WorldWideScience

Sample records for open-source software platform

  1. Beyond Open Source Software: Solving Common Library Problems Using the Open Source Hardware Arduino Platform

    Directory of Open Access Journals (Sweden)

    Jonathan Younker

    2013-06-01

    Full Text Available Using open source hardware platforms like the Arduino, libraries have the ability to quickly and inexpensively prototype custom hardware solutions to common library problems. The authors present the Arduino environment, what it is, what it does, and how it was used at the James A. Gibson Library at Brock University to create a production portable barcode-scanning utility for in-house use statistics collection as well as a prototype for a service desk statistics tabulation program’s hardware interface.

  2. SOFTWARE OPEN SOURCE, SOFTWARE GRATIS?

    Directory of Open Access Journals (Sweden)

    Nur Aini Rakhmawati

    2006-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Berlakunya Undang – undang Hak Atas Kekayaan Intelektual (HAKI, memunculkan suatu alternatif baru untuk menggunakan software open source. Penggunaan software open source menyebar seiring dengan isu global pada Information Communication Technology (ICT saat ini. Beberapa organisasi dan perusahaan mulai menjadikan software open source sebagai pertimbangan. Banyak konsep mengenai software open source ini. Mulai dari software yang gratis sampai software tidak berlisensi. Tidak sepenuhnya isu software open source benar, untuk itu perlu dikenalkan konsep software open source mulai dari sejarah, lisensi dan bagaimana cara memilih lisensi, serta pertimbangan dalam memilih software open source yang ada. Kata kunci :Lisensi, Open Source, HAKI

  3. Open source hardware and software platform for robotics and artificial intelligence applications

    Science.gov (United States)

    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.

  4. POLITO- A new open-source, platform independent software for generating high-quality lithostratigraphic columns

    Directory of Open Access Journals (Sweden)

    Cipran C. Stremtan

    2010-08-01

    Full Text Available POLITO is a free, open-source, and platform-independent software which can automatically generate lithostratigraphic columns from field data. Its simple and easy to use interface allows users to manipulate large datasets and create high-quality graphical outputs, either in editable vector or raster format, or as PDF files. POLITO uses USGS standard lithology patterns and can be downloaded from its Sourceforge project page (http://sourceforge.net/projects/polito/.

  5. Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

    Science.gov (United States)

    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.

  6. Open Source Software Acquisition

    DEFF Research Database (Denmark)

    Holck, Jesper; Kühn Pedersen, Mogens; Holm Larsen, Michael

    2005-01-01

    Lately we have seen a growing interest from both public and private organisations to adopt OpenSource Software (OSS), not only for a few, specific applications but also on a more general levelthroughout the organisation. As a consequence, the organisations' decisions on adoption of OSS arebecoming...

  7. BENEFITS AND SUCCESS FACTORS OF OPEN-SOURCE WEB SERVICES DEVELOPMENT PLATFORMS FOR SMALL SOFTWARE HOUSES

    Directory of Open Access Journals (Sweden)

    Valter de Assis Moreno Jr.

    2012-12-01

    Full Text Available It is usually difficult for companies to keep up with the development of new information technologies and adapt to them in face of the opportunities and threats their advances may represent. This is especially true for small and medium enterprises (SME in emerging economies, where resources tend to be scarce and markets more volatile. This paper describes an action research conducted in a small Brazilian software house that adopted an open-source Web Services development platform in order to improve its software development process. Data analysis revealed critical success factors (CSF in the adoption process, as well as specific benefits and barriers prone to be faced by small software houses in their adoption efforts. In the process of overcoming such barriers, SME may acquire intellectual capital that represents an essential resource to ensure their competitiveness and survival in emerging economies.

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

    Directory of Open Access Journals (Sweden)

    Luke eCampagnola

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  11. An Open Source Software Platform for Visualizing and Teaching Conservation Tasks in Architectural Heritage Environments

    Science.gov (United States)

    San Jose, I. Ignacio; Martinez, J.; Alvarez, N.; Fernandez, J. J.; Delgado, F.; Martinez, R.; Puche, J. C.; Finat, J.

    2013-07-01

    In this work we present a new software platform for interactive volumetric visualization of complex architectural objects and their applications to teaching and training conservation interventions in Architectural Cultural Heritage. Photogrammetric surveying is performed by processing the information arising from image- and range-based devices. Our visualization application is based on an adaptation of WebGL open standard; the performed adaptation allows to import open standards and an interactive navigation of 3D models in ordinary web navigators with a good performance. The Visualization platform is scalable and can be applied to urban environments, provided open source files be used; CityGML is an open standard based on a geometry -driven Ontology which is compatible with this approach. We illustrate our results with examples concerning to very damaged churches and a urban district of Segovia (World Cultural Heritage). Their connection with appropriate database eases the building evolution and interventions tracking. We have incorporated some preliminary examples to illustrate Advanced Visualization Tools and architectural e-Learning software platform which have been created for assessing conservation and restoration tasks in very damaged buildings. First version of the Advanced Visualization application has been developed in the framework of ADISPA Spanish Project Results. Our results are illustrated with the application of these software applications to several very damaged cultural heritage buildings in rural zones of Castilla y Leon (Spain).

  12. Open Source Software Acquisition

    DEFF Research Database (Denmark)

    Holck, Jesper; Kühn Pedersen, Mogens; Holm Larsen, Michael

    2005-01-01

    Lately we have seen a growing interest from both public and private organisations to adopt OpenSource Software (OSS), not only for a few, specific applications but also on a more general levelthroughout the organisation. As a consequence, the organisations' decisions on adoption of OSS arebecoming......, in smaller organisations and in small-scale adoption of OSS, the cheapprice of OSS is a major enabler, as it provides a good opportunity for experiments and short-termeconomic benefits. For small organisations these experiments can lead to development of a commonIT-architecture, and in larger organisations...

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

    Science.gov (United States)

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

    2015-12-01

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

  14. OptFlux: an open-source software platform for in silico metabolic engineering.

    Science.gov (United States)

    Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; Patil, Kiran R; Ferreira, Eugénio C; Rocha, Miguel

    2010-04-19

    Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization

  15. OptFlux: an open-source software platform for in silico metabolic engineering

    Directory of Open Access Journals (Sweden)

    Pinto José P

    2010-04-01

    Full Text Available Abstract Background Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. Conclusions The OptFlux software is freely available, together with documentation and other resources, thus

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

    Science.gov (United States)

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

    2014-12-01

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

  17. When to make proprietary software open source

    NARCIS (Netherlands)

    Caulkins, J.P.; Feichtinger, G.; Grass, D.; Hartl, R.F.; Kort, P.M.; Seidl, A.

    2013-01-01

    Software can be distributed closed source (proprietary) or open source (developed collaboratively). While a firm cannot sell open source software, and so loses potential sales revenue, the open source software development process can have a substantial positive impact on the quality of a software, i

  18. Web accessibility and open source software.

    Science.gov (United States)

    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 RISCOSS Platform for Risk Management in Open Source Software Adoption

    OpenAIRE

    Franch Gutiérrez, Javier; Kenett, Ron; Mancinelli, Fabio; Susi, Angelo; Ameller, David; Annosi, Maria Carmela; Ben-Jacob, Ron; Blumenfeld, Yehuda; Franco Bedoya, Óscar Hernán; Gross, Daniel; López Cuesta, Lidia; Morandini, Mirko; Oriol Hilari, Marc; Siena, Alberto

    2015-01-01

    Part 4: Adoption, Use, and Impact; International audience; Managing risks related to OSS adoption is a must for organizations that need to smoothly integrate OSS-related practices in their development processes. Adequate tool support may pave the road to effective risk management and ensure the sustainability of such activity. In this paper, we present the RISCOSS platform for managing risks in OSS adoption. RISCOSS builds upon a highly configurable data model that allows customization to sev...

  20. OptFlux: an open-source software platform for in silico metabolic engineering

    DEFF Research Database (Denmark)

    Rocha, I.; Maia, P.; Evangelista, P.

    2010-01-01

    software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed Opt......, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization...... algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition...

  1. An Open-Source Based ITS Platform

    DEFF Research Database (Denmark)

    Andersen, Ove; Krogh, Benjamin Bjerre; Torp, Kristian

    2013-01-01

    In this paper, a complete platform used to compute travel times from GPS data is described. Two approaches to computing travel time are proposed one based on points and one based on trips. Overall both approaches give reasonable results compared to existing manual estimated travel times. However......, the trip-based approach requires more GPS data and of a higher quality than the point-based approach. The platform has been completely implemented using open-source software. The main conclusion is that large quantity of GPS data can be managed, with a limited budget and that GPS data is a good source...

