a Chip. The feasibility of the measurement instrument was tested both in laboratory with a signal generator and in the Minerve reactor. It is shown that the instrument provides reliable and robust count rate estimation over a wide reactor power range based on the third order statistics of the fission chamber signal. In addition, the system is able to identify whether the measured count rate change is due to the malfunction of the detector or due to the change in the neutron flux. The applied self-monitoring method is based on the spectral properties of the fission chamber signal. During the experimental verification, the considered malfunction was the change of the polarization voltage.

  20. Update on single-screw expander geometry model integrated into an open-source simulation tool

    NASA Astrophysics Data System (ADS)

    Ziviani, D.; Bell, I. H.; De Paepe, M.; van den Broek, M.

    2015-08-01

    In this paper, a mechanistic steady-state model of a single-screw expander is described with emphasis on the geometric description. Insights into the calculation of the main parameters and the definition of the groove profile are provided. Additionally, the adopted chamber model is discussed. The model has been implemented by means of the open-source software PDSim (Positive Displacement SIMulation), written in the Python language, and the solution algorithm is described. The single-screw expander model is validated with a set of steady-state measurement points collected from a 11 kWe organic Rankine cycle test-rig with SES36 and R245fa as working fluid. The overall performance and behavior of the expander are also further analyzed.

  1. Ontology-Based Data Integration of Open Source Electronic Medical Record and Data Capture Systems

    ERIC Educational Resources Information Center

    Guidry, Alicia F.

    2013-01-01

    In low-resource settings, the prioritization of clinical care funding is often determined by immediate health priorities. As a result, investment directed towards the development of standards for clinical data representation and exchange are rare and accordingly, data management systems are often redundant. Open-source systems such as OpenMRS and…

  2. Development and evaluation of a lightweight sensor system for emission sampling from open area sources

    EPA Science Inventory

    A new sensor system for mobile and aerial emission sampling was developed for open area sources, such as open burning. The sensor system, termed “Kolibri”, consists of multiple low-cost air quality sensors measuring CO2, CO, and black carbon, samplers for particulate matter with ...

  3. Limitations of Phased Array Beamforming in Open Rotor Noise Source Imaging

    NASA Technical Reports Server (NTRS)

    Horvath, Csaba; Envia, Edmane; Podboy, Gary G.

    2013-01-01

    Phased array beamforming results of the F31/A31 historical baseline counter-rotating open rotor blade set were investigated for measurement data taken on the NASA Counter-Rotating Open Rotor Propulsion Rig in the 9- by 15-Foot Low-Speed Wind Tunnel of NASA Glenn Research Center as well as data produced using the LINPROP open rotor tone noise code. The planar microphone array was positioned broadside and parallel to the axis of the open rotor, roughly 2.3 rotor diameters away. The results provide insight as to why the apparent noise sources of the blade passing frequency tones and interaction tones appear at their nominal Mach radii instead of at the actual noise sources, even if those locations are not on the blades. Contour maps corresponding to the sound fields produced by the radiating sound waves, taken from the simulations, are used to illustrate how the interaction patterns of circumferential spinning modes of rotating coherent noise sources interact with the phased array, often giving misleading results, as the apparent sources do not always show where the actual noise sources are located. This suggests that a more sophisticated source model would be required to accurately locate the sources of each tone. The results of this study also have implications with regard to the shielding of open rotor sources by airframe empennages.

  4. Edaq530: A Transparent, Open-End and Open-Source Measurement Solution in Natural Science Education

    ERIC Educational Resources Information Center

    Kopasz, Katalin; Makra, Peter; Gingl, Zoltan

    2011-01-01

    We present Edaq530, a low-cost, compact and easy-to-use digital measurement solution consisting of a thumb-sized USB-to-sensor interface and measurement software. The solution is fully open-source, our aim being to provide a viable alternative to professional solutions. Our main focus in designing Edaq530 has been versatility and transparency. In…

  5. Open-Source web-based Geographical Information System for health exposure assessment.

    PubMed

    Evans, Barry; Sabel, Clive E

    2012-01-01

    This paper presents the design and development of an open source web-based Geographical Information System allowing users to visualise, customise and interact with spatial data within their web browser. The developed application shows that by using solely Open Source software it was possible to develop a customisable web based GIS application that provides functions necessary to convey health and environmental data to experts and non-experts alike without the requirement of proprietary software.

  6. Anatomy of BioJS, an open source community for the life sciences

    PubMed Central

    Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel

    2015-01-01

    BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects. DOI: http://dx.doi.org/10.7554/eLife.07009.001 PMID:26153621

  7. Anatomy of BioJS, an open source community for the life sciences.

    PubMed

    Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel

    2015-01-01

    BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects. PMID:26153621

  8. Anatomy of BioJS, an open source community for the life sciences.

    PubMed

    Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel

    2015-07-08

    BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

  9. 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

  10. MANTA--an open-source, high density electrophysiology recording suite for MATLAB.

    PubMed

    Englitz, B; David, S V; Sorenson, M D; Shamma, S A

    2013-01-01

    The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point.

  11. MANTA--an open-source, high density electrophysiology recording suite for MATLAB.

    PubMed

    Englitz, B; David, S V; Sorenson, M D; Shamma, S A

    2013-01-01

    The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point. PMID:23653593

  12. MANTA—an open-source, high density electrophysiology recording suite for MATLAB

    PubMed Central

    Englitz, B.; David, S. V.; Sorenson, M. D.; Shamma, S. A.

    2013-01-01

    The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point. PMID:23653593

  13. Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

    PubMed Central

    Helmus, Jonathan J.; Jaroniec, Christopher P.

    2013-01-01

    Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

  14. JBioWH: an open-source Java framework for bioinformatics data integration.

    PubMed

    Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

    2013-01-01

    The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

  15. Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

    PubMed

    Helmus, Jonathan J; Jaroniec, Christopher P

    2013-04-01

    Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

  16. Open source information on the U.S. infrastructure

    NASA Astrophysics Data System (ADS)

    Freiwald, David A.

    1995-05-01

    Terrorism is expected to increase on a global scale, with the US also becoming more of a target. Since there has not been a war in the lower 48 states of the continental US since about the turn of the century, the US has been quite open and lax about publishing information on our infrastructure, namely details on locations of power lines, gas and oil pipelines, etc.-- information not publically available in Europe. Examples are given, along with comments on the potential implications. Finally, brief remarks are given on some ways to address the situation.

  17. Styrofoam Debris as a Source of Hazardous Additives for Marine Organisms.

    PubMed

    Jang, Mi; Shim, Won Joon; Han, Gi Myung; Rani, Manviri; Song, Young Kyoung; Hong, Sang Hee

    2016-05-17

    There is growing concern over plastic debris and their fragments as a carrier for hazardous substances in marine ecosystem. The present study was conducted to provide field evidence for the transfer of plastic-associated chemicals to marine organisms. Hexabromocyclododecanes (HBCDs), brominated flame retardants, were recently detected in expanded polystyrene (styrofoam) marine debris. We hypothesized that if styrofoam debris acts as a source of the additives in the marine environment, organisms inhabiting such debris might be directly influenced by them. Here we investigated the characteristics of HBCD accumulation by mussels inhabiting styrofoam. For comparison, mussels inhabiting different substrates, such as high-density polyethylene (HDPE), metal, and rock, were also studied. The high HBCD levels up to 5160 ng/g lipid weight and the γ-HBCD dominated isomeric profiles in mussels inhabiting styrofoam strongly supports the transfer of HBCDs from styrofoam substrate to mussels. Furthermore, microsized styrofoam particles were identified inside mussels, probably originating from their substrates.

  18. Styrofoam Debris as a Source of Hazardous Additives for Marine Organisms.

    PubMed

    Jang, Mi; Shim, Won Joon; Han, Gi Myung; Rani, Manviri; Song, Young Kyoung; Hong, Sang Hee

    2016-05-17

    There is growing concern over plastic debris and their fragments as a carrier for hazardous substances in marine ecosystem. The present study was conducted to provide field evidence for the transfer of plastic-associated chemicals to marine organisms. Hexabromocyclododecanes (HBCDs), brominated flame retardants, were recently detected in expanded polystyrene (styrofoam) marine debris. We hypothesized that if styrofoam debris acts as a source of the additives in the marine environment, organisms inhabiting such debris might be directly influenced by them. Here we investigated the characteristics of HBCD accumulation by mussels inhabiting styrofoam. For comparison, mussels inhabiting different substrates, such as high-density polyethylene (HDPE), metal, and rock, were also studied. The high HBCD levels up to 5160 ng/g lipid weight and the γ-HBCD dominated isomeric profiles in mussels inhabiting styrofoam strongly supports the transfer of HBCDs from styrofoam substrate to mussels. Furthermore, microsized styrofoam particles were identified inside mussels, probably originating from their substrates. PMID:27100560

  19. Open source drug discovery--a new paradigm of collaborative research in tuberculosis drug development.

    PubMed

    Bhardwaj, Anshu; Scaria, Vinod; Raghava, Gajendra Pal Singh; Lynn, Andrew Michael; Chandra, Nagasuma; Banerjee, Sulagna; Raghunandanan, Muthukurussi V; Pandey, Vikas; Taneja, Bhupesh; Yadav, Jyoti; Dash, Debasis; Bhattacharya, Jaijit; Misra, Amit; Kumar, Anil; Ramachandran, Srinivasan; Thomas, Zakir; Brahmachari, Samir K

    2011-09-01

    It is being realized that the traditional closed-door and market driven approaches for drug discovery may not be the best suited model for the diseases of the developing world such as tuberculosis and malaria, because most patients suffering from these diseases have poor paying capacity. To ensure that new drugs are created for patients suffering from these diseases, it is necessary to formulate an alternate paradigm of drug discovery process. The current model constrained by limitations for collaboration and for sharing of resources with confidentiality hampers the opportunities for bringing expertise from diverse fields. These limitations hinder the possibilities of lowering the cost of drug discovery. The Open Source Drug Discovery project initiated by Council of Scientific and Industrial Research, India has adopted an open source model to power wide participation across geographical borders. Open Source Drug Discovery emphasizes integrative science through collaboration, open-sharing, taking up multi-faceted approaches and accruing benefits from advances on different fronts of new drug discovery. Because the open source model is based on community participation, it has the potential to self-sustain continuous development by generating a storehouse of alternatives towards continued pursuit for new drug discovery. Since the inventions are community generated, the new chemical entities developed by Open Source Drug Discovery will be taken up for clinical trial in a non-exclusive manner by participation of multiple companies with majority funding from Open Source Drug Discovery. This will ensure availability of drugs through a lower cost community driven drug discovery process for diseases afflicting people with poor paying capacity. Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery.

  20. 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.

  1. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

    PubMed

    Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

    2014-02-01

    De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

  2. Investigation of a corrugated channel flow with an open source PIV software

    NASA Astrophysics Data System (ADS)

    Sivas, Deniz; Bahadır Olcay, A.; Ahn, Hojin

    2016-03-01

    In this study, the corrugated channel flow was investigated by using an open-source particle image velocimetry (PIV) software. The open-source software called OpenPIV was first verified by using images of an earlier experimental work of a vortex ring formation. The corrugated channel flow images were taken with 200 W power LED light source and a high speed camera and those images were analysed with these spatial and temporal tools of OpenPIV. Laminar, transient and turbulent flow regimes were identified when Reynolds number was below 1100, in between 1100 and 2000 and higher than 2000, respectively. The velocity vectors were found to be about 20% lower than the previous study results. The flow inside the grooves was also investigated with OpenPIV and flow characteristics at the grooves were captured when interrogation window size was lowered. The visualization of the flow was presented for different Reynolds numbers with the relative scale values. As a result of this study, OpenPIV software was determined as promising open source PIV analysis software.

  3. Open-Source Python Modules to Estimate Level Ice Thickness from Ice Charts

    NASA Astrophysics Data System (ADS)

    Geiger, C. A.; Deliberty, T. L.; Bernstein, E. R.; Helfrich, S.

    2012-12-01

    A collaborative research effort between the University of Delaware (UD) and National Ice Center (NIC) addresses the task of providing open-source translations of sea ice stage-of-development into level ice thickness estimates on a 4km grid for the Interactive Multisensor Snow and Ice Mapping System (IMS). The characteristics for stage-of-development are quantified from remote sensing imagery with estimates of level ice thickness categories originating from World Meteorological Organization (WMO) egg coded ice charts codified since the 1970s. Conversions utilize Python scripting modules which transform electronic ice charts with WMO egg code characteristics into five level ice thickness categories, in centimeters, (0-10, 10-30, 30-70, 70-120, >120cm) and five ice types (open water, first year pack ice, fast ice, multiyear ice, and glacial ice with a reserve slot for deformed ice fractions). Both level ice thickness categories and ice concentration fractions are reported with uncertainties propagated based on WMO ice stage ranges which serve as proxy estimates for standard deviation. These products are in preparation for use by NCEP, CMC, and NAVO by 2014 based on their modeling requirements for daily products in near-real time. In addition to development, continuing research tests the value of these estimated products against in situ observations to improve both value and uncertainty estimates.

  4. pvsR: An Open Source Interface to Big Data on the American Political Sphere.

    PubMed

    Matter, Ulrich; Stutzer, Alois

    2015-01-01

    Digital data from the political sphere is abundant, omnipresent, and more and more directly accessible through the Internet. Project Vote Smart (PVS) is a prominent example of this big public data and covers various aspects of U.S. politics in astonishing detail. Despite the vast potential of PVS' data for political science, economics, and sociology, it is hardly used in empirical research. The systematic compilation of semi-structured data can be complicated and time consuming as the data format is not designed for conventional scientific research. This paper presents a new tool that makes the data easily accessible to a broad scientific community. We provide the software called pvsR as an add-on to the R programming environment for statistical computing. This open source interface (OSI) serves as a direct link between a statistical analysis and the large PVS database. The free and open code is expected to substantially reduce the cost of research with PVS' new big public data in a vast variety of possible applications. We discuss its advantages vis-à-vis traditional methods of data generation as well as already existing interfaces. The validity of the library is documented based on an illustration involving female representation in local politics. In addition, pvsR facilitates the replication of research with PVS data at low costs, including the pre-processing of data. Similar OSIs are recommended for other big public databases. PMID:26132154

  5. pvsR: An Open Source Interface to Big Data on the American Political Sphere

    PubMed Central

    2015-01-01

    Digital data from the political sphere is abundant, omnipresent, and more and more directly accessible through the Internet. Project Vote Smart (PVS) is a prominent example of this big public data and covers various aspects of U.S. politics in astonishing detail. Despite the vast potential of PVS’ data for political science, economics, and sociology, it is hardly used in empirical research. The systematic compilation of semi-structured data can be complicated and time consuming as the data format is not designed for conventional scientific research. This paper presents a new tool that makes the data easily accessible to a broad scientific community. We provide the software called pvsR as an add-on to the R programming environment for statistical computing. This open source interface (OSI) serves as a direct link between a statistical analysis and the large PVS database. The free and open code is expected to substantially reduce the cost of research with PVS’ new big public data in a vast variety of possible applications. We discuss its advantages vis-à-vis traditional methods of data generation as well as already existing interfaces. The validity of the library is documented based on an illustration involving female representation in local politics. In addition, pvsR facilitates the replication of research with PVS data at low costs, including the pre-processing of data. Similar OSIs are recommended for other big public databases. PMID:26132154

  6. 10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY... holder. (a) Each licensee shall visually check source holders, logging tools, and source handling tools... holders, logging tools, injection tools, source handling tools, storage containers, transport...