  2. Usability in open source software development

    DEFF Research Database (Denmark)

    Andreasen, M. S.; Nielsen, H. V.; Schrøder, S. O.

    2006-01-01

    Open Source Software (OSS) development has gained significant importance in the production of soft-ware products. Open Source Software developers have produced systems with a functionality that is competitive with similar proprietary software developed by commercial software organizations. Yet OSS...

  3. Practical open source software for libraries

    CERN Document Server

    Engard, Nicole

    2010-01-01

    Open source refers to an application whose source code is made available for use or modification as users see fit. This means libraries gain more flexibility and freedom than with software purchased with license restrictions. Both the open source community and the library world live by the same rules and principles. Practical Open Source Software for Libraries explains the facts and dispels myths about open source. Chapters introduce librarians to open source and what it means for libraries. The reader is provided with links to a toolbox full of freely available open source products to use in

  4. Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation.

    Science.gov (United States)

    Wang, Yu; Helminen, Emily; Jiang, Jingfeng

    2015-09-01

    Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time

  5. Free for All: Open Source Software

    Science.gov (United States)

    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…

  6. Free for All: Open Source Software

    Science.gov (United States)

    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…

  7. Free software and open source databases

    Directory of Open Access Journals (Sweden)

    Napoleon Alexandru SIRITEANU

    2006-01-01

    Full Text Available The emergence of free/open source software -FS/OSS- enterprises seeks to push software development out of the academic stream into the commercial mainstream, and as a result, end-user applications such as open source database management systems (PostgreSQL, MySQL, Firebird are becoming more popular. Companies like Sybase, Oracle, Sun, IBM are increasingly implementing open source strategies and porting programs/applications into the Linux environment. Open source software is redefining the software industry in general and database development in particular.

  8. Building Energy Management Open Source Software

    Energy Technology Data Exchange (ETDEWEB)

    2017-06-20

    This is the repository for Building Energy Management Open Source Software (BEMOSS), which is an open source operating system that is engineered to improve sensing and control of equipment in small- and medium-sized commercial buildings. BEMOSS offers the following key features: (1) Open source, open architecture – BEMOSS is an open source operating system that is built upon VOLTTRON – a distributed agent platform developed by Pacific Northwest National Laboratory (PNNL). BEMOSS was designed to make it easy for hardware manufacturers to seamlessly interface their devices with BEMOSS. Software developers can also contribute to adding additional BEMOSS functionalities and applications. (2) Plug & play – BEMOSS was designed to automatically discover supported load controllers (including smart thermostats, VAV/RTUs, lighting load controllers and plug load controllers) in commercial buildings. (3) Interoperability – BEMOSS was designed to work with load control devices form different manufacturers that operate on different communication technologies and data exchange protocols. (4) Cost effectiveness – Implementation of BEMOSS deemed to be cost-effective as it was built upon a robust open source platform that can operate on a low-cost single-board computer, such as Odroid. This feature could contribute to its rapid deployment in small- or medium-sized commercial buildings. (5) Scalability and ease of deployment – With its multi-node architecture, BEMOSS provides a distributed architecture where load controllers in a multi-floor and high occupancy building could be monitored and controlled by multiple single-board computers hosting BEMOSS. This makes it possible for a building engineer to deploy BEMOSS in one zone of a building, be comfortable with its operation, and later on expand the deployment to the entire building to make it more energy efficient. (6) Ability to provide local and remote monitoring – BEMOSS provides both local and remote monitoring

  9. 构建云计算平台的开源软件综述%Survey of Open Source Software for Building Cloud Computing Platforms

    Institute of Scientific and Technical Information of China (English)

    林利; 石文昌

    2012-01-01

    The emergence of open source software for cloud computing facilitates the building of cloud computing platforms, but meanwhile it challenges the choosing of appropriate ones from these pool of software. To figure out how to build a cloud computing platform, research on existing open source software for building cloud computing platforms is necessary. This paper investigated the development of these kinds of open source software and analyzed their architectures from the perspective of service models. Through comparison and analysis of representatives of them, effective ways were proposed for developers to choose appropriate pieces of software to build a specific cloud computing platform.%云计算开源软件的涌现为云计算平台的构建提供了便利,同时也为人们从中选择合适的软件带来了挑战.为明确如何构建云计算平台,研究现有用于构建云计算平台的开源软件十分必要.考察构建云计算平台的开源软件的发展状况,从提供服务的角度对各种服务模型的开源软件体系结构进行剖析,通过对比分析当前典型的用于构建云计算平台的开源软件,来为云计算平台建设者利用此类软件构建符合特定需求的云计算环境提供有效的途径.

  10. Building Energy Management Open Source Software

    Energy Technology Data Exchange (ETDEWEB)

    Rahman, Saifur [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)

    2017-08-25

    Funded by the U.S. Department of Energy in November 2013, a Building Energy Management Open Source Software (BEMOSS) platform was engineered to improve sensing and control of equipment in small- and medium-sized commercial buildings. According to the Energy Information Administration (EIA), small- (5,000 square feet or smaller) and medium-sized (between 5,001 to 50,000 square feet) commercial buildings constitute about 95% of all commercial buildings in the U.S. These buildings typically do not have Building Automation Systems (BAS) to monitor and control building operation. While commercial BAS solutions exist, including those from Siemens, Honeywell, Johnsons Controls and many more, they are not cost effective in the context of small- and medium-sized commercial buildings, and typically work with specific controller products from the same company. BEMOSS targets small and medium-sized commercial buildings to address this gap.

  11. Refurbishment and open source software

    CSIR Research Space (South Africa)

    Mabuza, S

    2006-11-01

    Full Text Available  & Open Source Software Electronic Waste Management Conference 2006 Sibongile Mabuza 2 Presentation Outline  About Meraka Institute Open Source Centre  Background to OSS  Extending life span using OSS  Different choices for different situations  Examples... Linux  Thin Client   LTSP (Linux Terminal Server Project)  12 Linux Applications for Old  computers  Linux LiveCD Router  FreeS/WAN  Print Server 13 Examples of OSS use on  Refurbished computers Open Source Centre – Soweto Tux...

  12. Cost Optimization Through Open Source Software

    Directory of Open Access Journals (Sweden)

    Mark VonFange

    2010-12-01

    Full Text Available The cost of information technology (IT as a percentage of overall operating and capital expenditures is growing as companies modernize their operations and as IT becomes an increasingly indispensable part of company resources. The price tag associated with IT infrastructure is a heavy one, and, in today's economy, companies need to look for ways to reduce overhead while maintaining quality operations and staying current with technology. With its advancements in availability, usability, functionality, choice, and power, free/libre open source software (F/LOSS provides a cost-effective means for the modern enterprise to streamline its operations. iXsystems wanted to quantify the benefits associated with the use of open source software at their company headquarters. This article is the outgrowth of our internal analysis of using open source software instead of commercial software in all aspects of company operations.

  13. Free and Open Source Software for Development

    CERN Document Server

    van Reijswoud, Victor

    2008-01-01

    Development organizations and International Non-Governmental Organizations have been emphasizing the high potential of Free and Open Source Software for the Less Developed Countries. Cost reduction, less vendor dependency and increased potential for local capacity development have been their main arguments. In spite of its advantages, Free and Open Source Software is not widely adopted at the African continent. In this book the authors will explore the grounds on with these expectations are based. Where do they come from and is there evidence to support these expectations? Over the past years several projects have been initiated and some good results have been achieved, but at the same time many challenges were encountered. What lessons can be drawn from these experiences and do these experiences contain enough evidence to support the high expectations? Several projects and their achievements will be considered. In the final part of the book the future of Free and Open Source Software for Development will be ...

  14. Usability in open source software development

    DEFF Research Database (Denmark)

    Andreasen, M. S.; Nielsen, H. V.; Schrøder, S. O.

    2006-01-01

    Open Source Software (OSS) development has gained significant importance in the production of soft-ware products. Open Source Software developers have produced systems with a functionality that is competitive with similar proprietary software developed by commercial software organizations. Yet OSS...... is usually designed for and by power-users, and OSS products have been criticized for having little or no emphasis on usability. We have conducted an empirical study of the developers’ opinions about usability and the way usability engineering is practiced in a variety of OSS projects. The study included...... a questionnaire survey and a series of interviews, where we interviewed OSS contributors with both technical and usability backgrounds. Overall we found that OSS developers are interested in usability, but in practice it is not top priority, and OSS projects rarely employs systematic usability evaluation. Most...

  15. Weather forecasting with open source software

    Science.gov (United States)

    Rautenhaus, Marc; Dörnbrack, Andreas

    2013-04-01

    To forecast the weather situation during aircraft-based atmospheric field campaigns, we employ a tool chain of existing and self-developed open source software tools and open standards. Of particular value are the Python programming language with its extension libraries NumPy, SciPy, PyQt4, Matplotlib and the basemap toolkit, the NetCDF standard with the Climate and Forecast (CF) Metadata conventions, and the Open Geospatial Consortium Web Map Service standard. These open source libraries and open standards helped to implement the "Mission Support System", a Web Map Service based tool to support weather forecasting and flight planning during field campaigns. The tool has been implemented in Python and has also been released as open source (Rautenhaus et al., Geosci. Model Dev., 5, 55-71, 2012). In this presentation we discuss the usage of free and open source software for weather forecasting in the context of research flight planning, and highlight how the field campaign work benefits from using open source tools and open standards.

  16. Open source software migration: Best practices

    CSIR Research Space (South Africa)

    Molefe, Onkgopotse M

    2010-09-01

    Full Text Available Open source software (OSS) has gained prominence worldwide, largely due to cost savings and security considerations. This has caused a change in the IT sector and has led to the migration of desktops from proprietary to OSS. The problem...

  17. An open-source thermodynamic software library

    DEFF Research Database (Denmark)

    Ritschel, Tobias Kasper Skovborg; Gaspar, Jozsef; Capolei, Andrea

    This is a technical report which accompanies the article ”An open-source thermodynamic software library” which describes an efficient Matlab and C implementation for evaluation of thermodynamic properties. In this technical report we present the model equations, that are also presented in the paper...

  18. Communal Resources in Open Source Software Development

    Science.gov (United States)

    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…

  19. Intrinsic Motivation in Open Source Software Development

    DEFF Research Database (Denmark)

    Bitzer, J.; W., Schrettl,; Schröder, Philipp

    2004-01-01

    This papers sheds light on the puzzling evidence that even though open source software (OSS) is a public good, it is developed for free by highly qualified, young and motivated individuals, and evolves at a rapid pace. We show that once OSS development is understood as the private provision...

  20. Software development an open source approach

    CERN Document Server

    Tucker, Allen; de Silva, Chamindra

    2011-01-01

    Overview and Motivation Software Free and Open Source Software (FOSS)Two Case Studies Working with a Project Team Key FOSS Activities Client-Oriented vs. Community-Oriented Projects Working on a Client-Oriented Project Joining a Community-Oriented Project Using Project Tools Collaboration Tools Code Management Tools Run-Time System ConstraintsSoftware Architecture Architectural Patterns Layers, Cohesion, and Coupling Security Concurrency, Race Conditions, and DeadlocksWorking with Code Bad Smells and Metrics Refactoring Testing Debugging Extending the Software for a New ProjectDeveloping the D

  1. Open source software to control Bioflo bioreactors.

    Directory of Open Access Journals (Sweden)

    David A Burdge

    Full Text Available 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.

  2. Open source software to control Bioflo bioreactors.

    Science.gov (United States)

    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.

  3. Open Source Software: All You Do Is Put It Together

    NARCIS (Netherlands)

    Obrenovic, Z.; Gasevic, D.

    2007-01-01

    The authors propose an infrastructure for rapidly prototyping applications from open source software components. The Adaptable Multi-Interface Communicator infrastructure (AMICO) is based on ideas of middleware platforms for component integration, but it focuses on pragmatic aspects of OSS integrati

  4. An Open-Source ITS Platform

    DEFF Research Database (Denmark)

    Andersen, Ove; Torp, Kristian

    2012-01-01

    , the trip-based approach requires more GPS data and of a higher quality than the point-based approach. The system has been completely implemented using open-source software and is in production. A detailed performance study, using a desktop PC, shows that the system can handle large data sizes...... and that the performance scales, for some components, linearly with the number of processor cores available. The main conclusion is that large quantity of GPS data can, with a very limited budget, used for estimating travel times, if enough GPS data is available....

  5. Repositorios digitales y software open source

    Directory of Open Access Journals (Sweden)

    Doria, María Vanesa

    2015-06-01

    Full Text Available En la actualidad las universidades se encuentran en constante evolución, fruto de la transformación generada por la sociedad de la información y el conocimiento, donde la transversalidad son las Tecnologías de la Información y Comunicación (TIC, que tienen como objetivo ampliar el acceso a la información y el conocimiento a través de su herramienta digital más distinguida, Internet. Las universidades retroalimentan su conocimiento e información, mediante las producciones científicasacadémicas, y para promover el acceso a ellas, muchas universidades están inclinándose al movimiento del Acceso Abierto (AA siguiendo la vía verde en el desarrollo de repositorios digitales (RD. Para la creación de RD es necesario analizar los software open source disponibles, dado que estos son las herramientas que facilitan la automatización de los mismos. El presente estudio se centra en el análisis de los software open source existentes en el mercado.

  6. GeolOkit 1.0: a new Open Source, Cross-Platform software for geological data visualization in Google Earth environment

    Science.gov (United States)

    Triantafyllou, Antoine; Bastin, Christophe; Watlet, Arnaud

    2016-04-01

    GIS software suites are today's essential tools to gather and visualise geological data, to apply spatial and temporal analysis and in fine, to create and share interactive maps for further geosciences' investigations. For these purposes, we developed GeolOkit: an open-source, freeware and lightweight software, written in Python, a high-level, cross-platform programming language. GeolOkit software is accessible through a graphical user interface, designed to run in parallel with Google Earth. It is a super user-friendly toolbox that allows 'geo-users' to import their raw data (e.g. GPS, sample locations, structural data, field pictures, maps), to use fast data analysis tools and to plot these one into Google Earth environment using KML code. This workflow requires no need of any third party software, except Google Earth itself. GeolOkit comes with large number of geosciences' labels, symbols, colours and placemarks and may process : (i) multi-points data, (ii) contours via several interpolations methods, (iii) discrete planar and linear structural data in 2D or 3D supporting large range of structures input format, (iv) clustered stereonets and rose diagram, (v) drawn cross-sections as vertical sections, (vi) georeferenced maps and vectors, (vii) field pictures using either geo-tracking metadata from a camera built-in GPS module, or the same-day track of an external GPS. We are looking for you to discover all the functionalities of GeolOkit software. As this project is under development, we are definitely looking to discussions regarding your proper needs, your ideas and contributions to GeolOkit project.

  7. International free and open source software law review

    National Research Council Canada - National Science Library

    2009-01-01

    "The International Free and Open Source Software Law Review (IFOSS L. Rev.) is a collaborative legal publication aiming to increase knowledge and understanding among lawyers about Free and Open Source Software issues...

  8. Open Source Software The Challenge Ahead

    CERN Document Server

    CERN. Geneva

    2007-01-01

    The open source community has done amazingly well in terms of challenging the historical epicenter of computing - the supercomputer and data center - and driving change there. Linux now represents a healthy and growing share of infrastructure in large organisations globally. Apache and other infrastructural components have established the new de facto standard for software in the back office: freedom. It would be easy to declare victory. But the real challenge lies ahead - taking free software to the mass market, to your grandparents, to your nieces and nephews, to your friends. This is the next wave, and if we are to be successful we need to articulate the audacious goals clearly and loudly - because that's how the community process works best. Speaker Bio: Mark Shuttleworth founded the Ubuntu Project in early 2004. Ubuntu is an enterprise Linux distribution that is freely available worldwide and has both desktop and enterprise server editions. Mark studied finance and information technology at the Universit...

  9. An open-source software platform for data management, visualisation, model building and model sharing in water, energy and other resource modelling domains.

    Science.gov (United States)

    Knox, S.; Meier, P.; Mohammed, K.; Korteling, B.; Matrosov, E. S.; Hurford, A.; Huskova, I.; Harou, J. J.; Rosenberg, D. E.; Thilmant, A.; Medellin-Azuara, J.; Wicks, J.

    2015-12-01

    Capacity expansion on resource networks is essential to adapting to economic and population growth and pressures such as climate change. Engineered infrastructure systems such as water, energy, or transport networks require sophisticated and bespoke models to refine management and investment strategies. Successful modeling of such complex systems relies on good data management and advanced methods to visualize and share data.Engineered infrastructure systems are often represented as networks of nodes and links with operating rules describing their interactions. Infrastructure system management and planning can be abstracted to simulating or optimizing new operations and extensions of the network. By separating the data storage of abstract networks from manipulation and modeling we have created a system where infrastructure modeling across various domains is facilitated.We introduce Hydra Platform, a Free Open Source Software designed for analysts and modelers to store, manage and share network topology and data. Hydra Platform is a Python library with a web service layer for remote applications, called Apps, to connect. Apps serve various functions including network or results visualization, data export (e.g. into a proprietary format) or model execution. This Client-Server architecture allows users to manipulate and share centrally stored data. XML templates allow a standardised description of the data structure required for storing network data such that it is compatible with specific models.Hydra Platform represents networks in an abstract way and is therefore not bound to a single modeling domain. It is the Apps that create domain-specific functionality. Using Apps researchers from different domains can incorporate different models within the same network enabling cross-disciplinary modeling while minimizing errors and streamlining data sharing. Separating the Python library from the web layer allows developers to natively expand the software or build web

  10. Open Source Testing Capability for Geospatial Software

    Science.gov (United States)

    Bermudez, L. E.