  7. A Bayesian Machine Learning Model for Estimating Building Occupancy from Open Source Data

    DOE PAGES

    Stewart, Robert N.; Urban, Marie L.; Duchscherer, Samantha E.; Kaufman, Jason; Morton, April M.; Thakur, Gautam; Piburn, Jesse; Moehl, Jessica

    2016-01-01

    Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the artmore » by introducing the Population Data Tables (PDT), a Bayesian based informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000ft2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information

  8. A Bayesian Machine Learning Model for Estimating Building Occupancy from Open Source Data

    SciTech Connect

    Stewart, Robert N.; Urban, Marie L.; Duchscherer, Samantha E.; Kaufman, Jason; Morton, April M.; Thakur, Gautam; Piburn, Jesse; Moehl, Jessica

    2016-01-01

    Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the art by introducing the Population Data Tables (PDT), a Bayesian based informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000ft2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including

  9. Utilization of open source electronic health record around the world: A systematic review

    PubMed Central

    Aminpour, Farzaneh; Sadoughi, Farahnaz; Ahamdi, Maryam

    2014-01-01

    Many projects on developing Electronic Health Record (EHR) systems have been carried out in many countries. The current study was conducted to review the published data on the utilization of open source EHR systems in different countries all over the world. Using free text and keyword search techniques, six bibliographic databases were searched for related articles. The identified papers were screened and reviewed during a string of stages for the irrelevancy and validity. The findings showed that open source EHRs have been wildly used by source limited regions in all continents, especially in Sub-Saharan Africa and South America. It would create opportunities to improve national healthcare level especially in developing countries with minimal financial resources. Open source technology is a solution to overcome the problems of high-costs and inflexibility associated with the proprietary health information systems. PMID:24672566

  10. GIS-Based Noise Simulation Open Source Software: N-GNOIS

    NASA Astrophysics Data System (ADS)

    Vijay, Ritesh; Sharma, A.; Kumar, M.; Shende, V.; Chakrabarti, T.; Gupta, Rajesh

    2015-12-01

    Geographical information system (GIS)-based noise simulation software (N-GNOIS) has been developed to simulate the noise scenario due to point and mobile sources considering the impact of geographical features and meteorological parameters. These have been addressed in the software through attenuation modules of atmosphere, vegetation and barrier. N-GNOIS is a user friendly, platform-independent and open geospatial consortia (OGC) compliant software. It has been developed using open source technology (QGIS) and open source language (Python). N-GNOIS has unique features like cumulative impact of point and mobile sources, building structure and honking due to traffic. Honking is the most common phenomenon in developing countries and is frequently observed on any type of roads. N-GNOIS also helps in designing physical barrier and vegetation cover to check the propagation of noise and acts as a decision making tool for planning and management of noise component in environmental impact assessment (EIA) studies.

  11. Quantifying atmospheric processing of mineral dust as a source of bioavailable phosphorus to the open oceans

    NASA Astrophysics Data System (ADS)

    Herbert, Ross; Stockdale, Anthony; Carslaw, Ken; Krom, Michael

    2016-04-01

    The transport and deposition of mineral dust is known to be the dominant source of phosphorus (P) to the surface waters of the open oceans. However, the fraction of this P that is deemed available for primary productivity remains a key uncertainty due to a limited understanding of the processes occurring during transport of the dust. Through a series of detailed laboratory experiments using desert dust and dust precursors, we show that the dissolution behaviour of P in these samples is controlled by a surface-bound labile pool, and an additional mineral pool primarily consisting of apatite. The acid dissolution of the apatite occurs rapidly and is controlled by the absolute number of H+ ions present in the solution surrounding the dust. Using these results we develop a new conceptual model that reproduces the major processes controlling P dissolution in the atmosphere. We then use a global aerosol microphysics model with a global soil database to quantify the deposition of bioavailable P to the open oceans and ice sheets. We show that, globally, the labile pool contributes 2.4 Gg P a-1 to the oceans and, from a potential pool of 11.5 Gg P a-1, the dissolved apatite pool contributes 0.24 Gg P a-1. A series of sensitivity studies identifying sources of acid in the atmosphere show that anthropogenic emissions of SO2 contribute 61% of the global mass of dissolved apatite, volcanic events contribute 11%, and DMS emissions contribute 10%. Finally, we show that the fraction of mineral dust P that is available for primary productivity varies, regionally, from <20% in the North Atlantic Ocean to >50% in the South Pacific Ocean; this explains the variability in the fraction of bioavailable P commonly observed in important oceanic regions.

  12. 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.

  13. Quantifying atmospheric processing of mineral dust as a source of bioavailable phosphorus to the open oceans

    NASA Astrophysics Data System (ADS)

    Herbert, Ross; Stockdale, Anthony; Carslaw, Ken; Krom, Michael

    2016-04-01

    The transport and deposition of mineral dust is known to be the dominant source of phosphorus (P) to the surface waters of the open oceans. However, the fraction of this P that is deemed available for primary productivity remains a key uncertainty due to a limited understanding of the processes occurring during transport of the dust. Through a series of detailed laboratory experiments using desert dust and dust precursors, we show that the dissolution behaviour of P in these samples is controlled by a surface-bound labile pool, and an additional mineral pool primarily consisting of apatite. The acid dissolution of the apatite occurs rapidly and is controlled by the absolute number of H+ ions present in the solution surrounding the dust. Using these results we develop a new conceptual model that reproduces the major processes controlling P dissolution in the atmosphere. We then use a global aerosol microphysics model with a global soil database to quantify the deposition of bioavailable P to the open oceans and ice sheets. We show that, globally, the labile pool contributes 2.4 Gg P a‑1 to the oceans and, from a potential pool of 11.5 Gg P a‑1, the dissolved apatite pool contributes 0.24 Gg P a‑1. A series of sensitivity studies identifying sources of acid in the atmosphere show that anthropogenic emissions of SO2 contribute 61% of the global mass of dissolved apatite, volcanic events contribute 11%, and DMS emissions contribute 10%. Finally, we show that the fraction of mineral dust P that is available for primary productivity varies, regionally, from <20% in the North Atlantic Ocean to >50% in the South Pacific Ocean; this explains the variability in the fraction of bioavailable P commonly observed in important oceanic regions.

  14. An open-source, mobile-friendly search engine for public medical knowledge.

    PubMed

    Samwald, Matthias; Hanbury, Allan

    2014-01-01

    The World Wide Web has become an important source of information for medical practitioners. To complement the capabilities of currently available web search engines we developed FindMeEvidence, an open-source, mobile-friendly medical search engine. In a preliminary evaluation, the quality of results from FindMeEvidence proved to be competitive with those from TRIP Database, an established, closed-source search engine for evidence-based medicine.

  15. Building an open-source robotic stereotaxic instrument.

    PubMed

    Coffey, Kevin R; Barker, David J; Ma, Sisi; West, Mark O

    2013-10-29

    This protocol includes the designs and software necessary to upgrade an existing stereotaxic instrument to a robotic (CNC) stereotaxic instrument for around $1,000 (excluding a drill), using industry standard stepper motors and CNC controlling software. Each axis has variable speed control and may be operated simultaneously or independently. The robot's flexibility and open coding system (g-code) make it capable of performing custom tasks that are not supported by commercial systems. Its applications include, but are not limited to, drilling holes, sharp edge craniotomies, skull thinning, and lowering electrodes or cannula. In order to expedite the writing of g-coding for simple surgeries, we have developed custom scripts that allow individuals to design a surgery with no knowledge of programming. However, for users to get the most out of the motorized stereotax, it would be beneficial to be knowledgeable in mathematical programming and G-Coding (simple programming for CNC machining). The recommended drill speed is greater than 40,000 rpm. The stepper motor resolution is 1.8°/Step, geared to 0.346°/Step. A standard stereotax has a resolution of 2.88 μm/step. The maximum recommended cutting speed is 500 μm/sec. The maximum recommended jogging speed is 3,500 μm/sec. The maximum recommended drill bit size is HP 2.

  16. Building An Open-source Robotic Stereotaxic Instrument

    PubMed Central

    Coffey, Kevin R.; Barker, David J.; Ma, Sisi; West, Mark O.

    2013-01-01

    This protocol includes the designs and software necessary to upgrade an existing stereotaxic instrument to a robotic (CNC) stereotaxic instrument for around $1,000 (excluding a drill), using industry standard stepper motors and CNC controlling software. Each axis has variable speed control and may be operated simultaneously or independently. The robot's flexibility and open coding system (g-code) make it capable of performing custom tasks that are not supported by commercial systems. Its applications include, but are not limited to, drilling holes, sharp edge craniotomies, skull thinning, and lowering electrodes or cannula. In order to expedite the writing of g-coding for simple surgeries, we have developed custom scripts that allow individuals to design a surgery with no knowledge of programming. However, for users to get the most out of the motorized stereotax, it would be beneficial to be knowledgeable in mathematical programming and G-Coding (simple programming for CNC machining). The recommended drill speed is greater than 40,000 rpm. The stepper motor resolution is 1.8°/Step, geared to 0.346°/Step. A standard stereotax has a resolution of 2.88 μm/step. The maximum recommended cutting speed is 500 μm/sec. The maximum recommended jogging speed is 3,500 μm/sec. The maximum recommended drill bit size is HP 2. PMID:24192514

  17. Building an open-source robotic stereotaxic instrument.

    PubMed

    Coffey, Kevin R; Barker, David J; Ma, Sisi; West, Mark O

    2013-01-01

    This protocol includes the designs and software necessary to upgrade an existing stereotaxic instrument to a robotic (CNC) stereotaxic instrument for around $1,000 (excluding a drill), using industry standard stepper motors and CNC controlling software. Each axis has variable speed control and may be operated simultaneously or independently. The robot's flexibility and open coding system (g-code) make it capable of performing custom tasks that are not supported by commercial systems. Its applications include, but are not limited to, drilling holes, sharp edge craniotomies, skull thinning, and lowering electrodes or cannula. In order to expedite the writing of g-coding for simple surgeries, we have developed custom scripts that allow individuals to design a surgery with no knowledge of programming. However, for users to get the most out of the motorized stereotax, it would be beneficial to be knowledgeable in mathematical programming and G-Coding (simple programming for CNC machining). The recommended drill speed is greater than 40,000 rpm. The stepper motor resolution is 1.8°/Step, geared to 0.346°/Step. A standard stereotax has a resolution of 2.88 μm/step. The maximum recommended cutting speed is 500 μm/sec. The maximum recommended jogging speed is 3,500 μm/sec. The maximum recommended drill bit size is HP 2. PMID:24192514

  18. Workshop - Serious Games and Open Source: Practice and Futures

    NASA Astrophysics Data System (ADS)

    Backlund, Per; Lundell, Björn; Scacchi, Walt

    Computer games are increasingly used throughout our society with people playing on the bus, at home and at work. Computer games thus affect larger and larger number of people and areas in the society of today. There are even scholars who advocate that games create better environments for learning than traditional classrooms. This situation motivates the use of games and game technology for additional purposes, e.g. education, training, health care or marketing.

  19. Emission source strengths of gasoline-filling processes determined by open-path spectroscopic techniques and inverse modeling

    NASA Astrophysics Data System (ADS)

    Schaefer, Klaus; Stockhause, Martina; Hoffmann, Herbert; Sedlmaier, Achim; Emeis, Stefan M.

    1998-12-01

    Up to now emission source strengths of diffuse and heterogenous emission of important VOCs are not well known especially from gas stations and gasoline tank farms. To estimate the total emission of these sources non-intrusive measurements were performed by a differential optical absorption spectroscopy (DOAS) system to determine the path- integrated concentrations of exhaust compounds downwind of the source through the whole exhaust plume. Simultaneously, the meteorological parameters were measured for modeling the dispersion of the plume inversely to obtain the emission source strengths of these compounds. The emissions by road traffic were determined by an additional open-path DOAS measurement. Measurement campaigns were performed during different wether conditions and at different sources which were characterized by well defined and easy air flow conditions. The emission source strengths were calculated with the Gaussian model PAL. The determined total emission of gas stations with gasoline vapor recovery system are about 20 mg benzene per kg refueled gasoline and the emission from refueling activities vary between 1 and 9 benzene per kg refueled gasoline depending on the technical behavior of the gasoline vapor recovery system. These values which were found from measurements during times with a and without refueling activities show a high amount of diffuse emissions. The emission rates from a gasoline taken farm were measured on an open path through the middle of that area and a maximum of 8 (mu) g/(m2s) was determined.

  20. Flood simulation using an open source quadtree grid shallow water flow solver

    NASA Astrophysics Data System (ADS)

    An, H.; Yu, S.

    2012-12-01

    We carry out performance testing of Gerris for flood simulation. Gerris Flow Solver is open source software and has the capability of adaptive quadtree grid generation. In particular, the shallow water flow solver within Gerris Flow Solver implements second-order accurate Gudunov type numerical schemes, with preserving the balance of source and flux terms on quadtree cut cell grids. The combination of quadtree grids with the cut cell method improves the flexibility of quadtree grids for grid generation. In addition, the model has the capacity of adaptive meshing in an easy and effective way, which can improve computational efficiency in 2D modeling. Pre- and post-processors are already well equipped for users. Finally, an extension such as bed erosion or sediment transport can be added if needed. Two flood events, Malpasset dam break in France and Baeksan levee failure in Korea, are simulated using Gerris, with adaptively refining meshes near water fronts and the river boundary. Simulation results are compared with survey data, experimental data as well as simulation results by other researchers. The simulation results demonstrate that the adaptive quadtree model can save approximately 95% of the computational cost while preserving the accuracy. Gerris is a very attractive alternative for flood managers given the favorable features demonstrated in this paper.

  1. 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

  2. OpenSourcePACS: an extensible infrastructure for medical image management.

    PubMed

    Bui, Alex A T; Morioka, Craig; Dionisio, John David N; Johnson, David B; Sinha, Usha; Ardekani, Siamak; Taira, Ricky K; Aberle, Denise R; El-Saden, Suzie; Kangarloo, Hooshang

    2007-01-01

    The development of comprehensive picture archive and communication systems (PACS) has mainly been limited to proprietary developments by vendors, though a number of freely available software projects have addressed specific image management tasks. The openSourcePACS project aims to provide an open source, common foundation upon which not only can a basic PACS be readily implemented, but to also support the evolution of new PACS functionality through the development of novel imaging applications and services. openSourcePACS consists of four main software modules: 1) image order entry, which enables the ordering and tracking of structured image requisitions; 2) an agent-based image server framework that coordinates distributed image services including routing, image processing, and querying beyond the present digital image and communications in medicine (DICOM) capabilities; 3) an image viewer, supporting standard display and image manipulation tools, DICOM presentation states, and structured reporting; and 4) reporting and result dissemination, supplying web-based widgets for creating integrated reports. All components are implemented using Java to encourage cross-platform deployment. To demonstrate the usage of openSourcePACS, a preliminary application supporting primary care/specialist communication was developed and is described herein. Ultimately, the goal of openSourcePACS is to promote the wide-scale development and usage of PACS and imaging applications within academic and research communities.

  3. The CERN antiproton source: Controls aspects of the additional collector ring and fast sampling devices

    NASA Astrophysics Data System (ADS)

    Chohan, V.

    1990-08-01

    The upgrade of the CERN antiproton source, meant to gain an order of magnitude in antiproton flux, required the construction of an additional ring to complement the existing antiproton accumulator (AA) and an entire rebuild of the target zone. The AA also needed major modifications to handle the increased flux and perform purely as an accumulator, preceded by collection in the collector ring (AC). The upgrade, known as the ACOL (antiproton collector) project, was approved under strict time and budgetary constraints and the existing AA control system, based on the Proton Synchrotron (PS) Divisional norms of CAMAC and Norsk-Data computers, had to be extended in the light of this. The limited (9 months) installation period for the whole upgrade meant that substantial preparatory and planning activities had to be carried out during the normal running of the AA. Advantage was taken of the upgrade to improve and consolidate the AA. Some aspects of the control system related to this upgrade are discussed together with the integration of new applications and instrumentation. The overall machine installation and running-in was carried out within the defined milestones and the project has now achieved the physics design goals.

  4. Elite sport is not an additional source of distress for adolescents with high stress levels.

    PubMed

    Gerber, Markus; Holsboer-Trachsler, Edith; Pühse, Uwe; Brand, Serge

    2011-04-01

    This study examined whether participation in elite sport interacts with stress in decreasing or increasing symptoms of depression and anxiety among adolescents, and further, whether the interplay between participation in high-performance sport and stress is related to the perceived quality of sleep. 434 adolescents (278 girls, 156 boys; age: M = 17.2 yr.) from 15 "Swiss Olympic Sport Classes" and 9 conventional classes answered a questionnaire and completed a 7-day sleep log. Analyses of covariance showed that heightened stress was related to more depressive symptoms and higher scores for trait-anxiety. Moreover, those classified as having poor sleep by a median split cutoff reported higher levels of depressive symptoms. No significant (multivariate) main effects were found for high-performance sport athletes. Similarly, no significant two- or three-way interaction effects were found. These results caution against exaggerated expectations concerning sport participation as a stress buffer. Nevertheless, participation in high-performance sport was not found to be an additional source of distress for adolescents who reported high stress levels despite prior research that has pointed toward such a relationship.

  5. GALE: a generic open source extensible adaptation engine

    NASA Astrophysics Data System (ADS)

    De Bra, Paul; Knutov, Evgeny; Smits, David; Stash, Natalia; Ramos, Vinicius F. C.