    2013-12-01

    resource for technologists responsible for interoperability among scientific tools that are used for sharing data and linking models, both within and between Earth science disciplines. This presentation will focus on the OGC compliance infrastructure and its open source tools, open source tests and and open issue tracker that can be used to improve scientific software. [1] http://www.opengeospatial.org/resource/products/stats [2] http://cite.opengeospatial.org/teamengine/ [3] http://cite.opengeospatial.org/te2

  11. Intrinsic Motivation in Open Source Software Development

    DEFF Research Database (Denmark)

    Bitzer, J.; W., Schrettl,; Schröder, Philipp

    2004-01-01

    of a public good, these features emerge quite naturally. We adapt a dynamic private-provision-of-public-goods model to reflects key aspects of the OSS phenomenon. In particular, instead of relying on extrinsic motives for programmers (e.g. signaling) the present model is driven by intrinsic motives of OSS...... programmers, such as user-programmers, play value or \\emph{homo ludens} payoff, and gift culture benefits. Such intrinsic motives feature extensively in the wider OSS literature and turn out to add new insights to the economic analysis.......This papers sheds light on the puzzling evidence that even though open source software (OSS) is a public good, it is developed for free by highly qualified, young and motivated individuals, and evolves at a rapid pace. We show that once OSS development is understood as the private provision...

  12. An Analysis of Open Source Security Software Products Downloads

    Science.gov (United States)

    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…

  13. An Analysis of Open Source Security Software Products Downloads

    Science.gov (United States)

    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. Analyzing huge pathology images with open source software.

    Science.gov (United States)

    Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

    2013-06-06

    Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here

  15. Open Source Next Generation Visualization Software for Interplanetary Missions

    Science.gov (United States)

    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).

  16. REUSABILITY ASSESSMENT OF OPEN SOURCE COMPONENTS FOR SOFTWARE PRODUCT LINES

    OpenAIRE

    Fazal-e- Amin; Ahmad Kamil Mahmood; Alan Oxley

    2011-01-01

    Software product lines and open source software are two emerging paradigms in software engineering. A common theme in both of these paradigms is „reuse‟. Software product lines are a reuse centered approach that makes use of existing assets to develop new products. At the moment, a motivation for using open source software is so as to gain access to source code, which can then be reused. The product line community is being attracted to open source components. The use of open source softwa...

  17. Management of Astronomical Software Projects with Open Source Tools

    Science.gov (United States)

    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.

  18. Proprietary software versus Open Source Software for Education

    Directory of Open Access Journals (Sweden)

    N. Pankaja

    2013-07-01

    Full Text Available The Internet has brought learning "online" and offers many advantages. It is convenient, available at any time of the day, and can be accessed nearly anywhere in the world. Recently, Cloud computing is all the rage. E-Learning offers tremendous potential to increase the availability and convenience of education. Today, online content is varied and can include: text on a website, digital audio, digital video, animated images, and virtual reality environments. This content can be created in a variety of ways by utilizing a variety of authoring tools and softwares. These days, we observe a movement in higher education leading from proprietary software to open source, for e-learning applications (1 In fact, open source software (OSS development can provide the necessary flexibility to combine languages, scripts, learning objects and lesson plans, effectively, without the cost and rigidity of proprietary software. In recent years, numerous open access LMS software‟s have emerged as viable alternatives to costly proprietary and commercial products. Open source software‟s of Content Management Systems (CMS and Learning Management System (LMS are gaining popularity. We weigh the pro‟s and cons of utilizing the OSS and proprietary software in this paper.

  19. Open source software and minority languages: a priceless opportunity

    Directory of Open Access Journals (Sweden)

    Jordi Mas

    2003-04-01

    Full Text Available Open source software is a form of software that gives its users freedom. With the advent of the Internet, open source software has consolidated as a technically viable, financially sustainable alternative to proprietary software. Languages such as Breton, Galician, Gaelic and Catalan have seen very little development in the world of proprietary software because of the limitations imposed. In contrast, in the world of open source software these languages have been developed with notable success. Open source projects of the importance of the Mozilla browser, the GNOME environment and the GNU/Linux system have complete or partial translations in all these languages. Open source software presents an unprecedented opportunity for the development of minority languages, such as Catalan, in new technologies thanks to the freedom that they guarantee us.

  20. Open source software and minority languages: a priceless opportunity

    Directory of Open Access Journals (Sweden)

    Jordi Mas

    2003-04-01

    Full Text Available Open source software is a form of software that gives its users freedom. With the advent of the Internet, open source software has consolidated as a technically viable, financially sustainable alternative to proprietary software. Languages such as Breton, Galician, Gaelic and Catalan have seen very little development in the world of proprietary software because of the limitations imposed. In contrast, in the world of open source software these languages have been developed with notable success. Open source projects of the importance of the Mozilla browser, the GNOME environment and the GNU/Linux system have complete or partial translations in all these languages. Open source software presents an unprecedented opportunity for the development of minority languages, such as Catalan, in new technologies thanks to the freedom that they guarantee us.

  1. Open source software engineering for geoscientific modeling applications

    Science.gov (United States)

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

    2012-12-01

    OpenGeoSys (OGS) is a scientific open source project for numerical simulation of thermo-hydro-mechanical-chemical (THMC) processes in porous and fractured media. The OGS software development community is distributed all over the world and people with different backgrounds are contributing code to a complex software system. The following points have to be addressed for successful software development: - Platform independent code - A unified build system - A version control system - A collaborative project web site - Continuous builds and testing - Providing binaries and documentation for end users OGS should run on a PC as well as on a computing cluster regardless of the operating system. Therefore the code should not include any platform specific feature or library. Instead open source and platform independent libraries like Qt for the graphical user interface or VTK for visualization algorithms are used. A source code management and version control system is a definite requirement for distributed software development. For this purpose Git is used, which enables developers to work on separate versions (branches) of the software and to merge those versions at some point to the official one. The version control system is integrated into an information and collaboration website based on a wiki system. The wiki is used for collecting information such as tutorials, application examples and case studies. Discussions take place in the OGS mailing list. To improve code stability and to verify code correctness a continuous build and testing system, based on the Jenkins Continuous Integration Server, has been established. This server is connected to the version control system and does the following on every code change: - Compiles (builds) the code on every supported platform (Linux, Windows, MacOS) - Runs a comprehensive test suite of over 120 benchmarks and verifies the results Runs software development related metrics on the code (like compiler warnings, code complexity

  2. Awareness of Open Source Software (OSS: Promises, Reality and Future

    Directory of Open Access Journals (Sweden)

    Anil (Student of M.Tech.(CSE

    2011-10-01

    Full Text Available Open source is a development method for software that harnessesthe power of distributed peer review and transparency of process.The Open Source Initiative Approved License trademark andprogram creates a nexus of trust around which developers, users,corporations and governments can organize open sourcecooperation. The promise of open source is better quality, higherreliability, more flexibility, lower cost, and an end to predatoryvendor lock-in.

  3. ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers.

    Science.gov (United States)

    Cui, Yang; Hanley, Luke

    2015-06-01

    ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.

  4. Evaluation and Customization of Different Open Source Desktop GIS Software

    Institute of Scientific and Technical Information of China (English)

    QIU Ruqiong; LI Bing

    2012-01-01

    This paper gave a general evaluation on existing three popular free and open source desktop GIS projects,according to the selected evaluation criteria.To further the understanding of the open source software,this paper also presented a customization example of QGIS with python and PyQT.

  5. Epistemic Communities, Situated Learning and Open Source Software Development

    DEFF Research Database (Denmark)

    Edwards, Kasper

    2001-01-01

    This paper analyses open source software (OSS) development as an epistemic community where each individual project is perceived as a single epistemic community. OSS development is a learning process where the involved parties contribute to, and learn from the community. It is discovered that theory...... of epistemic communities does indeed contribute to the understanding of open source software development. But, the important learning process of open source software development is not readily explained. The paper then introduces situated learning and legitimate peripheral participation as theoretical...

  6. The Systems Biology Research Tool: evolvable open-source software

    Directory of Open Access Journals (Sweden)

    Wright Jeremiah

    2008-06-01

    Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

  7. Open-source software gets boost at UN

    CERN Multimedia

    Schenker, J L

    2003-01-01

    "A months-long backroom battle led by Brazil, with support from India, South Africa and China, against the United States over open-source software took center stage Wednesday at the UN information summit meeting" (1 page)

  8. Code Forking, Governance, and Sustainability in Open Source Software

    Directory of Open Access Journals (Sweden)

    Juho Lindman

    2013-01-01

    Full Text Available The right to fork open source code is at the core of open source licensing. All open source licenses grant the right to fork their code, that is to start a new development effort using an existing code as its base. Thus, code forking represents the single greatest tool available for guaranteeing sustainability in open source software. In addition to bolstering program sustainability, code forking directly affects the governance of open source initiatives. Forking, and even the mere possibility of forking code, affects the governance and sustainability of open source initiatives on three distinct levels: software, community, and ecosystem. On the software level, the right to fork makes planned obsolescence, versioning, vendor lock-in, end-of-support issues, and similar initiatives all but impossible to implement. On the community level, forking impacts both sustainability and governance through the power it grants the community to safeguard against unfavourable actions by corporations or project leaders. On the business-ecosystem level forking can serve as a catalyst for innovation while simultaneously promoting better quality software through natural selection. Thus, forking helps keep open source initiatives relevant and presents opportunities for the development and commercialization of current and abandoned programs.

  9. Open Source Software Compliance within the Government

    Science.gov (United States)

    2016-12-01

    does not constitute an official endorsement or approval of the use of such commercial products. All product names and trademarks cited are the property...public license (MPL) ..................................................................................... 18 3 Program Administration and Management...ITL SR-16-32 7 the public release of the software or code is not further restricted by any other law or regulation. An example of such regulations

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

    Directory of Open Access Journals (Sweden)

    A. Panayides

    2013-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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…

  13. Agile Software Management for Successful Open Source Software Projects

    Science.gov (United States)

    Bermudez, L. E.

    2016-12-01

    The Open Geospatial Consortium (OGC), is the world leader industry consortium advancing geospatial technologies to help solve global challenges. The OGC brings the geospatial community together to advance standards, best practices and tools to improve sharing of geospatial data. The OGC Compliance program provides a free online testing facility [1], a process for certification [2] of compliant products, and coordination of a vibrant community of developers. The OGC testing facility is based on TEAM Engine, an open source software that is used by OGC and other geospatial communities to test web services, schemas, data and clients. The tests, which are also open source, are encoded in an XSLT like language called Compliance Testing language (CTL) and TestNG, a Java testing framework. TEAM Engine and related projects, as well as, each test have their own GitHub repository. The OGC Compliance program currently has more than 50 repositories. Releases of new revisions of tests and TEAM Engine are done every month, following a time boxed model. GitHub issue trackers are also use due to the easiness and close integration to the source code. However, GitHub issue trackers lack of the ability to order issues following an Agile methodology. Modern project management systems use a Kanban [3] approach to manage issues in a more efficient and focused way. About 10 organizations support the compliance program. A developer of an organization can take the lead of one or more projects and can participate on issues in other projects. However, coordinating the work to be done by one developer can be challenging due to the developer's participation in different projects and the difficulty of using a Kanban [3] approach directly from GitHub. This talk will provide a practical insight to manage projects using the Agile and Kanban methodologies when multiple developers participate in multiple GitHub projects. The ideas discussed in this talk will help organizations create more efficiently

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

    Science.gov (United States)

    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…

  15. Impact of Open Source software on the environmental protection

    Directory of Open Access Journals (Sweden)

    D. Viduka

    2015-03-01

    Full Text Available Ongoing development of computer hardware contributes to the constant throwing old computers ie. direct increase of electric and electronic equipment waste. This type of waste is a major threat to human health and the environment. By applying Open Source software solutions all users of computer hardware can significantly effect on the reduction of this type of waste. The aim of this paper is to present the advantages of using Open Source software package in terms of preserving and protecting the environment. This paper presents the results of testing MS Windows and Linux operating systems on an older computer, the results are obtained by applying the benchmark software GeekBench.

  16. The Case for Open Source Software in Digital Forensics

    Science.gov (United States)

    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

  17. Willingness to Cooperate Within the Open Source Software Domain

    NARCIS (Netherlands)

    Ravesteijn, J.P.P.; Silvius, A.J.G.

    2008-01-01

    Open Source Software (OSS) is an increasingly hot topic in the business domain. One of the key benefits mentioned is the unlimited access to the source code, which enables large communities to continuously improve a software application and prevents vendor lock-in. How attractive these benefits may

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

    Science.gov (United States)

    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. © 2016 Society for Laboratory Automation and Screening.

  19. ARLearn - Open source mobile application platform for learning

    NARCIS (Netherlands)

    Börner, Dirk; Ternier, Stefaan; Klemke, Roland; Schmitz, Birgit; Kalz, Marco; Tabuenca, Bernardo; Specht, Marcus

    2013-01-01

    Börner, D., Ternier, S., Klemke, R., Schmitz, B., Kalz, M., Tabuenca, B., & Specht, M. (2013). ARLearn - Open source mobile application platform for learning. In D. Hernández-Leo et al. (Eds.), Scaling up Learning for Sustained Impact. Proceedings of the 8th European Conference on Technology Enhance

  20. Dilemmas within Commercial Involvement in Open Source Software

    DEFF Research Database (Denmark)

    Ciesielska, Malgorzata; Westenholz, Ann

    2016-01-01

    Purpose – The purpose of this paper is to contribute to the literature about the commercial involvement in open source software, levels of this involvement and consequences of attempting to mix various logics of action. Design/methodology/approach – This paper uses the case study approach based...... on mixed methods: literature reviews and news searches, electronic surveys, qualitative interviews and observations. It combines discussions from several research projects as well as previous publications to present the scope of commercial choices within open source software and their consequences....... Findings – The findings show that higher levels of involvement in open source software communities poses important questions about the balance between economic, technological, and social logics as well as the benefits of being autonomous, having access to collaborative networks and minimizing risks related...

  1. Investigating Advances in the Acquisition of Systems Based on Open Architecture and Open Source Software

    Science.gov (United States)

    2011-08-01

    Copyright 2003-2008 Rodrigo B. Oliveira 4. UnityScript, Copyright 2005-2008 Rodrigo B. Oliveira 5. OpenAL cross platform audio library, Copyright...not know. ACM Computing Surveys, (in press). [5] Hauge, O., Ayala , C. and Conradi, R. (2010). Adoption of Open Source Software in Software- Intensive

  2. How Open Source Has Changed the Software Industry: Perspectives from Open Source Entrepreneurs

    Directory of Open Access Journals (Sweden)

    Risto Rajala

    2012-01-01

    Full Text Available The emergence of F/LOSS (free/libre open source software has triggered several changes in the software industry. F/LOSS has been cited as an archetypal form of open innovation; it consists of the convergence and collaboration of like-minded parties. An increasing number of software firms have taken upon this approach to link outsiders into their service development and product design. Also, software firms have been increasingly grounded their business models on user-centric and service-oriented operations. This article describes a study that investigates these changes from the perspective of F/LOSS entrepreneurs. The findings are summarized into four issues that are critical in managing an F/LOSS business: i dealing with organizational changes in the innovation process; ii mastering user involvement; iii successfully using resources; and iv designing revenue models.

  3. The Challenges of Open Source Software in IT Adoption

    DEFF Research Database (Denmark)

    Holm Larsen, Michael; Holck, Jesper; Pedersen, Mogens Kuhn

    2004-01-01

    Abstract: The paper presents an explorative study of Open Source Software (OSS) focusing on the managerial decisions for acquisition of OSS. Based on three case studies we argue that whereas small organizations often may chose adoption of OSS expecting significant cost savings, a major barrier...... for larger organizations' adoption of OSS lies in the organizations' consolidation of the enterprise architectures, in addition to that OSS will not be adopted before satisfactory delivery and procurement models for OSS are established. Keywords: Open Source Software, OSS, Enterprise Architecture, Total Cost...

  4. Open Source Software Reliability Growth Model by Considering Change- Point

    Directory of Open Access Journals (Sweden)

    Mashaallah Basirzadeh

    2012-01-01

    Full Text Available The modeling technique for Software Reliability is reaching its prosperity. Software reliability growth models have been used extensively for closed source software. The design and development of open source software (OSS is different from closed source software. We observed some basic characteristics for open source software like (i more instructions execution and code coverage taking place with respect to time, (ii release early, release often (iii frequent addition of patches (iv heterogeneity in fault density and effort expenditure (v Frequent release activities seem to have changed the bug dynamics significantly (vi Bug reporting on bug tracking system drastically increases and decreases. Due to this reason bug reported on bug tracking system keeps an irregular state and fluctuations. Therefore, fault detection/removal process can not be smooth and may be changed at some time point called change-point. In this paper, an instructions executed dependent software reliability growth model has been developed by considering change-point in order to cater diverse and huge user profile, irregular state of bug tracking system and heterogeneity in fault distribution. We have analyzed actual software failure count data to show numerical examples of software reliability assessment for the OSS. We also compare our model with the conventional in terms of goodness-of-fit for actual data. We have shown that the proposed model can assist improvement of quality for OSS systems developed under the open source project.