    2013-06-01

    This paper motivates and describes GALE, the Generic Adaptation Language and Engine that came out of the GRAPPLE EU FP7 project. The main focus of the paper is the extensible nature of GALE. The purpose of this description is to illustrate how a single core adaptation engine can be used for different types of adaptation, applied to different types of information items and documents. We illustrate the adaptive functionality on some examples of hypermedia documents. In April 2012, David Smits defended the world's first adaptive PhD thesis on this topic. The thesis, available for download and direct adaptive access at http://gale.win.tue.nl/thesis, shows that a single source of information can serve different audiences and at the same time also allows more freedom of navigation than is possible in any paper or static hypermedia document. The same can be done for course texts, hyperfiction, encyclopedia, museum, or other cultural heritage websites, etc. We explain how to add functionality to GALE if desired, to adapt the system's behavior to whatever the application requires. This stresses our main objective: to provide a technological base for adaptive (hypermedia) system researchers on which they can build extensions for the specific research they have in mind.

  6. OpenMS – An open-source software framework for mass spectrometry

    PubMed Central

    Sturm, Marc; Bertsch, Andreas; Gröpl, Clemens; Hildebrandt, Andreas; Hussong, Rene; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Zerck, Alexandra; Reinert, Knut; Kohlbacher, Oliver

    2008-01-01

    Background Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow. Results We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies. Conclusion OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at . PMID:18366760

  7. Open source large-scale high-resolution environmental modelling with GEMS

    NASA Astrophysics Data System (ADS)

    Baarsma, Rein; Alberti, Koko; Marra, Wouter; Karssenberg, Derek

    2016-04-01

    Many environmental, topographic and climate data sets are freely available at a global scale, creating the opportunities to run environmental models for every location on Earth. Collection of the data necessary to do this and the consequent conversion into a useful format is very demanding however, not to mention the computational demand of a model itself. We developed GEMS (Global Environmental Modelling System), an online application to run environmental models on various scales directly in your browser and share the results with other researchers. GEMS is open-source and uses open-source platforms including Flask, Leaflet, GDAL, MapServer and the PCRaster-Python modelling framework to process spatio-temporal models in real time. With GEMS, users can write, run, and visualize the results of dynamic PCRaster-Python models in a browser. GEMS uses freely available global data to feed the models, and automatically converts the data to the relevant model extent and data format. Currently available data includes the SRTM elevation model, a selection of monthly vegetation data from MODIS, land use classifications from GlobCover, historical climate data from WorldClim, HWSD soil information from WorldGrids, population density from SEDAC and near real-time weather forecasts, most with a ±100m resolution. Furthermore, users can add other or their own datasets using a web coverage service or a custom data provider script. With easy access to a wide range of base datasets and without the data preparation that is usually necessary to run environmental models, building and running a model becomes a matter hours. Furthermore, it is easy to share the resulting maps, timeseries data or model scenarios with other researchers through a web mapping service (WMS). GEMS can be used to provide open access to model results. Additionally, environmental models in GEMS can be employed by users with no extensive experience with writing code, which is for example valuable for using models

  8. Integrating open-source software applications to build molecular dynamics systems.

    PubMed

    Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

    2014-04-01

    Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability.

  9. The Open Source DataTurbine Initiative: Streaming Data Middleware for Environmental Observing Systems

    NASA Technical Reports Server (NTRS)

    Fountain T.; Tilak, S.; Shin, P.; Hubbard, P.; Freudinger, L.

    2009-01-01

    The Open Source DataTurbine Initiative is an international community of scientists and engineers sharing a common interest in real-time streaming data middleware and applications. The technology base of the OSDT Initiative is the DataTurbine open source middleware. Key applications of DataTurbine include coral reef monitoring, lake monitoring and limnology, biodiversity and animal tracking, structural health monitoring and earthquake engineering, airborne environmental monitoring, and environmental sustainability. DataTurbine software emerged as a commercial product in the 1990 s from collaborations between NASA and private industry. In October 2007, a grant from the USA National Science Foundation (NSF) Office of Cyberinfrastructure allowed us to transition DataTurbine from a proprietary software product into an open source software initiative. This paper describes the DataTurbine software and highlights key applications in environmental monitoring.

  10. Solar neutrinos and the influences of opacity, thermal instability, additional neutrino sources, and a central black hole on solar models

    NASA Technical Reports Server (NTRS)

    Stothers, R. B.; Ezer, D.

    1972-01-01

    Significant quantities that affect the internal structure of the sun are examined for factors that reduce the temperature near the sun's center. The four factors discussed are: opacity, central black hole, thermal instability, and additional neutrino sources.

  11. Point Cloud Visualization in AN Open Source 3d Globe

    NASA Astrophysics Data System (ADS)

    De La Calle, M.; Gómez-Deck, D.; Koehler, O.; Pulido, F.

    2011-09-01

    During the last years the usage of 3D applications in GIS is becoming more popular. Since the appearance of Google Earth, users are familiarized with 3D environments. On the other hand, nowadays computers with 3D acceleration are common, broadband access is widespread and the public information that can be used in GIS clients that are able to use data from the Internet is constantly increasing. There are currently several libraries suitable for this kind of applications. Based on these facts, and using libraries that are already developed and connected to our own developments, we are working on the implementation of a real 3D GIS with analysis capabilities. Since a 3D GIS such as this can be very interesting for tasks like LiDAR or Laser Scanner point clouds rendering and analysis, special attention is given to get an optimal handling of very large data sets. Glob3 will be a multidimensional GIS in which 3D point clouds could be explored and analysed, even if they are consist of several million points.The latest addition to our visualization libraries is the development of a points cloud server that works regardless of the cloud's size. The server receives and processes petitions from a 3d client (for example glob3, but could be any other, such as one based on WebGL) and delivers the data in the form of pre-processed tiles, depending on the required level of detail.

  12. Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

    NASA Astrophysics Data System (ADS)

    Liu, H. S.; Liao, H. M.

    2015-08-01

    Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS) to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data - a data processing system could be constructed.

  13. The Starchive: An open access, open source archive of nearby and young stars and their planets

    NASA Astrophysics Data System (ADS)

    Tanner, Angelle; Gelino, Chris; Elfeki, Mario

    2015-12-01

    Historically, astronomers have utilized a piecemeal set of archives such as SIMBAD, the Washington Double Star Catalog, various exoplanet encyclopedias and electronic tables from the literature to cobble together stellar and exo-planetary parameters in the absence of corresponding images and spectra. As the search for planets around young stars through direct imaging, transits and infrared/optical radial velocity surveys blossoms, there is a void in the available set of to create comprehensive lists of the stellar parameters of nearby stars especially for important parameters such as metallicity and stellar activity indicators. For direct imaging surveys, we need better resources for downloading existing high contrast images to help confirm new discoveries and find ideal target stars. Once we have discovered new planets, we need a uniform database of stellar and planetary parameters from which to look for correlations to better understand the formation and evolution of these systems. As a solution to these issues, we are developing the Starchive - an open access stellar archive in the spirit of the open exoplanet catalog, the Kepler Community Follow-up Program and many others. The archive will allow users to download various datasets, upload new images, spectra and metadata and will contain multiple plotting tools to use in presentations and data interpretations. While we will highly regulate and constantly validate the data being placed into our archive the open nature of its design is intended to allow the database to be expanded efficiently and have a level of versatility which is necessary in today's fast moving, big data community. Finally, the front-end scripts will be placed on github and users will be encouraged to contribute new plotting tools. Here, I will introduce the community to the content and expected capabilities of the archive and query the audience for community feedback.

  14. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond

    PubMed Central

    Van Voorhis, Wesley C.; Adams, John H.; Adelfio, Roberto; Ahyong, Vida; Akabas, Myles H.; Alano, Pietro; Alday, Aintzane; Alemán Resto, Yesmalie; Alsibaee, Aishah; Alzualde, Ainhoa; Andrews, Katherine T.; Avery, Simon V.; Avery, Vicky M.; Ayong, Lawrence; Baker, Mark; Baker, Stephen; Ben Mamoun, Choukri; Bhatia, Sangeeta; Bickle, Quentin; Bounaadja, Lotfi; Bowling, Tana; Bosch, Jürgen; Boucher, Lauren E.; Boyom, Fabrice F.; Brea, Jose; Brennan, Marian; Burton, Audrey; Caffrey, Conor R.; Camarda, Grazia; Carrasquilla, Manuela; Carter, Dee; Belen Cassera, Maria; Chih-Chien Cheng, Ken; Chindaudomsate, Worathad; Chubb, Anthony; Colon, Beatrice L.; Colón-López, Daisy D.; Corbett, Yolanda; Crowther, Gregory J.; Cowan, Noemi; D’Alessandro, Sarah; Le Dang, Na; Delves, Michael; Du, Alan Y.; Duffy, Sandra; Abd El-Salam El-Sayed, Shimaa; Ferdig, Michael T.; Fernández Robledo, José A.; Fidock, David A.; Florent, Isabelle; Fokou, Patrick V. T.; Galstian, Ani; Gamo, Francisco Javier; Gold, Ben; Golub, Todd; Goldgof, Gregory M.; Guha, Rajarshi; Guiguemde, W. Armand; Gural, Nil; Guy, R. Kiplin; Hansen, Michael A. E.; Hanson, Kirsten K.; Hemphill, Andrew; Hooft van Huijsduijnen, Rob; Horii, Takaaki; Horrocks, Paul; Hughes, Tyler B.; Huston, Christopher; Igarashi, Ikuo; Ingram-Sieber, Katrin; Itoe, Maurice A.; Jadhav, Ajit; Naranuntarat Jensen, Amornrat; Jensen, Laran T.; Jiang, Rays H. Y.; Kaiser, Annette; Keiser, Jennifer; Ketas, Thomas; Kicka, Sebastien; Kim, Sunyoung; Kirk, Kiaran; Kumar, Vidya P.; Kyle, Dennis E.; Lafuente, Maria Jose; Landfear, Scott; Lee, Nathan; Lee, Sukjun; Lehane, Adele M.; Li, Fengwu; Little, David; Liu, Liqiong; Llinás, Manuel; Loza, Maria I.; Lubar, Aristea; Lucantoni, Leonardo; Lucet, Isabelle; Maes, Louis; Mancama, Dalu; Mansour, Nuha R.; March, Sandra; McGowan, Sheena; Medina Vera, Iset; Meister, Stephan; Mercer, Luke; Mestres, Jordi; Mfopa, Alvine N.; Misra, Raj N.; Moon, Seunghyun; Moore, John P.; Morais Rodrigues da Costa, Francielly; Müller, Joachim; Muriana, Arantza; Nakazawa Hewitt, Stephen; Nare, Bakela; Nathan, Carl; Narraidoo, Nathalie; Nawaratna, Sujeevi; Ojo, Kayode K.; Ortiz, Diana; Panic, Gordana; Papadatos, George; Parapini, Silvia; Patra, Kailash; Pham, Ngoc; Prats, Sarah; Plouffe, David M.; Poulsen, Sally-Ann; Pradhan, Anupam; Quevedo, Celia; Quinn, Ronald J.; Rice, Christopher A.; Abdo Rizk, Mohamed; Ruecker, Andrea; St. Onge, Robert; Salgado Ferreira, Rafaela; Samra, Jasmeet; Robinett, Natalie G.; Schlecht, Ulrich; Schmitt, Marjorie; Silva Villela, Filipe; Silvestrini, Francesco; Sinden, Robert; Smith, Dennis A.; Soldati, Thierry; Spitzmüller, Andreas; Stamm, Serge Maximilian; Sullivan, David J.; Sullivan, William; Suresh, Sundari; Suzuki, Brian M.; Suzuki, Yo; Swamidass, S. Joshua; Taramelli, Donatella; Tchokouaha, Lauve R. Y.; Theron, Anjo; Thomas, David; Tonissen, Kathryn F.; Townson, Simon; Tripathi, Abhai K.; Trofimov, Valentin; Udenze, Kenneth O.; Ullah, Imran; Vallieres, Cindy; Vigil, Edgar; Vinetz, Joseph M.; Voong Vinh, Phat; Vu, Hoan; Watanabe, Nao-aki; Weatherby, Kate; White, Pamela M.; Wilks, Andrew F.; Winzeler, Elizabeth A.; Wojcik, Edward; Wree, Melanie; Wu, Wesley; Yokoyama, Naoaki; Zollo, Paul H. A.; Abla, Nada; Blasco, Benjamin; Burrows, Jeremy; Laleu, Benoît; Leroy, Didier; Spangenberg, Thomas; Wells, Timothy; Willis, Paul A.

    2016-01-01

    A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal

  15. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.

    PubMed

    Van Voorhis, Wesley C; Adams, John H; Adelfio, Roberto; Ahyong, Vida; Akabas, Myles H; Alano, Pietro; Alday, Aintzane; Alemán Resto, Yesmalie; Alsibaee, Aishah; Alzualde, Ainhoa; Andrews, Katherine T; Avery, Simon V; Avery, Vicky M; Ayong, Lawrence; Baker, Mark; Baker, Stephen; Ben Mamoun, Choukri; Bhatia, Sangeeta; Bickle, Quentin; Bounaadja, Lotfi; Bowling, Tana; Bosch, Jürgen; Boucher, Lauren E; Boyom, Fabrice F; Brea, Jose; Brennan, Marian; Burton, Audrey; Caffrey, Conor R; Camarda, Grazia; Carrasquilla, Manuela; Carter, Dee; Belen Cassera, Maria; Chih-Chien Cheng, Ken; Chindaudomsate, Worathad; Chubb, Anthony; Colon, Beatrice L; Colón-López, Daisy D; Corbett, Yolanda; Crowther, Gregory J; Cowan, Noemi; D'Alessandro, Sarah; Le Dang, Na; Delves, Michael; DeRisi, Joseph L; Du, Alan Y; Duffy, Sandra; Abd El-Salam El-Sayed, Shimaa; Ferdig, Michael T; Fernández Robledo, José A; Fidock, David A; Florent, Isabelle; Fokou, Patrick V T; Galstian, Ani; Gamo, Francisco Javier; Gokool, Suzanne; Gold, Ben; Golub, Todd; Goldgof, Gregory M; Guha, Rajarshi; Guiguemde, W Armand; Gural, Nil; Guy, R Kiplin; Hansen, Michael A E; Hanson, Kirsten K; Hemphill, Andrew; Hooft van Huijsduijnen, Rob; Horii, Takaaki; Horrocks, Paul; Hughes, Tyler B; Huston, Christopher; Igarashi, Ikuo; Ingram-Sieber, Katrin; Itoe, Maurice A; Jadhav, Ajit; Naranuntarat Jensen, Amornrat; Jensen, Laran T; Jiang, Rays H Y; Kaiser, Annette; Keiser, Jennifer; Ketas, Thomas; Kicka, Sebastien; Kim, Sunyoung; Kirk, Kiaran; Kumar, Vidya P; Kyle, Dennis E; Lafuente, Maria Jose; Landfear, Scott; Lee, Nathan; Lee, Sukjun; Lehane, Adele M; Li, Fengwu; Little, David; Liu, Liqiong; Llinás, Manuel; Loza, Maria I; Lubar, Aristea; Lucantoni, Leonardo; Lucet, Isabelle; Maes, Louis; Mancama, Dalu; Mansour, Nuha R; March, Sandra; McGowan, Sheena; Medina Vera, Iset; Meister, Stephan; Mercer, Luke; Mestres, Jordi; Mfopa, Alvine N; Misra, Raj N; Moon, Seunghyun; Moore, John P; Morais Rodrigues da Costa, Francielly; Müller, Joachim; Muriana, Arantza; Nakazawa Hewitt, Stephen; Nare, Bakela; Nathan, Carl; Narraidoo, Nathalie; Nawaratna, Sujeevi; Ojo, Kayode K; Ortiz, Diana; Panic, Gordana; Papadatos, George; Parapini, Silvia; Patra, Kailash; Pham, Ngoc; Prats, Sarah; Plouffe, David M; Poulsen, Sally-Ann; Pradhan, Anupam; Quevedo, Celia; Quinn, Ronald J; Rice, Christopher A; Abdo Rizk, Mohamed; Ruecker, Andrea; St Onge, Robert; Salgado Ferreira, Rafaela; Samra, Jasmeet; Robinett, Natalie G; Schlecht, Ulrich; Schmitt, Marjorie; Silva Villela, Filipe; Silvestrini, Francesco; Sinden, Robert; Smith, Dennis A; Soldati, Thierry; Spitzmüller, Andreas; Stamm, Serge Maximilian; Sullivan, David J; Sullivan, William; Suresh, Sundari; Suzuki, Brian M; Suzuki, Yo; Swamidass, S Joshua; Taramelli, Donatella; Tchokouaha, Lauve R Y; Theron, Anjo; Thomas, David; Tonissen, Kathryn F; Townson, Simon; Tripathi, Abhai K; Trofimov, Valentin; Udenze, Kenneth O; Ullah, Imran; Vallieres, Cindy; Vigil, Edgar; Vinetz, Joseph M; Voong Vinh, Phat; Vu, Hoan; Watanabe, Nao-Aki; Weatherby, Kate; White, Pamela M; Wilks, Andrew F; Winzeler, Elizabeth A; Wojcik, Edward; Wree, Melanie; Wu, Wesley; Yokoyama, Naoaki; Zollo, Paul H A; Abla, Nada; Blasco, Benjamin; Burrows, Jeremy; Laleu, Benoît; Leroy, Didier; Spangenberg, Thomas; Wells, Timothy; Willis, Paul A

    2016-07-01

    A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal

  16. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.

    PubMed

    Van Voorhis, Wesley C; Adams, John H; Adelfio, Roberto; Ahyong, Vida; Akabas, Myles H; Alano, Pietro; Alday, Aintzane; Alemán Resto, Yesmalie; Alsibaee, Aishah; Alzualde, Ainhoa; Andrews, Katherine T; Avery, Simon V; Avery, Vicky M; Ayong, Lawrence; Baker, Mark; Baker, Stephen; Ben Mamoun, Choukri; Bhatia, Sangeeta; Bickle, Quentin; Bounaadja, Lotfi; Bowling, Tana; Bosch, Jürgen; Boucher, Lauren E; Boyom, Fabrice F; Brea, Jose; Brennan, Marian; Burton, Audrey; Caffrey, Conor R; Camarda, Grazia; Carrasquilla, Manuela; Carter, Dee; Belen Cassera, Maria; Chih-Chien Cheng, Ken; Chindaudomsate, Worathad; Chubb, Anthony; Colon, Beatrice L; Colón-López, Daisy D; Corbett, Yolanda; Crowther, Gregory J; Cowan, Noemi; D'Alessandro, Sarah; Le Dang, Na; Delves, Michael; DeRisi, Joseph L; Du, Alan Y; Duffy, Sandra; Abd El-Salam El-Sayed, Shimaa; Ferdig, Michael T; Fernández Robledo, José A; Fidock, David A; Florent, Isabelle; Fokou, Patrick V T; Galstian, Ani; Gamo, Francisco Javier; Gokool, Suzanne; Gold, Ben; Golub, Todd; Goldgof, Gregory M; Guha, Rajarshi; Guiguemde, W Armand; Gural, Nil; Guy, R Kiplin; Hansen, Michael A E; Hanson, Kirsten K; Hemphill, Andrew; Hooft van Huijsduijnen, Rob; Horii, Takaaki; Horrocks, Paul; Hughes, Tyler B; Huston, Christopher; Igarashi, Ikuo; Ingram-Sieber, Katrin; Itoe, Maurice A; Jadhav, Ajit; Naranuntarat Jensen, Amornrat; Jensen, Laran T; Jiang, Rays H Y; Kaiser, Annette; Keiser, Jennifer; Ketas, Thomas; Kicka, Sebastien; Kim, Sunyoung; Kirk, Kiaran; Kumar, Vidya P; Kyle, Dennis E; Lafuente, Maria Jose; Landfear, Scott; Lee, Nathan; Lee, Sukjun; Lehane, Adele M; Li, Fengwu; Little, David; Liu, Liqiong; Llinás, Manuel; Loza, Maria I; Lubar, Aristea; Lucantoni, Leonardo; Lucet, Isabelle; Maes, Louis; Mancama, Dalu; Mansour, Nuha R; March, Sandra; McGowan, Sheena; Medina Vera, Iset; Meister, Stephan; Mercer, Luke; Mestres, Jordi; Mfopa, Alvine N; Misra, Raj N; Moon, Seunghyun; Moore, John P; Morais Rodrigues da Costa, Francielly; Müller, Joachim; Muriana, Arantza; Nakazawa Hewitt, Stephen; Nare, Bakela; Nathan, Carl; Narraidoo, Nathalie; Nawaratna, Sujeevi; Ojo, Kayode K; Ortiz, Diana; Panic, Gordana; Papadatos, George; Parapini, Silvia; Patra, Kailash; Pham, Ngoc; Prats, Sarah; Plouffe, David M; Poulsen, Sally-Ann; Pradhan, Anupam; Quevedo, Celia; Quinn, Ronald J; Rice, Christopher A; Abdo Rizk, Mohamed; Ruecker, Andrea; St Onge, Robert; Salgado Ferreira, Rafaela; Samra, Jasmeet; Robinett, Natalie G; Schlecht, Ulrich; Schmitt, Marjorie; Silva Villela, Filipe; Silvestrini, Francesco; Sinden, Robert; Smith, Dennis A; Soldati, Thierry; Spitzmüller, Andreas; Stamm, Serge Maximilian; Sullivan, David J; Sullivan, William; Suresh, Sundari; Suzuki, Brian M; Suzuki, Yo; Swamidass, S Joshua; Taramelli, Donatella; Tchokouaha, Lauve R Y; Theron, Anjo; Thomas, David; Tonissen, Kathryn F; Townson, Simon; Tripathi, Abhai K; Trofimov, Valentin; Udenze, Kenneth O; Ullah, Imran; Vallieres, Cindy; Vigil, Edgar; Vinetz, Joseph M; Voong Vinh, Phat; Vu, Hoan; Watanabe, Nao-Aki; Weatherby, Kate; White, Pamela M; Wilks, Andrew F; Winzeler, Elizabeth A; Wojcik, Edward; Wree, Melanie; Wu, Wesley; Yokoyama, Naoaki; Zollo, Paul H A; Abla, Nada; Blasco, Benjamin; Burrows, Jeremy; Laleu, Benoît; Leroy, Didier; Spangenberg, Thomas; Wells, Timothy; Willis, Paul A

    2016-07-01

    A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal

  17. iPhone forensics based on Macintosh open source and freeware tools

    NASA Astrophysics Data System (ADS)

    Höne, Thomas; Creutzburg, Reiner

    2011-02-01

    The aim of this article is to show the usefulness of Mac OS X based open source tools for forensic investigation of modern iPhones. It demonstrates how important data stored in the iPhone is investigated. Two different scenarios of investigations are presented that are well-suited for a forensics lab work in university. This work shows how to analyze an Apple iPhone using open source and freeware tools. Important data used in a forensics investigation, which are possibly stored on a mobile device are presented. Also the superstructure and functions of the iPhone are explained.

  18. Modeling community population dynamics with the open-source language R.

    PubMed

    Green, Robin; Shou, Wenying

    2014-01-01

    The ability to explain biological phenomena with mathematics and to generate predictions from mathematical models is critical for understanding and controlling natural systems. Concurrently, the rise in open-source software has greatly increased the ease at which researchers can implement their own mathematical models. With a reasonably sound understanding of mathematics and programming skills, a researcher can quickly and easily use such tools for their own work. The purpose of this chapter is to expose the reader to one such tool, the open-source programming language R, and to demonstrate its practical application to studying population dynamics. We use the Lotka-Volterra predator-prey dynamics as an example.

  19. Open-source meteor detection software for low-cost single-board computers

    NASA Astrophysics Data System (ADS)

    Vida, D.; Zubović, D.; Šegon, D.; Gural, P.; Cupec, R.

    2016-01-01

    This work aims to overcome the current price threshold of meteor stations which can sometimes deter meteor enthusiasts from owning one. In recent years small card-sized computers became widely available and are used for numerous applications. To utilize such computers for meteor work, software which can run on them is needed. In this paper we present a detailed description of newly-developed open-source software for fireball and meteor detection optimized for running on low-cost single board computers. Furthermore, an update on the development of automated open-source software which will handle video capture, fireball and meteor detection, astrometry and photometry is given.

  20. Evaluation of an open source tool for indexing and searching enterprise radiology and pathology reports

    NASA Astrophysics Data System (ADS)

    Kim, Woojin; Boonn, William

    2010-03-01

    Data mining of existing radiology and pathology reports within an enterprise health system can be used for clinical decision support, research, education, as well as operational analyses. In our health system, the database of radiology and pathology reports exceeds 13 million entries combined. We are building a web-based tool to allow search and data analysis of these combined databases using freely available and open source tools. This presentation will compare performance of an open source full-text indexing tool to MySQL's full-text indexing and searching and describe implementation procedures to incorporate these capabilities into a radiology-pathology search engine.

  1. PyEEG: an open source Python module for EEG/MEG feature extraction.

    PubMed

    Bao, Forrest Sheng; Liu, Xin; Zhang, Christina

    2011-01-01

    Computer-aided diagnosis of neural diseases from EEG signals (or other physiological signals that can be treated as time series, e.g., MEG) is an emerging field that has gained much attention in past years. Extracting features is a key component in the analysis of EEG signals. In our previous works, we have implemented many EEG feature extraction functions in the Python programming language. As Python is gaining more ground in scientific computing, an open source Python module for extracting EEG features has the potential to save much time for computational neuroscientists. In this paper, we introduce PyEEG, an open source Python module for EEG feature extraction.

  2. Long-term Science Data Curation Using a Digital Object Model and Open-Source Frameworks

    NASA Astrophysics Data System (ADS)

    Pan, J.; Lenhardt, W.; Wilson, B. E.; Palanisamy, G.; Cook, R. B.

    2010-12-01

    Scientific digital content, including Earth Science observations and model output, has become more heterogeneous in format and more distributed across the Internet. In addition, data and metadata are becoming necessarily linked internally and externally on the Web. As a result, such content has become more difficult for providers to manage and preserve and for users to locate, understand, and consume. Specifically, it is increasingly harder to deliver relevant metadata and data processing lineage information along with the actual content consistently. Readme files, data quality information, production provenance, and other descriptive metadata are often separated in the storage level as well as in the data search and retrieval interfaces available to a user. Critical archival metadata, such as auditing trails and integrity checks, are often even more difficult for users to access, if they exist at all. We investigate the use of several open-source software frameworks to address these challenges. We use Fedora Commons Framework and its digital object abstraction as the repository, Drupal CMS as the user-interface, and the Islandora module as the connector from Drupal to Fedora Repository. With the digital object model, metadata of data description and data provenance can be associated with data content in a formal manner, so are external references and other arbitrary auxiliary information. Changes are formally audited on an object, and digital contents are versioned and have checksums automatically computed. Further, relationships among objects are formally expressed with RDF triples. Data replication, recovery, metadata export are supported with standard protocols, such as OAI-PMH. We provide a tentative comparative analysis of the chosen software stack with the Open Archival Information System (OAIS) reference model, along with our initial results with the existing terrestrial ecology data collections at NASA’s ORNL Distributed Active Archive Center for

  3. Open Source Based Sensor Platform for Mobile Environmental Monitoring and Data Acquisition

    NASA Astrophysics Data System (ADS)

    Schima, Robert; Goblirsch, Tobias; Misterek, René; Salbach, Christoph; Schlink, Uwe; Francyk, Bogdan; Dietrich, Peter; Bumberger, Jan

    2016-04-01

    The impact of global change, urbanization and complex interactions between humans and the environment show different effects on different scales. However, the desire to obtain a better understanding of ecosystems and process dynamics in nature accentuates the need for observing these processes in higher temporal and spatial resolutions. Especially with regard to the process dynamics and heterogeneity of urban areas, a comprehensive monitoring of these effects remains to be a challenging issue. Open source based electronics and cost-effective sensors are offering a promising approach to explore new possibilities of mobile data acquisition and innovative strategies and thereby support a comprehensive ad-hoc monitoring and the capturing of environmental processes close to real time. Accordingly, our project aims the development of new strategies for mobile data acquisition and real-time processing of user-specific environmental data, based on a holistic and integrated process. To this end, the concept of our monitoring system covers the data collection, data processing and data integration as well as the data provision within one infrastructure. This ensures a consistent data stream and a rapid data processing. However, the overarching goal is the provision of an integrated service instead of lengthy and arduous data acquisition by hand. Therefore, the system also serves as a data acquisition assistant and gives guidance during the measurements. In technical terms, our monitoring system consists of mobile sensor devices, which can be controlled and managed by a smart phone app (Android). At the moment, the system is able to acquire temperature and humidity in space (GPS) and time (real-time clock) as a built in function. In addition, larger system functionality can be accomplished by adding further sensors for the detection of e.g. fine dust, methane or dissolved organic compounds. From the IT point of view, the system includes a smart phone app and a web service for

  4. Reflection on the Process of Open Sourcing Software Based on Ten Years of Development of RAPID

    NASA Astrophysics Data System (ADS)

    David, C. H.; Famiglietti, J. S.; Yang, Z. L.; Habets, F.; Maidment, D.

    2015-12-01

    As the number and size of geoscience datasets persist in their constant rise, geoscientists increasingly express their yearning for further sharing of their data and software, and for facilitation of the associated academic credits. We present here our experience based on the open source development of an Earth System Model focusing on the propagation of water flow waves in large river networks: the Routing Application for Parallel computatIon of Discharge (RAPID). Since inception of RAPID ten years ago in January 2006, the community of its users has grown slowly but steadily, and now includes researchers in industry, academia, and government organizations. This growth of the RAPID users community can be explained - at least in part - by its open availability. However, despite an increasing support for open science (software and data), the mechanics of sharing still remain mysterious to many geoscientists… as they were for the authors. The purpose of this presentation is therefore to shed light on the steps involved in opening software and data based on a decade of experience related to the development and release of an Earth System Model. Three distinct steps of open sourcing are highlighted here: opening, exposing, and automatic testing. Each one of these steps is presented as an independent and tractable increment at various stages of development that is justified based on the size of the users community. Topics covered include software and data licenses, code and data repositories, unit testing, and continuous integration.

  5. Developing a low-cost open-source CTD for research and outreach

    NASA Astrophysics Data System (ADS)

    Thaler, A. D.; Sturdivant, K.

    2013-12-01

    Developing a low-cost open-source CTD for research and outreach Andrew David Thaler and Kersey Sturdivant Conductivity, temperature, and depth (CTD). With these three measurements, marine scientists can unlock ocean patterns hidden beneath the waves. The ocean is not uniform, it its filled with swirling eddies, temperature boundaries, layers of high and low salinity, changing densities, and many other physical characteristics. To reveal these patterns, oceanographers use a tool called the CTD. A CTD is found on almost every major research vessel. Rare is the scientific expedition-whether it be coastal work in shallow estuaries or journeys to the deepest ocean trenches-that doesn't begin with the humble CTD cast. The CTD is not cheap. Commercial CTD's start at more the 5,000 and can climb as high as 25,000 or more. We believe that the prohibitive cost of a CTD is an unacceptable barrier to open science. The price tag excludes individuals and groups who lack research grants or significant private funds from conducting oceanographic research. We want to make this tool-the workhorse of oceanographic research-available to anyone with an interest in the oceans. The OpenCTD is a low-cost, open-source CTD suitable for both educators and scientists. The platform is built using readily available parts and is powered by an Arduino-based microcontroller. Our goal is to create a device that is accurate enough to be used for scientific research and can be constructed for less than $200. Source codes, circuit diagrams, and building plans will be freely available. The final instrument will be effective to 200 meters depth. Why 200 meters? For many coastal regions, 200 meters of water depth covers the majority of the ocean that is accessible by small boat. The OpenCTD is targeted to people working in this niche, where entire research projects can be conducted for less than the cost of a commercial CTD. However, the Open CTD is scalable, and anyone with the inclination can adapt our

  6. Aerostat-lofted instrument and sampling method for determination of emissions from open area sources.

    PubMed

    Aurell, Johanna; Gullett, Brian K; Pressley, Christopher; Tabor, Dennis G; Gribble, Robert D

    2011-10-01

    An aerostat-borne instrument and sampling method was developed to characterize air samples from area sources, such as emissions from open burning. The 10 kg battery-powered instrument system, termed "the Flyer", is lofted with a helium-filled aerostat of 4m nominal diameter and maneuvered by means of one or two tethers. The Flyer can be configured variously for continuous CO₂ monitoring, batch sampling of semi-volatile organic compounds (SVOCs), volatile organic compounds (VOCs), black carbon, metals, and PM by size. The samplers are controlled by a trigger circuit to avoid unnecessary dilution from background sampling when not within the source plume. The aerostat/Flyer method was demonstrated by sampling emissions from open burning (OB) and open detonation (OD) of military ordnance. A carbon balance approach was used to derive emission factors that showed excellent agreement with published values.