  5. Some Observations On Open Source Software Development On Software Engineering Perspectives

    Directory of Open Access Journals (Sweden)

    Vinay Tiwari

    2010-12-01

    Full Text Available Several argument has been made that open source software development process some times also referred as free and open source software development (FOSSD violates the traditional softwareengineering principles and researches advocates to rethink and re-evaluate the studies and concepts of software engineering. The aim of this paper is to investigate the software development process models of Open source software on the software engineering perspectives. In this paper a discussion on some of development models of OSS and their comparison with the traditional development models is made and the software engineering practices followed in open source development environment is also been discussed. Principle difference and similarities of these development models with the conventional models are also discussed. The ultimate goal is to understand how open source software development processesare similar to or different from software engineering processes and to bring better understanding to the development process of Open Source Software.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  7. Open-source software for generating electrocardiogram signals

    CERN Document Server

    McSharry, P E; Sharry, Patrick E. Mc; Cifford, Gari D.

    2004-01-01

    ECGSYN, a dynamical model that faithfully reproduces the main features of the human electrocardiogram (ECG), including heart rate variability, RR intervals and QT intervals is presented. Details of the underlying algorithm and an open-source software implementation in Matlab, C and Java are described. An example of how this model will facilitate comparisons of signal processing techniques is provided.

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

    Science.gov (United States)

    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…

  9. The Economics of Open Source Software Development: An Introduction

    DEFF Research Database (Denmark)

    2006-01-01

    This chapter introduces the fundamentals of Open Source Software, its nature, the central economic aspects and the key mechanisms of its development. Furthermore, we present the themes of the book and provide a first overview for the reader by giving short summaries of its chapters....

  10. Digital Preservation in Open-Source Digital Library Software

    Science.gov (United States)

    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…

  11. Exploring Coordination Structures in Open Source Software Development

    NARCIS (Netherlands)

    Amrit, Chintan; Hegeman, J.H.; Hillegersberg, van Jos; Hillegersberg, van Jos; Harmsen, Frank; Amrit, Chintan; Geisberger, Eva; Keil, Patrick; Kuhrmann, Marco

    2007-01-01

    Coordination is difficult to achieve in a large globally distributed project setting. The problem is multiplied in open source software development projects, where most of the traditional means of coordination such as plans, system-level designs, schedules and defined process are not used. In order

  12. Intrinsic Motivation versus Signaling in Open Source Software Development

    DEFF Research Database (Denmark)

    Bitzer, J; Schrettl, W; Schröder, P

    This papers sheds light on the puzzling fact that even though open source software (OSS) is a public good, it is developed for free by highly qualified, young, motivated individuals, and evolves at a rapid pace. We show that when OSS development is understood as the private provision of a public...

  13. [Osirix: free and open-source software for medical imagery].

    Science.gov (United States)

    Jalbert, F; Paoli, J R

    2008-02-01

    Osirix is a tool for diagnostic imagery, teaching and research tasks, which presents many possible applications in maxillofacial and oral surgery. It is a free and open-source software developed on Mac OS X (Apple) by Dr Antoine Rosset and Dr Osman Ratib, in the department of radiology and medical computing of Geneva (Switzerland).

  14. Digital Preservation in Open-Source Digital Library Software

    Science.gov (United States)

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

    Science.gov (United States)

    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…

  16. An Organizational Perspective on Free and Open Source Software Development

    DEFF Research Database (Denmark)

    Vujovic, Sladjana; Ulhøi, John Parm

    2006-01-01

    , there are various combinations or hybrids, in the following referred to as free/open source-based (F/OS-based) agency. In the discussions, practical examples from software production are included. In conclusion, the paper identifies avenues for future research as well as important managerial and policy implications....

  17. Standard Interfaces for Open Source Infrastructure as a Service Platforms

    Directory of Open Access Journals (Sweden)

    Andrei IONESCU

    2015-01-01

    Full Text Available To reduce vendor lock-in and fragmentation and to evolve into a transparent platform, IaaS platforms must adhere to open standards. All the major open source IaaS Platforms offer interfaces compatible with the de facto standards but mostly lacks support for the de jure, open efforts of standardization. Available implementations of open standards are not part of their main development efforts. More development resources as well as consolidation of open standards are needed to achieve increased portability and interoperability.

  18. 基于开源软件的私有云计算平台构建%Construction of Private Cloud Computing Platform Based on Open Source Software

    Institute of Scientific and Technical Information of China (English)

    姜毅; 王伟军; 曹丽; 刘凯; 陈桂强

    2013-01-01

    介绍了私有云的应用范围,讨论了自行开发、商业和开源解决方案各自的特点,分析了开源方案的主要优势,比较了主流的开源云计算项目Eucalyptus、OpenStack、OpenNebula和Nimbus,重点研究了OpenStack架构.在此基础上,讨论了基于OpenStack的私有云计算平台构建方法,其主要过程包括基础环境配置,Nova、Glance、Swift、Keystone和Horizon组件安装,虚拟机部署等,最后给出了该平台在云计算软件测试项目中的应用实例.%This paper introduced the application range of the private cloud, discussed the characteristics of the self-developed and business and open source solutions, and analyzed the main advantage of the open source solution, then compared the mainstream projects of the open source cloud computing, such as Eucalyptus, OpenStack, OpenNebula and Nimbus, studied the structure of OpenStack mainly. Based on this, this paper presented the construction example of private cloud computing platform based on OpenStack, which major processes included configuration of base environment, components installation of Nova, Glance, Swift, Keystone and Horizon, deployment of virtual machines, and finally discussed the platform application examples in the cloud computing software testing.

  19. An Organizational Perspective on Free and Open Source Software Development

    DEFF Research Database (Denmark)

    Vujovic, Sladjana; Ulhøi, John Parm

    2006-01-01

    The traditional model of innovation, the restricted/close source (R/CS) model, is based on proprietary knowledge and private model of production. A fundamental different one, the open source model is based on non-proprietary knowledge and non-economic motives. Moreover, between the two......, there are various combinations or hybrids, in the following referred to as free/open source-based (F/OS-based) agency. In the discussions, practical examples from software production are included. In conclusion, the paper identifies avenues for future research as well as important managerial and policy implications....

  20. Free Open Source Software in Electronics Engineering Education: A Survey

    Directory of Open Access Journals (Sweden)

    Vijay Nehra

    2014-05-01

    Full Text Available Since the last two decades, much attention has been paid to Electronics Engineering (EE education in India. Various commercial software tools and simulator such as mathematical application packages, electronics CAD tools, learning management systems, multimedia tools and general purpose tools supports EE education. Traditionally, proprietary software packages such as OrCAD Pspice, MATLAB, LabView, Multisim and others too are widely practiced and well integrated in electronics engineering curricula of various Universities nationwide. In today’s market, there are plenty of software tools and packages; however, most of them are expensive. The high cost of standard commercial packages is often hardship for students and faculties. Selecting various appropriate tools for academic use is considered as one of the key challenges in EE education. Over recent years, an alternative trend based on Free Open Source Software (FOSS has gained momentum in higher education due to several benefits such as cost, license management flexibility, access to source code, security and stability etc. Presently, a plethora of open source software tools and resource related to EE can be deployed in teaching and learning process of EE education. In this communication, a short exposition of Free Open Source Software useful in electronics engineering education and research is presented. A brief outlook of FOSS packages, their web addresses and major highlights are also presented. The overall aim of this paper is to create awareness among instructors and students to impart active and self learning using FOSS.

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

    Science.gov (United States)

    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/).

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

    Science.gov (United States)

    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.

  3. A Survey of Open Source Products for Building a SIP Communication Platform

    Directory of Open Access Journals (Sweden)

    Pavel Segec

    2011-01-01

    Full Text Available The Session Initiation Protocol (SIP is a multimedia signalling protocol that has evolved into a widely adopted communication standard. The integration of SIP into existing IP networks has fostered IP networks becoming a convergence platform for both real-time and non-real-time multimedia communications. This converged platform integrates data, voice, video, presence, messaging, and conference services into a single network that offers new communication experiences for users. The open source community has contributed to SIP adoption through the development of open source software for both SIP clients and servers. In this paper, we provide a survey on open SIP systems that can be built using publically available software. We identify SIP features for service development and programming, services and applications of a SIP-converged platform, and the most important technologies supporting SIP functionalities. We propose an advanced converged IP communication platform that uses SIP for service delivery. The platform supports audio and video calls, along with media services such as audio conferences, voicemail, presence, and instant messaging. Using SIP Application Programming Interfaces (APIs, the platform allows the deployment of advanced integrated services. The platform is implemented with open source software. Architecture components run on standardized hardware with no need for special purpose investments.