  7. Open source hardware and software platform for robotics and artificial intelligence applications

    NASA Astrophysics Data System (ADS)

    Liang, S. Ng; Tan, K. O.; Lai Clement, T. H.; Ng, S. K.; Mohammed, A. H. Ali; Mailah, Musa; Azhar Yussof, Wan; Hamedon, Zamzuri; Yussof, Zulkifli

    2016-02-01

    Recent developments in open source hardware and software platforms (Android, Arduino, Linux, OpenCV etc.) have enabled rapid development of previously expensive and sophisticated system within a lower budget and flatter learning curves for developers. Using these platform, we designed and developed a Java-based 3D robotic simulation system, with graph database, which is integrated in online and offline modes with an Android-Arduino based rubbish picking remote control car. The combination of the open source hardware and software system created a flexible and expandable platform for further developments in the future, both in the software and hardware areas, in particular in combination with graph database for artificial intelligence, as well as more sophisticated hardware, such as legged or humanoid robots.

  8. Aerostat-lofted instrument and sampling method for determination of emissions from open area sources

    EPA Science Inventory

    An aerostat-borne instrument and sampling method was developed to characterize air samples from area sources, such as emissions from open burning. The 10 kg battery-powered instrument system, termed "the Flyer," is lofted with a helium-filled aerostat of 4 m nominal diameter and ...

  9. Development and evaluation of a lightweight sensor system for aerial emission sampling from open area sources

    EPA Science Inventory

    A new sensor system for mobile and aerial emission sampling was developed for open area pollutant sources, such as prescribed forest burns. The sensor system, termed “Kolibri”, consists of multiple low-cost air quality sensors measuring CO2, CO, samplers for particula...

  10. Learning and Best Practices for Learning in Open-Source Software Communities

    ERIC Educational Resources Information Center

    Singh, Vandana; Holt, Lila

    2013-01-01

    This research is about participants who use open-source software (OSS) discussion forums for learning. Learning in online communities of education as well as non-education-related online communities has been studied under the lens of social learning theory and situated learning for a long time. In this research, we draw parallels among these two…

  11. Promoting Conceptual Change through Active Learning Using Open Source Software for Physics Simulations

    ERIC Educational Resources Information Center

    Baser, Mustafa

    2006-01-01

    This paper reports upon an active learning approach that promotes conceptual change when studying direct current electricity circuits, using free open source software, "Qucs". The study involved a total of 102 prospective mathematics teacher students. Prior to instruction, students' understanding of direct current electricity was determined by a…

  12. Development and evaluation of a lightweight sensor system for aerial emission sampling from open area sources

    EPA Science Inventory

    A new sensor system for mobile and aerial emission sampling was developed for open area pollutant sources, such as prescribed forest burns. The sensor system, termed “Kolibri”, consists of multiple low-cost air quality sensors measuring CO2, CO, samplers for particulate matter wi...

  13. Development and methods for an open-sourced data visualization tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper presents an open source on-demand web tool, which is specifically addressed to scientists and researchers that are non-expert in converting time series data into a time surface visualization. Similar to a GIS environment the time surface shows time on two axes; time of day vs. day of year...

  14. Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

    ERIC Educational Resources Information Center

    Vanfretti, L.; Milano, F.

    2012-01-01

    This paper describes how the use of free and open-source software (FOSS) can facilitate the application of constructive alignment theory in power systems engineering education by enabling the deep learning approach in power system analysis courses. With this aim, this paper describes the authors' approach in using the Power System Analysis Toolbox…

  15. Introducing a new open source GIS user interface for the SWAT model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Soil and Water Assessment Tool (SWAT) model is a robust watershed modelling tool. It typically uses the ArcSWAT interface to create its inputs. ArcSWAT is public domain software which works in the licensed ArcGIS environment. The aim of this paper was to develop an open source user interface ...

  16. Makahiki: An Open Source Serious Game Framework for Sustainability Education and Conservation

    ERIC Educational Resources Information Center

    Xu, Yongwen; Johnson, Philip M.; Lee, George E.; Moore, Carleton A.; Brewer, Robert S.

    2014-01-01

    Sustainability education and conservation have become an international imperative due to the rising cost of energy, increasing scarcity of natural resource and irresponsible environmental practices. This paper presents Makahiki, an open source serious game framework for sustainability, which implements an extensible framework for different…

  17. Development of a system based on open source technology for DC resistor calibration

    NASA Astrophysics Data System (ADS)

    Geronymo, G. M.; Silva, M. C.

    2016-07-01

    This work present the development of a new system, based on open source technology, for the automation of DC resistor calibration. The new system is web-based, stores the measurement registers on a structured database and has new features that can increase the productivity of the laboratory. Some proposes of future development are presented, also.

  18. PyPedal, an open source software package for pedigree analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The open source software package PyPedal (http://pypedal.sourceforge.net/) was first released in 2002, and provided users with a set of simple tools for manipulating pedigrees. Its flexibility has been demonstrated by its used in a number of settings for large and small populations. After substantia...

  19. Tensor calculus with open-source software: the SageManifolds project

    NASA Astrophysics Data System (ADS)

    Gourgoulhon, Eric; Bejger, Michal; Mancini, Marco

    2015-04-01

    The SageManifolds project aims at extending the mathematics software system Sage towards differential geometry and tensor calculus. Like Sage, SageManifolds is free, open- source and is based on the Python programming language. We discuss here some details of the implementation, which relies on Sage's parent/element framework, and present a concrete example of use.

  20. Fac-Back-OPAC: An Open Source Interface to Your Library System

    ERIC Educational Resources Information Center

    Beccaria, Mike; Scott, Dan

    2007-01-01

    The new Fac-Back-OPAC (a faceted backup OPAC) is built on code that was originally developed by Casey Durfee in February 2007. It represents the convergence of two prominent trends in library tools: the decoupling of discovery tools from the traditional integrated library system (ILS) and the use of readily available open source components to…

  1. Shaping Software Engineering Curricula Using Open Source Communities: A Case Study

    ERIC Educational Resources Information Center

    Bowring, James; Burke, Quinn

    2016-01-01

    This paper documents four years of a novel approach to teaching a two-course sequence in software engineering as part of the ABET-accredited computer science curriculum at the College of Charleston. This approach is team-based and centers on learning software engineering in the context of open source software projects. In the first course, teams…

  2. Open Source in Higher Education: Towards an Understanding of Networked Universities

    ERIC Educational Resources Information Center

    Quint-Rapoport, Mia

    2012-01-01

    This article addresses the question of understanding more about networked universities by looking at open source software developers working in academic contexts. It sketches their identities and work as an emerging professional community that both relies upon and develops digitally mediated networks and contributes to the progress of academic…

  3. Challenges, Frustrations and Triumphs of Remixing an Open Source Game Engine for Educational Purposes

    ERIC Educational Resources Information Center

    Stowell, Timothy; Shelton, Brett E.

    2008-01-01

    The use, reuse, and remixing of commercial games has influenced the field of educational gaming. Part of this influence is felt though a number of popular game engines whose code has been released for the creation of games by other groups. This paper follows one group's progress of using the open-source and highly successful commercial game engine…

  4. Exploring the Factors Influencing the Adoption of Open Source Software in Western Cape Schools

    ERIC Educational Resources Information Center

    Johnston, Kevin; Begg, Shameemah; Tanner, Maureen

    2013-01-01

    Open Source Software (OSS) presents many benefits to both the private and the public sectors, and has proven to be a viable solution in schools. Although a policy mandating the use of OSS exists in the Western Cape province of South Africa, very few schools in the province have adopted OSS. The education system in South Africa is currently facing…

  5. Involving Software Engineering Students in Open Source Software Projects: Experiences from a Pilot Study

    ERIC Educational Resources Information Center

    Sowe, Sulayman K.; Stamelos, Ioannis G.

    2007-01-01

    Anecdotal and research evidences show that the Free and Open Source Software (F/OSS) development model has produced a paradigm shift in the way we develop, support, and distribute software. This shift is not only redefining the software industry but also the way we teach and learn in our software engineering (SE) courses. But for many universities…

  6. On the Prospects and Concerns of Integrating Open Source Software Environment in Software Engineering Education

    ERIC Educational Resources Information Center

    Kamthan, Pankaj

    2007-01-01

    Open Source Software (OSS) has introduced a new dimension in software community. As the development and use of OSS becomes prominent, the question of its integration in education arises. In this paper, the following practices fundamental to projects and processes in software engineering are examined from an OSS perspective: project management;…

  7. Application of Open-Source Enterprise Information System Modules: An Empirical Study

    ERIC Educational Resources Information Center

    Lee, Sang-Heui

    2010-01-01

    Although there have been a number of studies on large scale implementation of proprietary enterprise information systems (EIS), open-source software (OSS) for EIS has received limited attention in spite of its potential as a disruptive innovation. Cost saving is the main driver for adopting OSS among the other possible benefits including security…

  8. An Investigation of an Open-Source Software Development Environment in a Software Engineering Graduate Course

    ERIC Educational Resources Information Center

    Ge, Xun; Huang, Kun; Dong, Yifei

    2010-01-01

    A semester-long ethnography study was carried out to investigate project-based learning in a graduate software engineering course through the implementation of an Open-Source Software Development (OSSD) learning environment, which featured authentic projects, learning community, cognitive apprenticeship, and technology affordances. The study…

  9. Open Source Software in Medium Size Organizations: Key Factors for Adoption

    ERIC Educational Resources Information Center

    Solomon, Jerry T.

    2010-01-01

    For-profit organizations are constantly evaluating new technologies to gain competitive advantage. One such technology, application software, has changed significantly over the past 25 years with the introduction of Open Source Software (OSS). In contrast to commercial software that is developed by private companies and sold to organizations, OSS…

  10. Open Source Software in Teaching Physics: A Case Study on Vector Algebra and Visual Representations

    ERIC Educational Resources Information Center

    Cataloglu, Erdat

    2006-01-01

    This study aims to report the effort on teaching vector algebra using free open source software (FOSS). Recent studies showed that students have difficulties in learning basic physics concepts. Constructivist learning theories suggest the use of visual and hands-on activities in learning. We will report on the software used for this purpose. The…

  11. Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions

    PubMed Central

    Shenoy, Shailesh M.

    2016-01-01

    A challenge in any imaging laboratory, especially one that uses modern techniques, is to achieve a sustainable and productive balance between using open source and commercial software to perform quantitative image acquisition, analysis and visualization. In addition to considering the expense of software licensing, one must consider factors such as the quality and usefulness of the software’s support, training and documentation. Also, one must consider the reproducibility with which multiple people generate results using the same software to perform the same analysis, how one may distribute their methods to the community using the software and the potential for achieving automation to improve productivity. PMID:27516727

  12. Application of Open Source Software by the Lunar Mapping and Modeling Project

    NASA Astrophysics Data System (ADS)

    Ramirez, P.; Goodale, C. E.; Bui, B.; Chang, G.; Kim, R. M.; Law, E.; Malhotra, S.; Rodriguez, L.; Sadaqathullah, S.; Mattmann, C. A.; Crichton, D. J.

    2011-12-01

    The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is responsible for the development of an information system to support lunar exploration, decision analysis, and release of lunar data to the public. The data available through the lunar portal is predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). This project has created a gold source of data, models, and tools for lunar explorers to exercise and incorporate into their activities. At Jet Propulsion Laboratory (JPL), we focused on engineering and building the infrastructure to support cataloging, archiving, accessing, and delivery of lunar data. We decided to use a RESTful service-oriented architecture to enable us to abstract from the underlying technology choices and focus on interfaces to be used internally and externally. This decision allowed us to leverage several open source software components and integrate them by either writing a thin REST service layer or relying on the API they provided; the approach chosen was dependent on the targeted consumer of a given interface. We will discuss our varying experience using open source products; namely Apache OODT, Oracle Berkley DB XML, Apache Solr, and Oracle OpenSSO (now named OpenAM). Apache OODT, developed at NASA's Jet Propulsion Laboratory and recently migrated over to Apache, provided the means for ingestion and cataloguing of products within the infrastructure. Its usage was based upon team experience with the project and past benefit received on other projects internal and external to JPL. Berkeley DB XML, distributed by Oracle for both commercial and open source use, was the storage technology chosen for our metadata. This decision was in part based on our use Federal Geographic Data Committee (FGDC) Metadata, which is expressed in XML, and the desire to keep it in its native form and exploit other technologies built on

  13. CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

    PubMed

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

    2011-05-01

    NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension. PMID:21409563

  14. Open-source MFIX-DEM software for gas-solids flows: Part II Validation studies

    SciTech Connect

    Li, Tingwen; Garg, Rahul; Galvin, Janine; Pannala, Sreekanth

    2012-01-01

    With rapid advancements in computer hardware and numerical algorithms, computational fluid dynamics (CFD) has been increasingly employed as a useful tool for investigating the complex hydrodynamics inherent in multiphase flows. An important step during the development of a CFD model and prior to its application is conducting careful and comprehensive verification and validation studies. Accordingly, efforts to verify and validate the open-source MFIX-DEM software, which can be used for simulating the gas solids flow using an Eulerian reference frame for the continuum fluid and a Lagrangian discrete framework (Discrete Element Method) for the particles, have been made at the National Energy Technology Laboratory (NETL). In part I of this paper, extensive verification studies were presented and in this part, detailed validation studies of MFIX-DEM are presented. A series of test cases covering a range of gas solids flow applications were conducted. In particular the numerical results for the random packing of a binary particle mixture, the repose angle of a sandpile formed during a side charge process, velocity, granular temperature, and voidage profiles from a bounded granular shear flow, lateral voidage and velocity profiles from a monodisperse bubbling fluidized bed, lateral velocity profiles from a spouted bed, and the dynamics of segregation of a binary mixture in a bubbling bed were compared with available experimental data, and in some instances with empirical correlations. In addition, sensitivity studies were conducted for various parameters to quantify the error in the numerical simulation.

  15. Open-Source MFIX-DEM Software for Gas-Solids Flows: Part II - Validation Studies

    SciTech Connect

    Li, Tingwen

    2012-04-01

    With rapid advancements in computer hardware and numerical algorithms, computational fluid dynamics (CFD) has been increasingly employed as a useful tool for investigating the complex hydrodynamics inherent in multiphase flows. An important step during the development of a CFD model and prior to its application is conducting careful and comprehensive verification and validation studies. Accordingly, efforts to verify and validate the open-source MFIX-DEM software, which can be used for simulating the gas–solids flow using an Eulerian reference frame for the continuum fluid and a Lagrangian discrete framework (Discrete Element Method) for the particles, have been made at the National Energy Technology Laboratory (NETL). In part I of this paper, extensive verification studies were presented and in this part, detailed validation studies of MFIX-DEM are presented. A series of test cases covering a range of gas–solids flow applications were conducted. In particular the numerical results for the random packing of a binary particle mixture, the repose angle of a sandpile formed during a side charge process, velocity, granular temperature, and voidage profiles from a bounded granular shear flow, lateral voidage and velocity profiles from a monodisperse bubbling fluidized bed, lateral velocity profiles from a spouted bed, and the dynamics of segregation of a binary mixture in a bubbling bed were compared with available experimental data, and in some instances with empirical correlations. In addition, sensitivity studies were conducted for various parameters to quantify the error in the numerical simulation.

  16. VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy.

    PubMed

    Gray, Robert D M; Beerli, Corina; Pereira, Pedro Matos; Scherer, Kathrin Maria; Samolej, Jerzy; Bleck, Christopher Karl Ernst; Mercer, Jason; Henriques, Ricardo

    2016-01-01

    The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture. PMID:27374400

  17. jSPyDB, an open source database-independent tool for data management

    NASA Astrophysics Data System (ADS)

    Pierro, Giuseppe Antonio; Cavallari, Francesca; Di Guida, Salvatore; Innocente, Vincenzo

    2011-12-01

    Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web-based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. Moreover, thanks to jQuery libraries, this tool supports export of data in different formats, such as XML and JSON. Finally, by using a set of pre-defined functions, users are allowed to create their customized views for a better data visualization. In this way, we optimize the performance of database servers by avoiding short connections and concurrent sessions. In addition, security is enforced since we do not provide users the possibility to directly execute any SQL statement.

  18. VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy

    PubMed Central

    Gray, Robert D. M.; Beerli, Corina; Pereira, Pedro Matos; Scherer, Kathrin Maria; Samolej, Jerzy; Bleck, Christopher Karl Ernst; Mercer, Jason; Henriques, Ricardo

    2016-01-01

    The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and naïve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture. PMID:27374400

  19. Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy.

    PubMed

    Dedecker, Peter; Duwé, Sam; Neely, Robert K; Zhang, Jin

    2012-12-01

    We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies. PMID:23208219

  20. A new, open-source, multi-modality digital breast phantom

    NASA Astrophysics Data System (ADS)

    Graff, Christian G.