  4. pyLIMA : an open source microlensing software

    Science.gov (United States)

    Bachelet, Etienne

    2017-01-01

    Planetary microlensing is a unique tool to detect cold planets around low-mass stars which is approaching a watershed in discoveries as near-future missions incorporate dedicated surveys. NASA and ESA have decided to complement WFIRST-AFTA and Euclid with microlensing programs to enrich our statistics about this planetary population. Of the nany challenges in- herent in these missions, the data analysis is of primary importance, yet is often perceived as time consuming, complex and daunting barrier to participation in the field. We present the first open source modeling software to conduct a microlensing analysis. This software is written in Python and use as much as possible existing packages.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  7. Open Source Software Alternatives in Higher Education Following Computer Science Curricula 2013

    Directory of Open Access Journals (Sweden)

    Borislav Stoyanov

    2014-09-01

    Full Text Available In this study we overview the open source software, describe the advantages and disadvantages of using open source software in modern Higher Education following Computer Science Curricula 2013. The study’s main purposes are to clear the understanding of open source software, to present alternatives of the commercial software and demonstrate the potential benefits of integrating open source software in Higher Education.

  8. What makes computational open source software libraries successful?

    Science.gov (United States)

    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.

  9. An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Segre, Daniel [Boston Univ., MA (United States)

    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.

  10. Technical Evaluation Report 59: The Emergence of Open-Source Software in China

    Directory of Open Access Journals (Sweden)

    Curtis J. Bonk

    2007-03-01

    Full Text Available 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 the Chinese software market. Unlike the spontaneity of open-source movement in North America, open-source software development in China, such as Red Flag Linux, is an orchestrated activity wherein different levels of China's government play a vital role in sponsoring, incubating, and using open-source software, most conspicuously, Red Flag Linux. While there are no reports on open-source course management system in China, there are reports on the study and use of Western open-source course management systems for instruction and learning in Chinese higher education institutions. This paper discusses the current status of open-source software in China, including open-source course management software and associated tools and resources. Importantly, it describes the development model of Red Flag Linux, the most successful open-source software initiative in China. In addition, it explores the possibility of Chinese higher education institutions joining efforts to develop China’s own open-source course management system using the open-source development model established in North America. A timeline of current and major open-source projects of significance in China is provided. The paper concludes with a discussion of the potential for applying the open-source software development model to open and distance education in China.

  11. ABCD, an Open Source Software for Modern Libraries

    Directory of Open Access Journals (Sweden)

    Sangeeta Namdev Dhamdhere

    2011-12-01

    Full Text Available Nowadays, librarians are using various kinds of open source software for different purposes such as library automation, digitization, institutional repository, content management. ABCD, acronym for Automatisación de Bibliotécas y Centros de Documentación, is one of such software. It caters to almost all present needs of modern libraries of any sizes. It offers a solution to library automation with ISBD as well as local formats. It has excellent indexing and retrieval features based on UNESCO’s ISIS technology, a web OPAC, and a library Portal with integrated meta-search and content management system to manage online as well as offline digital resources and physical documents and media.

  12. An open-source automated continuous condition-based maintenance platform for commercial buildings

    Energy Technology Data Exchange (ETDEWEB)

    Katipamula, Srinivas; Gowri, Krishnan; Hernandez, George

    2016-09-09

    This paper describes one such reference process that can be deployed to provide continuous automated conditioned-based maintenance management for buildings that have BIM, a building automation system (BAS) and a computerized maintenance management software (CMMS) systems. The process can be deployed using an open source transactional network platform, VOLTTRON™, designed for distributed sensing and controls and supports both energy efficiency and grid services.

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

    Science.gov (United States)

    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…

  14. Social network of PESCA (Open Source Platform for eHealth).

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  16. Code forking in open-source software: a requirements perspective

    CERN Document Server

    Ernst, Neil A; Mylopoulos, John

    2010-01-01

    To fork a project is to copy the existing code base and move in a direction different than that of the erstwhile project leadership. Forking provides a rapid way to address new requirements by adapting an existing solution. However, it can also create a plethora of similar tools, and fragment the developer community. Hence, it is not always clear whether forking is the right strategy. In this paper, we describe a mixed-methods exploratory case study that investigated the process of forking a project. The study concerned the forking of an open-source tool for managing software projects, Trac. Trac was forked to address differing requirements in an academic setting. The paper makes two contributions to our understanding of code forking. First, our exploratory study generated several theories about code forking in open source projects, for further research. Second, we investigated one of these theories in depth, via a quantitative study. We conjectured that the features of the OSS forking process would allow new...

  17. Improving Data Catalogs with Free and Open Source Software

    Science.gov (United States)

    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

  18. Involving Software Engineering Students in Open Source Software Projects: Experiences from a Pilot Study

    Science.gov (United States)

    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…

  19. Fpocket: An open source platform for ligand pocket detection

    Directory of Open Access Journals (Sweden)

    Le Guilloux Vincent

    2009-06-01

    Full Text Available Abstract Background Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces. Results Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. The modular source code is organised around a central library of functions, a basis for three main programs: (i Fpocket, to perform pocket identification, (ii Tpocket, to organise pocket detection benchmarking on a set of known protein-ligand complexes, and (iii Dpocket, to collect pocket descriptor values on a set of proteins. Fpocket is written in the C programming language, which makes it a platform well suited for the scientific community willing to develop new scoring functions and extract various pocket descriptors on a large scale level. Fpocket 1.0, relying on a simple scoring function, is able to detect 94% and 92% of the pockets within the best three ranked pockets from the holo and apo proteins respectively, outperforming the standards of the field, while being faster. Conclusion Fpocket provides a rapid, open source and stable basis for further developments related to protein pocket detection, efficient pocket descriptor extraction, or drugablity prediction purposes. Fpocket is freely available under the GNU GPL license at http://fpocket.sourceforge.net.

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

    Science.gov (United States)

    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.

  1. Mahotas: Open source software for scriptable computer vision

    Directory of Open Access Journals (Sweden)

    Luis Pedro Coelho

    2013-07-01

    Full Text Available Mahotas is a computer vision library for Python. It contains traditional image processing functionality such as filtering and morphological operations as well as more modern computer vision functions for feature computation, including interest point detection and local descriptors. The interface is in Python, a dynamic programming language, which is appropriate for fast development, but the algorithms are implemented in C++ and are tuned for speed. The library is designed to fit in with the scientific software ecosystem in this language and can leverage the existing infrastructure developed in that language. Mahotas is released under a liberal open source license (MIT License and is available from http://github.com/luispedro/mahotas and from the Python Package Index (http://pypi.python.org/pypi/mahotas. Tutorials and full API documentation are available online at http://mahotas.readthedocs.org/.

  2. Open Source Software Success Model for Iran: End-User Satisfaction Viewpoint

    Directory of Open Access Journals (Sweden)

    Ali Niknafs

    2012-03-01

    Full Text Available The open source software development is notable option for software companies. Recent years, many advantages of this software type are cause of move to that in Iran. National security and international restrictions problems and also software and services costs and more other problems intensified importance of use of this software. Users and their viewpoints are the critical success factor in the software plans. But there is not an appropriate model for open source software case in Iran. This research tried to develop a measuring open source software success model for Iran. By use of data gathered from open source users and online survey the model was tested. The results showed that components by positive effect on open source success were user satisfaction, open source community services quality, open source quality, copyright and security.

  3. 76 FR 75875 - Defense Federal Acquisition Regulation Supplement; Open Source Software Public Meeting

    Science.gov (United States)

    2011-12-05

    ... Defense Acquisition Regulations System Defense Federal Acquisition Regulation Supplement; Open Source... 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 all...

  4. On the Prospects and Concerns of Integrating Open Source Software Environment in Software Engineering Education

    Science.gov (United States)

    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;…

  5. On the Prospects and Concerns of Integrating Open Source Software Environment in Software Engineering Education

    Science.gov (United States)

    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;…

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

    Science.gov (United States)

    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.

  7. Adoption of open source software in business models: a Red Hat and IBM case study

    CSIR Research Space (South Africa)

    Munga, N

    2009-10-01

    Full Text Available Free / Libre open source software (FLOSS/OSS) has gained increasing popularity and utilisation in commercial and governmental organisations. Universities like Harvard and Stanford now offer courses on open source as a business and also on how...