    2016-03-01

    An anthropomorphic digital breast phantom has been developed with the goal of generating random voxelized breast models that capture the anatomic variability observed in vivo. This is a new phantom and is not based on existing digital breast phantoms or segmentation of patient images. It has been designed at the outset to be modality agnostic (i.e., suitable for use in modeling x-ray based imaging systems, magnetic resonance imaging, and potentially other imaging systems) and open source so that users may freely modify the phantom to suit a particular study. In this work we describe the modeling techniques that have been developed, the capabilities and novel features of this phantom, and study simulated images produced from it. Starting from a base quadric, a series of deformations are performed to create a breast with a particular volume and shape. Initial glandular compartments are generated using a Voronoi technique and a ductal tree structure with terminal duct lobular units is grown from the nipple into each compartment. An additional step involving the creation of fat and glandular lobules using a Perlin noise function is performed to create more realistic glandular/fat tissue interfaces and generate a Cooper's ligament network. A vascular tree is grown from the chest muscle into the breast tissue. Breast compression is performed using a neo-Hookean elasticity model. We show simulated mammographic and T1-weighted MRI images and study properties of these images.

  1. CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

    PubMed

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

    2011-05-01

    NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.

  2. Development of an Open Source Image-Based Flow Modeling Software - SimVascular

    NASA Astrophysics Data System (ADS)

    Updegrove, Adam; Merkow, Jameson; Schiavazzi, Daniele; Wilson, Nathan; Marsden, Alison; Shadden, Shawn

    2014-11-01

    SimVascular (www.simvascular.org) is currently the only comprehensive software package that provides a complete pipeline from medical image data segmentation to patient specific blood flow simulation. This software and its derivatives have been used in hundreds of conference abstracts and peer-reviewed journal articles, as well as the foundation of medical startups. SimVascular was initially released in August 2007, yet major challenges and deterrents for new adopters were the requirement of licensing three expensive commercial libraries utilized by the software, a complicated build process, and a lack of documentation, support and organized maintenance. In the past year, the SimVascular team has made significant progress to integrate open source alternatives for the linear solver, solid modeling, and mesh generation commercial libraries required by the original public release. In addition, the build system, available distributions, and graphical user interface have been significantly enhanced. Finally, the software has been updated to enable users to directly run simulations using models and boundary condition values, included in the Vascular Model Repository (vascularmodel.org). In this presentation we will briefly overview the capabilities of the new SimVascular 2.0 release. National Science Foundation.

  3. An open-source engine for the processing of electron backscatter patterns: EBSD-image.

    PubMed

    Pinard, Philippe T; Lagacé, Marin; Hovington, Pierre; Thibault, Denis; Gauvin, Raynald

    2011-06-01

    An open source software package dedicated to processing stored electron backscatter patterns is presented. The package gives users full control over the type and order of operations that are performed on electron backscatter diffraction (EBSD) patterns as well as the results obtained. The current version of EBSD-Image (www.ebsd-image.org) offers a flexible and structured interface to calculate various quality metrics over large datasets. It includes unique features such as practical file formats for storing diffraction patterns and analysis results, stitching of mappings with automatic reorganization of their diffraction patterns, and routines for processing data on a distributed computer grid. Implementations of the algorithms used in the software are described and benchmarked using simulated diffraction patterns. Using those simulated EBSD patterns, the detection of Kikuchi bands in EBSD-Image was found to be comparable to commercially available EBSD systems. In addition, 24 quality metrics were evaluated based on the ability to assess the level of deformation in two samples (copper and iron) deformed using 220 grit SiC grinding paper. Fourteen metrics were able to properly measure the deformation gradient of the samples.

  4. Real Space Multigrid (RMG) Open Source Software Suite for Multi-Petaflops Electronic Structure Calculations

    NASA Astrophysics Data System (ADS)

    Briggs, Emil; Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry; Li, Yan

    RMG is a cross platform open source package for ab initio electronic structure calculations that uses real-space grids, multigrid pre-conditioning, and subspace diagonalization to solve the Kohn-Sham equations. The code has been successfully used for a wide range of problems ranging from complex bulk materials to multifunctional electronic devices and biological systems. RMG makes efficient use of GPU accelerators, if present, but does not require them. Recent work has extended GPU support to systems with multiple GPU's per computational node, as well as optimized both CPU and GPU memory usage to enable large problem sizes, which are no longer limited by the memory of the GPU board. Additional enhancements include increased portability, scalability and performance. New versions of the code are regularly released at sourceforge.net/projects/rmgdft/. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms.

  5. Imaging C. elegans Embryos using an Epifluorescent Microscope and Open Source Software

    PubMed Central

    Verbrugghe, Koen J. C.; Chan, Raymond C.

    2011-01-01

    Cellular processes, such as chromosome assembly, segregation and cytokinesis,are inherently dynamic. Time-lapse imaging of living cells, using fluorescent-labeled reporter proteins or differential interference contrast (DIC) microscopy, allows for the examination of the temporal progression of these dynamic events which is otherwise inferred from analysis of fixed samples1,2. Moreover, the study of the developmental regulations of cellular processes necessitates conducting time-lapse experiments on an intact organism during development. The Caenorhabiditis elegans embryo is light-transparent and has a rapid, invariant developmental program with a known cell lineage3, thus providing an ideal experiment model for studying questions in cell biology4,5and development6-9. C. elegans is amendable to genetic manipulation by forward genetics (based on random mutagenesis10,11) and reverse genetics to target specific genes (based on RNAi-mediated interference and targeted mutagenesis12-15). In addition, transgenic animals can be readily created to express fluorescently tagged proteins or reporters16,17. These traits combine to make it easy to identify the genetic pathways regulating fundamental cellular and developmental processes in vivo18-21. In this protocol we present methods for live imaging of C. elegans embryos using DIC optics or GFP fluorescence on a compound epifluorescent microscope. We demonstrate the ease with which readily available microscopes, typically used for fixed sample imaging, can also be applied for time-lapse analysis using open-source software to automate the imaging process. PMID:21490567

  6. radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar

    PubMed Central

    2010-01-01

    Background Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Results Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Conclusions Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets. PMID:20977735

  7. OOSTethys - Open Source Software for the Global Earth Observing Systems of Systems

    NASA Astrophysics Data System (ADS)

    Bridger, E.; Bermudez, L. E.; Maskey, M.; Rueda, C.; Babin, B. L.; Blair, R.

    2009-12-01

    An open source software project is much more than just picking the right license, hosting modular code and providing effective documentation. Success in advancing in an open collaborative way requires that the process match the expected code functionality to the developer's personal expertise and organizational needs as well as having an enthusiastic and responsive core lead group. We will present the lessons learned fromOOSTethys , which is a community of software developers and marine scientists who develop open source tools, in multiple languages, to integrate ocean observing systems into an Integrated Ocean Observing System (IOOS). OOSTethys' goal is to dramatically reduce the time it takes to install, adopt and update standards-compliant web services. OOSTethys has developed servers, clients and a registry. Open source PERL, PYTHON, JAVA and ASP tool kits and reference implementations are helping the marine community publish near real-time observation data in interoperable standard formats. In some cases publishing an OpenGeospatial Consortium (OGC), Sensor Observation Service (SOS) from NetCDF files or a database or even CSV text files could take only minutes depending on the skills of the developer. OOSTethys is also developing an OGC standard registry, Catalog Service for Web (CSW). This open source CSW registry was implemented to easily register and discover SOSs using ISO 19139 service metadata. A web interface layer over the CSW registry simplifies the registration process by harvesting metadata describing the observations and sensors from the “GetCapabilities” response of SOS. OPENIOOS is the web client, developed in PERL to visualize the sensors in the SOS services. While the number of OOSTethys software developers is small, currently about 10 around the world, the number of OOSTethys toolkit implementers is larger and growing and the ease of use has played a large role in spreading the use of interoperable standards compliant web services widely

  8. Open Source Subtitle Editor Software Study for Section 508 Close Caption Applications

    NASA Technical Reports Server (NTRS)

    Murphy, F. Brandon

    2013-01-01

    This paper will focus on a specific item within the NASA Electronic Information Accessibility Policy - Multimedia Presentation shall have synchronized caption; thus making information accessible to a person with hearing impairment. This synchronized caption will assist a person with hearing or cognitive disability to access the same information as everyone else. This paper focuses on the research and implementation for CC (subtitle option) support to video multimedia. The goal of this research is identify the best available open-source (free) software to achieve synchronized captions requirement and achieve savings, while meeting the security requirement for Government information integrity and assurance. CC and subtitling are processes that display text within a video to provide additional or interpretive information for those whom may need it or those whom chose it. Closed captions typically show the transcription of the audio portion of a program (video) as it occurs (either verbatim or in its edited form), sometimes including non-speech elements (such as sound effects). The transcript can be provided by a third party source or can be extracted word for word from the video. This feature can be made available for videos in two forms: either Soft-Coded or Hard-Coded. Soft-Coded is the more optional version of CC, where you can chose to turn them on if you want, or you can turn them off. Most of the time, when using the Soft-Coded option, the transcript is also provided to the view along-side the video. This option is subject to compromise, whereas the transcript is merely a text file that can be changed by anyone who has access to it. With this option the integrity of the CC is at the mercy of the user. Hard-Coded CC is a more permanent form of CC. A Hard-Coded CC transcript is embedded within a video, without the option of removal.

  9. Openwebglobe - AN Open Source Sdk for Creating Large-Scale Virtual Globes on a Webgl Basis

    NASA Astrophysics Data System (ADS)

    Loesch, B.; Christen, M.; Nebiker, S.

    2012-07-01

    This paper introduces the OpenWebGlobe project (www.openwebglobe.org) and the OpenWebGlobe SDK (Software Development Kit) - an open source virtual globe environment using WebGL. Unlike other (web-based) 3d geovisualisation technologies and toolkits, the OpenWebGlobe SDK not only supports the content authoring and web visualization aspects, but also the data processing functionality for generating multi-terabyte terrain, image, map and 3d point cloud data sets in high-performance and cloud-based parallel computing environments. The OpenWebGlobe architecture is described and the paper outlines the processing and the viewer functionality provided by the OpenWebGlobe SDK. It then discusses the generation and updating of a global 3d base map using OpenStreetMap data and finally presents two show cases employing the technology a) for implementing an interactive national 3d geoportal incorporating high resolution national geodata sets and b) for implementing a 3d geoinformation service supporting the real-time incorporation of 3d point cloud data.

  10. Phase 1 Validation Testing and Simulation for the WEC-Sim Open Source Code

    NASA Astrophysics Data System (ADS)

    Ruehl, K.; Michelen, C.; Gunawan, B.; Bosma, B.; Simmons, A.; Lomonaco, P.

    2015-12-01

    WEC-Sim is an open source code to model wave energy converters performance in operational waves, developed by Sandia and NREL and funded by the US DOE. The code is a time-domain modeling tool developed in MATLAB/SIMULINK using the multibody dynamics solver SimMechanics, and solves the WEC's governing equations of motion using the Cummins time-domain impulse response formulation in 6 degrees of freedom. The WEC-Sim code has undergone verification through code-to-code comparisons; however validation of the code has been limited to publicly available experimental data sets. While these data sets provide preliminary code validation, the experimental tests were not explicitly designed for code validation, and as a result are limited in their ability to validate the full functionality of the WEC-Sim code. Therefore, dedicated physical model tests for WEC-Sim validation have been performed. This presentation provides an overview of the WEC-Sim validation experimental wave tank tests performed at the Oregon State University's Directional Wave Basin at Hinsdale Wave Research Laboratory. Phase 1 of experimental testing was focused on device characterization and completed in Fall 2015. Phase 2 is focused on WEC performance and scheduled for Winter 2015/2016. These experimental tests were designed explicitly to validate the performance of WEC-Sim code, and its new feature additions. Upon completion, the WEC-Sim validation data set will be made publicly available to the wave energy community. For the physical model test, a controllable model of a floating wave energy converter has been designed and constructed. The instrumentation includes state-of-the-art devices to measure pressure fields, motions in 6 DOF, multi-axial load cells, torque transducers, position transducers, and encoders. The model also incorporates a fully programmable Power-Take-Off system which can be used to generate or absorb wave energy. Numerical simulations of the experiments using WEC-Sim will be

  11. NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

    NASA Astrophysics Data System (ADS)

    Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

    2010-09-01

    The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full

  12. DualSPHysics: Open-source parallel CFD solver based on Smoothed Particle Hydrodynamics (SPH)

    NASA Astrophysics Data System (ADS)

    Crespo, A. J. C.; Domínguez, J. M.; Rogers, B. D.; Gómez-Gesteira, M.; Longshaw, S.; Canelas, R.; Vacondio, R.; Barreiro, A.; García-Feal, O.

    2015-02-01

    DualSPHysics is a hardware accelerated Smoothed Particle Hydrodynamics code developed to solve free-surface flow problems. DualSPHysics is an open-source code developed and released under the terms of GNU General Public License (GPLv3). Along with the source code, a complete documentation that makes easy the compilation and execution of the source files is also distributed. The code has been shown to be efficient and reliable. The parallel power computing of Graphics Computing Units (GPUs) is used to accelerate DualSPHysics by up to two orders of magnitude compared to the performance of the serial version.

  13. tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform

    PubMed Central

    Scheufele, Elisabeth; Aronzon, Dina; Coopersmith, Robert; McDuffie, Michael T.; Kapoor, Manish; Uhrich, Christopher A.; Avitabile, Jean E.; Liu, Jinlei; Housman, Dan; Palchuk, Matvey B.

    2014-01-01

    The tranSMART knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. tranSMART bridges the prolific world of basic science and clinical practice data at the point of care by merging multiple types of data from disparate sources into a common environment. The application supports data harmonization and integration with analytical pipelines. The application code was released into the open source community in January 2012, with 32 instances in operation. tranSMART’s extensible data model and corresponding data integration processes, rapid data analysis features, and open source nature make it an indispensable tool in translational or clinical research. PMID:25717408

  14. tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform.

    PubMed

    Scheufele, Elisabeth; Aronzon, Dina; Coopersmith, Robert; McDuffie, Michael T; Kapoor, Manish; Uhrich, Christopher A; Avitabile, Jean E; Liu, Jinlei; Housman, Dan; Palchuk, Matvey B

    2014-01-01

    The tranSMART knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. tranSMART bridges the prolific world of basic science and clinical practice data at the point of care by merging multiple types of data from disparate sources into a common environment. The application supports data harmonization and integration with analytical pipelines. The application code was released into the open source community in January 2012, with 32 instances in operation. tranSMART's extensible data model and corresponding data integration processes, rapid data analysis features, and open source nature make it an indispensable tool in translational or clinical research. PMID:25717408

  15. tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform.

    PubMed

    Scheufele, Elisabeth; Aronzon, Dina; Coopersmith, Robert; McDuffie, Michael T; Kapoor, Manish; Uhrich, Christopher A; Avitabile, Jean E; Liu, Jinlei; Housman, Dan; Palchuk, Matvey B

    2014-01-01

    The tranSMART knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. tranSMART bridges the prolific world of basic science and clinical practice data at the point of care by merging multiple types of data from disparate sources into a common environment. The application supports data harmonization and integration with analytical pipelines. The application code was released into the open source community in January 2012, with 32 instances in operation. tranSMART's extensible data model and corresponding data integration processes, rapid data analysis features, and open source nature make it an indispensable tool in translational or clinical research.

  16. Sources of Free and Open Source Spatial Data for Natural Disasters and Principles for Use in Developing Country Contexts

    NASA Astrophysics Data System (ADS)

    Taylor, Faith E.; Malamud, Bruce D.; Millington, James D. A.

    2016-04-01

    Access to reliable spatial and quantitative datasets (e.g., infrastructure maps, historical observations, environmental variables) at regional and site specific scales can be a limiting factor for understanding hazards and risks in developing country settings. Here we present a 'living database' of >75 freely available data sources relevant to hazard and risk in Africa (and more globally). Data sources include national scientific foundations, non-governmental bodies, crowd-sourced efforts, academic projects, special interest groups and others. The database is available at http://tinyurl.com/africa-datasets and is continually being updated, particularly in the context of broader natural hazards research we are doing in the context of Malawi and Kenya. For each data source, we review the spatiotemporal resolution and extent and make our own assessments of reliability and usability of datasets. Although such freely available datasets are sometimes presented as a panacea to improving our understanding of hazards and risk in developing countries, there are both pitfalls and opportunities unique to using this type of freely available data. These include factors such as resolution, homogeneity, uncertainty, access to metadata and training for usage. Based on our experience, use in the field and grey/peer-review literature, we present a suggested set of guidelines for using these free and open source data in developing country contexts.

  17. An open source toolkit for the implementation of hypotheses driven, integrated water and solute fate models

    NASA Astrophysics Data System (ADS)

    Kraft, P.; Frede, H.-G.; Breuer, L.

    2012-04-01

    Hydrological models are composed of hypotheses concerning the flow regime in the landscape. Classical model applications do not test these implicit hypotheses, but solely calibrate the parameter set of this single model structure. This more or less blind use of modeling systems has been critically disputed in the last decade, due to the lack of a hypotheses guided methodology. Modular frameworks can help to formulate, implement and test hypotheses. The Catchment Modelling Framework, CMF, is such a modular framework, designed to be openly accessible and operating system independent. CMF is implemented in C++ as a library of objects for the design of problem oriented, catchment specific model structures. The objects of the library are assembled with the programming language Python, utilizing the vast amount of available scientific libraries. The model domain is discretized following a finite volume approach. Models are created as a web of water fluxes, where the finite volumes (water storages) and boundary conditions form the nodes, and equations for water fluxes (flux connections) form the edges. Using these objects as a model toolkit, a large range of different models can be realized: from physics based one dimensional percolation models, over two dimensional hillslope models to large scale lumped or semi-distributed approaches. Distinct hydrological features, like irrigation or drainage measures can be included into the model as additional flux connections. Due to the open interface of CMF, high frequency exchange of data with additional models can be implemented. By coupling models in depth with this mechanism, driven by a shared steering script, new integrated approaches are rapidly developed. This model coupling has been shown for biogeochemical models, for integrated nutrient transport and turnover modeling, where CMF acts as a lateral distributor, and the biogeochemical model calculates the reactive flux. In another study, a regional, steady state groundwater

  18. Impacts of carbon source addition on denitrification and phosphorus uptake in enhanced biological phosphorus removal systems.

    PubMed

    Begum, Shamim A; Batista, Jacimaria R

    2013-01-01

    In this study, simultaneous denitrification and phosphorus (P) removal were investigated in batch tests using nitrified mixed liquor and secondary wastewater influent from a full-scale treatment plant and different levels of acetate and propionate as supplemental carbon sources. Without supplemental carbon source, denitrification occurred at low rate and P release and P uptake was negatively affected (i.e., P removal of only 59.7%). When acetate and propionate were supplied, denitrification and P release occurred simultaneously under anoxic conditions. For acetate and propionate at a C/N stoichiometric ratio of 7.6, P release was negatively affected by denitrification. For acetate, the percent P removal and denitrification were very similar for C/N ratios of 22 (5X stoichiometric) and 59 (10X stoichiometric). For propionate, both percent P removal and denitrification deteriorated for C/N ratios of 22 (5X stoichiometric) and 45 (10X stoichiometric). It was observed that carbon source added in excess to stoichiometric ratio was consumed in the aerobic zone, but P was not taken up. This implies that PAO bacteria may utilize the excess carbon source in the aerobic zone rather than their polyhydroxyalkanoate (PHA) reserves, thereby promoting deterioration of the system.

  19. osni.info-Using free/libre/open source software to build a virtual international community for open source nursing informatics.

    PubMed

    Oyri, Karl; Murray, Peter J

    2005-12-01

    Many health informatics organizations seem to be slow to take up the advantages of dynamic, web-based technologies for providing services to, and interaction with, their members; these are often the very technologies they promote for use within healthcare environments. This paper aims to introduce some of the many free/libre/open source (FLOSS) applications that are now available to develop interactive websites and dynamic online communities as part of the structure of health informatics organizations, and to show how the Open Source Nursing Informatics Working Group (OSNI) of the special interest group in nursing informatics of the International Medical Informatics Association (IMIA-NI) is using some of these tools to develop an online community of nurse informaticians through their website, at . Some background introduction to FLOSS applications is used for the benefit of those less familiar with such tools, and examples of some of the FLOSS content management systems (CMS) being used by OSNI are described. The experiences of the OSNI will facilitate a knowledgeable nursing contribution to the wider discussions on the applications of FLOSS within health and healthcare, and provides a model that many other groups could adopt.

  20. Open-source computational model of a solid oxide fuel cell

    NASA Astrophysics Data System (ADS)

    Beale, Steven B.; Choi, Hae-Won; Pharoah, Jon G.; Roth, Helmut K.; Jasak, Hrvoje; Jeon, Dong Hyup

    2016-03-01

    The solid oxide fuel cell is an electro-chemical device which converts chemical energy into electricity and heat. To compete in today's market, design improvements, in terms of performance and life cycle, are required. Numerical prototypes can accelerate design and development progress. In this programme of research, a three-dimensional solid oxide fuel cell prototype, openFuelCell, based on open-source computational fluid dynamics software was developed and applied to a single cell. Transport phenomena, combined with the solution to the local Nernst equation for the open-circuit potential, as well as the Kirchhoff-Ohm relationship for the local current density, allow local electro-chemistry, fluid flow, multi-component species transport, and multi-region thermal analysis to be considered. The underlying physicochemical hydrodynamics, including porous-electrode and electro-chemical effects are described in detail. The openFuelCell program is developed in an object-oriented open-source C++ library. The code is available at

  1. ImTK: an open source multi-center information management toolkit

    NASA Astrophysics Data System (ADS)

    Alaoui, Adil; Ingeholm, Mary Lou; Padh, Shilpa; Dorobantu, Mihai; Desai, Mihir; Cleary, Kevin; Mun, Seong K.

    2008-03-01

    The Information Management Toolkit (ImTK) Consortium is an open source initiative to develop robust, freely available tools related to the information management needs of basic, clinical, and translational research. An open source framework and agile programming methodology can enable distributed software development while an open architecture will encourage interoperability across different environments. The ISIS Center has conceptualized a prototype data sharing network that simulates a multi-center environment based on a federated data access model. This model includes the development of software tools to enable efficient exchange, sharing, management, and analysis of multimedia medical information such as clinical information, images, and bioinformatics data from multiple data sources. The envisioned ImTK data environment will include an open architecture and data model implementation that complies with existing standards such as Digital Imaging and Communications (DICOM), Health Level 7 (HL7), and the technical framework and workflow defined by the Integrating the Healthcare Enterprise (IHE) Information Technology Infrastructure initiative, mainly the Cross Enterprise Document Sharing (XDS) specifications.

  2. Medical Subject Headings (MeSH) for indexing and retrieving open-source healthcare data.

    PubMed

    Marc, David T; Khairat, Saif S

    2014-01-01

    The US federal government initiated the Open Government Directive where federal agencies are required to publish high value datasets so that they are available to the public. Data.gov and the community site Healthdata.gov were initiated to disperse such datasets. However, data searches and retrieval for these sites are keyword driven and severely limited in performance. The purpose of this paper is to address the issue of extracting relevant open-source data by proposing a method of adopting the MeSH framework for indexing and data retrieval. A pilot study was conducted to compare the performance of traditional keywords to MeSH terms for retrieving relevant open-source datasets related to "mortality". The MeSH framework resulted in greater sensitivity with comparable specificity to the keyword search. MeSH showed promise as a method for indexing and retrieving data, yet future research should conduct a larger scale evaluation of the performance of the MeSH framework for retrieving relevant open-source healthcare datasets.

  3. Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology.

    PubMed

    Siegle, Joshua H; Hale, Gregory J; Newman, Jonathan P; Voigts, Jakob

    2015-06-01

    One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors. PMID:25528614

  4. Social network of PESCA (Open Source Platform for eHealth).

    PubMed

    Sanchez, Carlos L; Romero-Cuevas, Miguel; Lopez, Diego M; Lorca, Julio; Alcazar, Francisco J; Ruiz, Sergio; Mercado, Carmen; Garcia-Fortea, Pedro

    2008-01-01

    Information and Communication Technologies (ICTs) are revolutionizing how healthcare systems deliver top-quality care to citizens. In this way, Open Source Software (OSS) has demonstrated to be an important strategy to spread ICTs use. Several human and technological barriers in adopting OSS for healthcare have been identified. Human barriers include user acceptance, limited support, technical skillfulness, awareness, resistance to change, etc., while Technological barriers embrace need for open standards, heterogeneous OSS developed without normalization and metrics, lack of initiatives to evaluate existing health OSS and need for quality control and functional validation. The goals of PESCA project are to create a platform of interoperable modules to evaluate, classify and validate good practices in health OSS. Furthermore, a normalization platform will provide interoperable solutions in the fields of healthcare services, health surveillance, health literature, and health education, knowledge and research. Within the platform, the first goal to achieve is the setup of the collaborative work infrastructure. The platform is being organized as a Social Network which works to evaluate five scopes of every existing open source tools for eHealth: Open Source Software, Quality, Pedagogical, Security and privacy and Internationalization/I18N. In the meantime, the knowledge collected from the networking will configure a Good Practice Repository on eHealth promoting the effective use of ICT on behalf of the citizen's health.

  5. QuTiP: An open-source Python framework for the dynamics of open quantum systems

    NASA Astrophysics Data System (ADS)

    Johansson, J. R.; Nation, P. D.; Nori, Franco

    2012-08-01

    We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

  6. Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab.

    PubMed

    Boulos, Maged N Kamel; Honda, Kiyoshi

    2006-01-18

    Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft(R) Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described.

  7. OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine.

    PubMed

    Tharakan, Ravi; Martens, Lennart; Van Eyk, Jennifer E; Graham, David R

    2008-06-01

    We here present a user-friendly and extremely lightweight tool that can serve as a stand-alone front-end for the Open MS Search Algorithm (OMSSA) search engine, or that can directly be used as part of an informatics processing pipeline for MS driven proteomics. The OMSSA graphical user interface (OMSSAGUI) tool is written in Java, and is supported on Windows, Linux, and OSX platforms. It is an open source under the Apache 2 license and can be downloaded from http://code.google.com/p/mass-spec-gui/.

  8. An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

    SciTech Connect

    Segre, Daniel

    2014-08-14

    The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

  9. Can open-source drug R&D repower pharmaceutical innovation?

    PubMed

    Munos, B

    2010-05-01

    Open-source R&D initiatives are multiplying across biomedical research. Some of them-such as public-private partnerships-have achieved notable success in bringing new drugs to market economically, whereas others reflect the pharmaceutical industry's efforts to retool its R&D model. Is open innovation the answer to the innovation crisis? This Commentary argues that although it may likely be part of the solution, significant cultural, scientific, and regulatory barriers can prevent it from delivering on its promise.

  10. IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in Java

    PubMed Central

    Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

    2015-01-01

    Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM’s image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis. PMID:25612319

  11. IQM: an extensible and portable open source application for image and signal analysis in Java.

    PubMed

    Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

    2015-01-01

    Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM's image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis.

  12. Open Source Meets Virtual Reality--An Instructor's Journey Unearths New Opportunities for Learning, Community, and Academia

    ERIC Educational Resources Information Center

    O'Connor, Eileen A.

    2015-01-01

    Opening with the history, recent advances, and emerging ways to use avatar-based virtual reality, an instructor who has used virtual environments since 2007 shares how these environments bring more options to community building, teaching, and education. With the open-source movement, where the source code for virtual environments was made…

  13. Adopting Open-Source Software Applications in U. S. Higher Education: A Cross-Disciplinary Review of the Literature

    ERIC Educational Resources Information Center

    van Rooij, Shahron Williams

    2009-01-01

    Higher Education institutions in the United States are considering Open Source software applications such as the Moodle and Sakai course management systems and the Kuali financial system to build integrated learning environments that serve both academic and administrative needs. Open Source is presumed to be more flexible and less costly than…

  14. Cognitive Readiness Assessment and Reporting: An Open Source Mobile Framework for Operational Decision Support and Performance Improvement

    ERIC Educational Resources Information Center

    Heric, Matthew; Carter, Jenn

    2011-01-01

    Cognitive readiness (CR) and performance for operational time-critical environments are continuing points of focus for military and academic communities. In response to this need, we designed an open source interactive CR assessment application as a highly adaptive and efficient open source testing administration and analysis tool. It is capable…

  15. Open Source Software Development Experiences on the Students' Resumes: Do They Count?--Insights from the Employers' Perspectives

    ERIC Educational Resources Information Center

    Long, Ju

    2009-01-01

    Open Source Software (OSS) is a major force in today's Information Technology (IT) landscape. Companies are increasingly using OSS in mission-critical applications. The transparency of the OSS technology itself with openly available source codes makes it ideal for students to participate in the OSS project development. OSS can provide unique…

  16. Free and Open Source Software underpinning the European Forest Data Centre

    NASA Astrophysics Data System (ADS)

    Rodriguez Aseretto, Dario; Di Leo, Margherita; de Rigo, Daniele; Corti, Paolo; McInerney, Daniel; Camia, Andrea; San-Miguel-Ayanz, Jesús

    2013-04-01

    Worldwide, governments are growingly focusing [1] on free and open source software (FOSS) as a move toward transparency and the freedom to run, copy, study, change and improve the software [2]. The European Commission (EC) is also supporting the development of FOSS (see e.g., [3]). In addition to the financial savings, FOSS contributes to scientific knowledge freedom in computational science (CS) [4] and is increasingly rewarded in the science-policy interface within the emerging paradigm of open science [5-8]. Since complex computational science applications may be affected by software uncertainty [4,9-11], FOSS may help to mitigate part of the impact of software errors by CS community-driven open review, correction and evolution of scientific code [10,12-15]. The continental scale of EC science-based policy support implies wide networks of scientific collaboration. Thematic information systems also may benefit from this approach within reproducible [16] integrated modelling [4]. This is supported by the EC strategy on FOSS: "for the development of new information systems, where deployment is foreseen by parties outside of the EC infrastructure, [F]OSS will be the preferred choice and in any case used whenever possible" [17]. The aim of this contribution is to highlight how a continental scale information system may exploit and integrate FOSS technologies within the transdisciplinary research underpinning such a complex system. A European example is discussed where FOSS innervates both the structure of the information system itself and the inherent transdisciplinary research for modelling the data and information which constitute the system content. The information system. The European Forest Data Centre (EFDAC, http://forest.jrc.ec.europa.eu/efdac/) has been established at the EC Joint Research Centre (JRC) as the focal point for forest data and information in Europe to supply European decision-makers with processed, quality checked and timely policy relevant

  17. Proteus - A Free and Open Source Sensor Observation Service (SOS) Client

    NASA Astrophysics Data System (ADS)

    Henriksson, J.; Satapathy, G.; Bermudez, L. E.

    2013-12-01

    The Earth's 'electronic skin' is becoming ever more sophisticated with a growing number of sensors measuring everything from seawater salinity levels to atmospheric pressure. To further the scientific application of this data collection effort, it is important to make the data easily available to anyone who wants to use it. Making Earth Science data readily available will allow the data to be used in new and potentially groundbreaking ways. The US National Science and Technology Council made this clear in its most recent National Strategy for Civil Earth Observations report, when it remarked that Earth observations 'are often found to be useful for additional purposes not foreseen during the development of the observation system'. On the road to this goal the Open Geospatial Consortium (OGC) is defining uniform data formats and service interfaces to facilitate the discovery and access of sensor data. This is being done through the Sensor Web Enablement (SWE) stack of standards, which include the Sensor Observation Service (SOS), Sensor Model Language (SensorML), Observations & Measurements (O&M) and Catalog Service for the Web (CSW). End-users do not have to use these standards directly, but can use smart tools that leverage and implement them. We have developed such a tool named Proteus. Proteus is an open-source sensor data discovery client. The goal of Proteus is to be a general-purpose client that can be used by anyone for discovering and accessing sensor data via OGC-based services. Proteus is a desktop client and supports a straightforward workflow for finding sensor data. The workflow takes the user through the process of selecting appropriate services, bounding boxes, observed properties, time periods and other search facets. NASA World Wind is used to display the matching sensor offerings on a map. Data from any sensor offering can be previewed in a time series. The user can download data from a single sensor offering, or download data in bulk from all

  18. A radio/optical reference frame. 5: Additional source positions in the mid-latitude southern hemisphere

    NASA Technical Reports Server (NTRS)

    Russell, J. L.; Reynolds, J. E.; Jauncey, D. L.; De Vegt, C.; Zacharias, N.; Ma, C.; Fey, A. L.; Johnston, K. J.; Hindsley, R.; Hughes, J. A.

    1994-01-01

    We report new accurate radio position measurements for 30 sources, preliminary positions for two sources, improved radio postions for nine additional sources which had limited previous observations, and optical positions and optical-radio differences for six of the radio sources. The Very Long Baseline Interferometry (VLBI) observations are part of the continuing effort to establish a global radio reference frame of about 400 compact, flat spectrum sources, which are evenly distributed across the sky. The observations were made using Mark III data format in four separate sessions in 1988-89 with radio telescopes at Tidbinbilla, Australia, Kauai, USA, and Kashima, Japan. We observed a total of 54 sources, including ten calibrators and three which were undetected. The 32 new source positions bring the total number in the radio reference frame catalog to 319 (172 northern and 147 southern) and fill in the zone -25 deg greater than delta greater than -45 deg which, prior to this list, had the lowest source density. The VLBI positions have an average formal precision of less than 1 mas, although unknown radio structure effects of about 1-2 mas may be present. The six new optical postion measurements are part of the program to obtain positions of the optical counterparts of the radio reference frame source and to map accurately the optical on to the radio reference frames. The optical measurements were obtained from United States Naval Observatory (USNO) Black Birch astrograph plates and source plates from the AAT, and Kitt Peak National Observatory (KPNO) 4 m, and the European Southern Observatory (ESO) Schmidt. The optical positions have an average precision of 0.07 sec, mostly due to the zero point error when adjusted to the FK5 optical frame using the IRS catalog. To date we have measured optical positions for 46 sources.

  19. Applying Open Source Game Engine for Building Visual Simulation Training System of Fire Fighting

    NASA Astrophysics Data System (ADS)

    Yuan, Diping; Jin, Xuesheng; Zhang, Jin; Han, Dong

    There's a growing need for fire departments to adopt a safe and fair method of training to ensure that the firefighting commander is in a position to manage a fire incident. Visual simulation training systems, with their ability to replicate and interact with virtual fire scenarios through the use of computer graphics or VR, become an effective and efficient method for fire ground education. This paper describes the system architecture and functions of a visual simulated training system of fire fighting on oil storage, which adopting Delat3D, a open source game and simulation engine, to provide realistic 3D views. It presents that using open source technology provides not only the commercial-level 3D effects but also a great reduction of cost.

  20. Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes.

    PubMed

    Jurcău, Daniel-Alexandru; Stoicu-Tivadar, Vasile

    2016-01-01

    This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user's browser, and two popular open-source relational database management systems.

  1. The masked priming toolbox: an open-source MATLAB toolbox for masked priming researchers.

    PubMed

    Wilson, Andrew D; Tresilian, James; Schlaghecken, Friederike

    2011-03-01

    The Masked Priming Toolbox is an open-source collection of MATLAB functions that utilizes the free third-party PsychToolbox-3 (PTB3: Brainard, Spatial Vision, 10, 433-436, 1997; Kleiner, Brainard & Pelli, Perception, 36, 2007; Pelli, Spatial Vision, 10, 437-442, 1997). It is designed to allow a researcher to run masked (and unmasked) priming experiments using a variety of response devices (including keyboards, graphics tablets and force transducers). Very little knowledge of MATLAB is required; experiments are generated by creating a text file with the required parameters, and raw and analyzed data are output to Excel (as well as MATLAB) files for further analysis. The toolbox implements a variety of stimuli for use as primes and targets, as well as a variety of masks. Timing, size, location, and orientation of stimuli are all parameterizable. The code is open-source and made available on the Web under a Creative Commons License.

  2. Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes.

    PubMed

    Jurcău, Daniel-Alexandru; Stoicu-Tivadar, Vasile

    2016-01-01

    This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user's browser, and two popular open-source relational database management systems. PMID:27350484

  3. Validation of an open-source framework for the simulation of blood flow in biomedical devices

    NASA Astrophysics Data System (ADS)

    Quaini, Annalisa; Passerini, Tiziano; Villa, Umberto; Veneziani, Alessandro; Canic, Suncica

    2013-11-01

    We discuss the validation of an open source framework for the solution of problems arising in hemodynamics. The framework is assessed through experimental data for fluid flow in an idealized medical device with rigid boundaries. The core of the framework is an open source parallel finite element library that features several algorithms for fluid problems. The numerical results for the flow in the idealized medical device are in good quantitative agreement with the measured axial components of the velocity and pressures for flow rates corresponding to laminar, transitional, and turbulent regimes. A detailed account of the methods is provided. Support through grants NSF DMS-1109189 and NIH R01 HL70531 is gratefully acknowledged.

  4. Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

    PubMed Central

    2016-01-01

    The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work. PMID:27800551

  5. Low-cost, portable open-source gas monitoring device based on chemosensory technology

    NASA Astrophysics Data System (ADS)

    Gotor, Raúl; Gaviña, Pablo; Costero, Ana M.

    2015-08-01

    We report herein the construction of an electronic device to perform the real-time digitalization of the color state of the optical chemosensors used in the detection of dangerous gases. To construct the device, we used open-source modular electronics, such as Arduino and Sparkfun components, as well as free and open-source software (FOSS). The basic principle of the operation of this device is the continuous color measurement of a chemosensor-doped sensing film, whose color changes in the presence of a specific gas. The chemosensor-sensing film can be prepared by using any of the widely available chemosensors for the desired gas. Color measurement is taken by two TCS230 color sensor ICs, reported to the microcontroller, and the results are displayed on an LCD display and pushed through a USB serial port. By using a cyanide optical chemosensor, we demonstrated the operation of the device as a HCN gas detector at low concentrations.

  6. Decision tree approach for classification of remotely sensed satellite data using open source support

    NASA Astrophysics Data System (ADS)

    Sharma, Richa; Ghosh, Aniruddha; Joshi, P. K.

    2013-10-01

    In this study, an attempt has been made to develop a decision tree classification (DTC) algorithm for classification of remotely sensed satellite data (Landsat TM) using open source support. The decision tree is constructed by recursively partitioning the spectral distribution of the training dataset using WEKA, open source data mining software. The classified image is compared with the image classified using classical ISODATA clustering and Maximum Likelihood Classifier (MLC) algorithms. Classification result based on DTC method provided better visual depiction than results produced by ISODATA clustering or by MLC algorithms. The overall accuracy was found to be 90% (kappa = 0.88) using the DTC, 76.67% (kappa = 0.72) using the Maximum Likelihood and 57.5% (kappa = 0.49) using ISODATA clustering method. Based on the overall accuracy and kappa statistics, DTC was found to be more preferred classification approach than others.

  7. The development and design of an electronic patient record using open source web-based technology.

    PubMed

    Syed-Mohamad, Sharifa Mastura; Ali, Siti Hawa; Mat-Husin, Mohd Nazri

    2010-01-01

    This paper describes the method used to develop the One Stop Crisis Centre (OSCC) Portal, an open source web-based electronic patient record system (EPR) for the One Stop Crisis Center, Hospital Universiti Sains Malaysia (HUSM) in Kelantan, Malaysia. Features and functionalities of the system are presented to demonstrate the workflow. Use of the OSCC Portal improved data integration and data communication and contributed to improvements in care management. With implementation of the OSCC portal, improved coordination between disciplines and standardisation of data in HUSM were noticed. It is expected that this will in turn result in improved data confidentiality and data integrity. The collected data will also be useful for quality assessment and research. Other low-resource centers with limited computer hardware and access to open-source software could benefit from this endeavour. PMID:20335647

  8. Modeling community population dynamics with the open-source language R.

    PubMed

    Green, Robin; Shou, Wenying

    2014-01-01

    The ability to explain biological phenomena with mathematics and to generate predictions from mathematical models is critical for understanding and controlling natural systems. Concurrently, the rise in open-source software has greatly increased the ease at which researchers can implement their own mathematical models. With a reasonably sound understanding of mathematics and programming skills, a researcher can quickly and easily use such tools for their own work. The purpose of this chapter is to expose the reader to one such tool, the open-source programming language R, and to demonstrate its practical application to studying population dynamics. We use the Lotka-Volterra predator-prey dynamics as an example. PMID:24838889

  9. A distributed database system for sharing geological information using free and open source software

    NASA Astrophysics Data System (ADS)

    Nemoto, T.; Masumoto, S.; Nonogaki, S.; Raghavan, V.

    2013-12-01

    Recently, geological information, such as borehole data and geological maps, and seismic, volcanic or landslide hazard maps are published on the Internet by the national government, local governments, and research institutes in Japan. Most web systems that deliver such geological information consist of a centralized database, which are located and maintained in one location. It is easier to manage the centralized database system because all data resides in a single location. However, if the database breaks, the web service will not be available. In the present study, a distributed database system has been developed to continue delivering geological information even if a database breaks. The distributed database system has an advantage that the system remains available although an individual database is down. All the software used to construct the system is free and open source software. PostgreSQL and pgpool-II are utilized to construct a distributed database. PostgreSQL is a powerful relational database management system. Pgpool-II has a function for management of multiple PostgreSQL servers. OpenLayers is used for the web map clients. Replication and Parallel query modes with pgpool-II are utilized for distribution of a database. It is possible to create a real-time backup on 2 or more PostgreSQL clusters by replication mode. If a database breaks, the backup database will works to continue delivering geological information. Data can be split among multiple servers by using parallel query mode. The rules to send partitioned data to an appropriate cluster are contained in the System Database. If large-scale data is searched, the overall execution time will be reduced. The prototype for sharing 1500 borehole data has been successfully implemented by combination of PostgreSQL and pgpool-II on Linux server. Further development and improvement of the system are necessary to manage and analyze various spatial data in addition to borehole data. This study was supported

  10. Open-Source Conceptual Sizing Models for the Hyperloop Passenger Pod

    NASA Technical Reports Server (NTRS)

    Chin, Jeffrey C.; Gray, Justin S.; Jones, Scott M.; Berton, Jeffrey J.

    2015-01-01

    Hyperloop is a new mode of transportation proposed as an alternative to California's high speed rail project, with the intended benefits of higher performance at lower overall costs. It consists of a passenger pod traveling through a tube under a light vacuum and suspended on air bearings. The pod travels up to transonic speeds resulting in a 35 minute travel time between the intended route from Los Angeles and San Francisco. Of the two variants outlined, the smaller system includes a 1.1 meter tall passenger capsule traveling through a 2.2 meter tube at 700 miles per hour. The passenger pod features water-based heat exchangers as well as an on-board compression system that reduces the aerodynamic drag as it moves through the tube. Although the original proposal looks very promising, it assumes that tube and pod dimensions are independently sizable without fully acknowledging the constraints of the compressor system on the pod geometry. This work focuses on the aerodynamic and thermodynamic interactions between the two largest systems; the tube and the pod. Using open-source toolsets, a new sizing method is developed based on one-dimensional thermodynamic relationships that accounts for the strong interactions between these sub-systems. These additional considerations require a tube nearly twice the size originally considered and limit the maximum pod travel speed to about 620 miles per hour. Although the results indicate that Hyperloop will need to be larger and slightly slower than originally intended, the estimated travel time only increases by approximately five minutes, so the overall performance is not dramatically affected. In addition, the proposed on-board heat exchanger is not an ideal solution to achieve reasonable equilibrium air temperatures within the tube. Removal of this subsystem represents a potential reduction in weight, energy requirements and complexity of the pod. In light of these finding, the core concept still remains a compelling

  11. 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

  12. An open-source computational and data resource to analyze digital maps of immunopeptidomes

    SciTech Connect

    Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J.; Schuster, Heiko; Ternette, Nicola; Alpízar, Adán; Schittenhelm, Ralf B.; Ramarathinam, Sri H.; Lindestam Arlehamn, Cecilia S.; Chiek Koh, Ching; Gillet, Ludovic C.; Rabsteyn, Armin; Navarro, Pedro; Kim, Sangtae; Lam, Henry; Sturm, Theo; Marcilla, Miguel; Sette, Alessandro; Campbell, David S.; Deutsch, Eric W.; Moritz, Robert L.; Purcell, Anthony W.; Rammensee, Hans -Georg; Stevanovic, Stefan; Aebersold, Ruedi

    2015-07-08

    We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.

  13. ProteoCloud: a full-featured open source proteomics cloud computing pipeline.

    PubMed

    Muth, Thilo; Peters, Julian; Blackburn, Jonathan; Rapp, Erdmann; Martens, Lennart

    2013-08-01

    We here present the ProteoCloud pipeline, a freely available, full-featured cloud-based platform to perform computationally intensive, exhaustive searches in a cloud environment using five different peptide identification algorithms. ProteoCloud is entirely open source, and is built around an easy to use and cross-platform software client with a rich graphical user interface. This client allows full control of the number of cloud instances to initiate and of the spectra to assign for identification. It also enables the user to track progress, and to visualize and interpret the results in detail. Source code, binaries and documentation are all available at http://proteocloud.googlecode.com.

  14. Open-Source as a strategy for operational software - the case of Enki

    NASA Astrophysics Data System (ADS)

    Kolberg, Sjur; Bruland, Oddbjørn

    2014-05-01

    Since 2002, SINTEF Energy has been developing what is now known as the Enki modelling system. This development has been financed by Norway's largest hydropower producer Statkraft, motivated by a desire for distributed hydrological models in operational use. As the owner of the source code, Statkraft has recently decided on Open Source as a strategy for further development, and for migration from an R&D context to operational use. A current cooperation project is currently carried out between SINTEF Energy, 7 large Norwegian hydropower producers including Statkraft, three universities and one software company. Of course, the most immediate task is that of software maturing. A more important challenge, however, is one of gaining experience within the operational hydropower industry. A transition from lumped to distributed models is likely to also require revision of measurement program, calibration strategy, use of GIS and modern data sources like weather radar and satellite imagery. On the other hand, map based visualisations enable a richer information exchange between hydrologic forecasters and power market traders. The operating context of a distributed hydrology model within hydropower planning is far from settled. Being both a modelling framework and a library of plugin-routines to build models from, Enki supports the flexibility needed in this situation. Recent development has separated the core from the user interface, paving the way for a scripting API, cross-platform compilation, and front-end programs serving different degrees of flexibility, robustness and security. The open source strategy invites anyone to use Enki and to develop and contribute new modules. Once tested, the same modules are available for the operational versions of the program. A core challenge is to offer rigid testing procedures and mechanisms to reject routines in an operational setting, without limiting the experimentation with new modules. The Open Source strategy also has

  15. SPIM-fluid: open source light-sheet based platform for high-throughput imaging.

    PubMed

    Gualda, Emilio J; Pereira, Hugo; Vale, Tiago; Estrada, Marta Falcão; Brito, Catarina; Moreno, Nuno

    2015-11-01

    Light sheet fluorescence microscopy has recently emerged as the technique of choice for obtaining high quality 3D images of whole organisms/embryos with low photodamage and fast acquisition rates. Here we present an open source unified implementation based on Arduino and Micromanager, which is capable of operating Light Sheet Microscopes for automatized 3D high-throughput imaging on three-dimensional cell cultures and model organisms like zebrafish, oriented to massive drug screening. PMID:26601007

  16. Open-Source, Web-Based Dashboard Components for DICOM Connectivity.

    PubMed

    Bustamante, Catalina; Pineda, Julian; Rascovsky, Simon; Arango, Andres

    2016-08-01

    The administration of a DICOM network within an imaging healthcare institution requires tools that allow for monitoring of connectivity and availability for adequate uptime measurements and help guide technology management strategies. We present the implementation of an open-source widget for the Dashing framework that provides basic dashboard functionality allowing for monitoring of a DICOM network using network "ping" and DICOM "C-ECHO" operations. PMID:26856347

  17. The C-Cat Wordnet Package: An Open Source Package for modifying andapplying Wordnet

    SciTech Connect

    Stevens, K; Huang, T; Buttler, D

    2011-09-16

    We present the C-Cat Wordnet package, an open source library for using and modifying Wordnet. The package includes four key features: an API for modifying Synsets; implementations of standard similarity metrics, implementations of well known Word Sense Disambiguation algorithms, and an implementation of the Castanet algorithm. The library is easily extendible and usable in many runtime environments. We demonstrate it's use on two standard Word Sense Disambiguation tasks and apply the Castanet algorithm to a corpus.

  18. DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

    PubMed

    Dryden, Michael D M; Wheeler, Aaron R

    2015-01-01

    Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

  19. The Trick Simulation Toolkit: A NASA/Open source Framework for Running Time Based Physics Models

    NASA Technical Reports Server (NTRS)

    Penn, John M.; Lin, Alexander S.

    2016-01-01

    This paper describes the design and use at of the Trick Simulation Toolkit, a simulation development environment for creating high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. It describes Trick's design goals and how the development environment attempts to achieve those goals. It describes how Trick is used in some of the many training and engineering simulations at NASA. Finally it describes the Trick NASA/Open source project on Github.

  20. CosmoBolognaLib: Open source C++ libraries for cosmological calculations

    NASA Astrophysics Data System (ADS)

    Marulli, Federico; Veropalumbo, Alfonso; Moresco, Michele

    2015-11-01

    CosmoBolognaLib contains numerical libraries for cosmological calculations; written in C++, it is intended to define a common numerical environment for cosmological investigations of the large-scale structure of the Universe. The software aids in handling real and simulated astronomical catalogs by measuring one-point, two-point and three-point statistics in configuration space and performing cosmological analyses. These open source libraries can be included in either C++ or Python codes.