  8. Open Source Software in Education: a Report of Experience

    Directory of Open Access Journals (Sweden)

    Hagen HÖPFNER

    2003-04-01

    Full Text Available Most students use computers without thinking about how the software and the hardware works internally. So, their occupational outlook depends strictly on the equipment used by a potential employer. Obviously, in case of shoals of applications students which know about the handling of miscellaneous systems are preferred. The concept behind UNIX, BSD or Linux is to provide a set of small but efficient and specialised chiefly tools. More complex problems can be resolved by combining these tools. So, learning how to work with a UNIX-like operating system is learning how to break down a problem into manageable subproblems. But, schools are typically under-funded. That means, that they are unable to bye commercial UNIX-systems. A solution for this dilemma is the usage of Open Source Software like Linux. This paper presents a report of experience which is based on three lectures and practical courses on UNIX/Linux. We will show how to introduce the concepts of Linux as well as how to advance the motivation of students by facilitate individual successes.

  9. Moodle: How we built a community around open source software

    CERN Document Server

    CERN. Geneva

    2010-01-01

    Martin will talk about the continuing growth of Moodle from an idea into a worldwide project helping millions of people. He'll talk about the factors that have contributed to Moodle's current success, some that were integrated from the beginning of the project and some that were learned along the way.About the speakerMartin Dougiamas is best known as the founder of Moodle, the popular free course management system used by millions of teachers around the world.As the executive director of Moodle Pty Ltd in Perth, Western Australia, he leads the team of software developers at the heart of the Moodle project and the global network of 54 Moodle Partner service companies that help provide funding for this independent open source software project.Martin has a mixed academic background with post-graduate degrees in Computer Science and Education, and continues to focus on researching how educators approach internet-based education. His major goal for the future is to improve the quality of education by encouraging ...

  10. An Open Source modular platform for hydrological model implementation

    Science.gov (United States)

    Kolberg, Sjur; Bruland, Oddbjørn

    2010-05-01

    : Write or compile computer code, handle file IO for each modules, • Routine implementation and testing. Implementation of new process-simulating methods/equations, specialised objective functions or quality control routines, testing of these in an existing framework. o Need not: Implement user or model interface for the new routine, IO handling, administration of model setup and run, calibration and validation routines etc. From being developed for Norway's largest hydropower producer Statkraft, ENKI is now being turned into an Open Source project. At the time of writing, the licence and the project administration is not established. Also, it remains to port the application to other compilers and computer platforms. However, we hope that ENKI will prove useful for both academic and operational users.

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

    Science.gov (United States)

    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.

  12. A Study of Language Usage Evolution in Open Source Software

    CERN Document Server

    Karus, Siim

    2011-01-01

    The use of programming languages such as Java and C in Open Source Software (OSS) has been well studied. However, many other popular languages such as XSL or XML have received minor attention. In this paper, we discuss some trends in OSS development that we observed when considering multiple programming language evolution of OSS. Based on the revision data of 22 OSS projects, we tracked the evolution of language usage and other artefacts such as documentation files, binaries and graphics files. In these systems several different languages and artefact types including C/C++, Java, XML, XSL, Makefile, Groovy, HTML, Shell scripts, CSS, Graphics files, JavaScript, JSP, Ruby, Phyton, XQuery, OpenDocument files, PHP, etc. have been used. We found that the amount of code written in different languages differs substantially. Some of our findings can be summarized as follows: (1) JavaScript and CSS files most often co-evolve with XSL; (2) Most Java developers but only every second C/C++ developer work with XML; (3) an...

  13. Automatic Image Registration Using Free and Open Source Software

    Science.gov (United States)

    Giri Babu, D.; Raja Shekhar, S. S.; Chandrasekar, K.; Sesha Sai, M. V. R.; Diwakar, P. G.; Dadhwal, V. K.

    2014-11-01

    Image registration is the most critical operation in remote sensing applications to enable location based referencing and analysis of earth features. This is the first step for any process involving identification, time series analysis or change detection using a large set of imagery over a region. Most of the reliable procedures involve time consuming and laborious manual methods of finding the corresponding matching features of the input image with respect to reference. Also the process, as it involves human interaction, does not converge with multiple operations at different times. Automated procedures rely on accurately determining the matching locations or points from both the images under comparison and the procedures are robust and consistent over time. Different algorithms are available to achieve this, based on pattern recognition, feature based detection, similarity techniques etc. In the present study and implementation, Correlation based methods have been used with a improvement over newly developed technique of identifying and pruning the false points of match. Free and Open Source Software (FOSS) have been used to develop the methodology to reach a wider audience, without any dependency on COTS (Commercially off the shelf) software. Standard deviation from foci of the ellipse of correlated points, is a statistical means of ensuring the best match of the points of interest based on both intensity values and location correspondence. The methodology is developed and standardised by enhancements to meet the registration requirements of remote sensing imagery. Results have shown a performance improvement, nearly matching the visual techniques and have been implemented in remote sensing operational projects. The main advantage of the proposed methodology is its viability in production mode environment. This paper also shows that the visualization capabilities of MapWinGIS, GDAL's image handling abilities and OSSIM's correlation facility can be efficiently

  14. tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform.

    Science.gov (United States)

    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.

  15. An Investigation of an Open-Source Software Development Environment in a Software Engineering Graduate Course

    Science.gov (United States)

    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…

  16. An Investigation of an Open-Source Software Development Environment in a Software Engineering Graduate Course

    Science.gov (United States)

    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…

  17. A comparative study of challenges in integrating Open Source Software and Inner Source Software

    NARCIS (Netherlands)

    Stol, Klaas-Jan; Babar, Muhammad Ali; Avgeriou, Paris; Fitzgerald, Brian

    2011-01-01

    Context: Several large software-developing organizations have adopted Open Source Software development (OSSD) practices to develop in-house components that are subsequently integrated into products. This phenomenon is also known as "Inner Source". While there have been several reports of successful

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  20. Open Source Seismic Hazard Analysis Software Framework (OpenSHA)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — OpenSHA is an effort to develop object-oriented, web- & GUI-enabled, open-source, and freely available code for conducting Seismic Hazard Analyses (SHA). Our...

  1. Open source PIV software applied to streaming, time-resolved PIV data

    Science.gov (United States)

    Taylor, Zachary; Gurka, Roi; Liberzon, Alex; Kopp, Gregory

    2008-11-01

    The data handling requirements for time resolved PIV data have increased substantially in recent years as the advent in high speed imaging and real time streaming. Therefore, there is a need for new hardware and software solutions for data storage and analysis. The presented solution is based on open source software (OSS) which has proven to be a successful means of development. This includes the PIV algorithms and flow analysis software. The solution, based on OSS known as ``URAPIV,'' originally was developed in Matlab and recently available in Python. The advantage of these scripting languages lies within their highly customizable platform; however, their routines cannot compete with commercially available software for computational speed. Thus, an effort has been undertaken to develop URAPIV-C++, a GUI based on the Qt 4 cross-platform open source library. This provides users with features commonly found in commercial packages and is comparable in processing speed to the commercial packages. The uniqueness of this package is in its complete handling of PIV experiments from the algorithms to post analysis under OSS license for large data sets. The package and its features are utilized in the recent STR-PIV system, which will be operable at the Advanced Facility for Avian Research at UWO. The wake flow behind an elongated body will be presented as a demonstration.

  2. Performance Evaluation of Block Acquisition and Tracking Algorithms Using an Open Source GPS Receiver Platform

    Science.gov (United States)

    Ramachandran, Ganesh K.; Akopian, David; Heckler, Gregory W.; Winternitz, Luke B.

    2011-01-01

    Location technologies have many applications in wireless communications, military and space missions, etc. US Global Positioning System (GPS) and other existing and emerging Global Navigation Satellite Systems (GNSS) are expected to provide accurate location information to enable such applications. While GNSS systems perform very well in strong signal conditions, their operation in many urban, indoor, and space applications is not robust or even impossible due to weak signals and strong distortions. The search for less costly, faster and more sensitive receivers is still in progress. As the research community addresses more and more complicated phenomena there exists a demand on flexible multimode reference receivers, associated SDKs, and development platforms which may accelerate and facilitate the research. One of such concepts is the software GPS/GNSS receiver (GPS SDR) which permits a facilitated access to algorithmic libraries and a possibility to integrate more advanced algorithms without hardware and essential software updates. The GNU-SDR and GPS-SDR open source receiver platforms are such popular examples. This paper evaluates the performance of recently proposed block-corelator techniques for acquisition and tracking of GPS signals using open source GPS-SDR platform.

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

    Science.gov (United States)

    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…

  4. An open-source platform to study uniaxial stress effects on nanoscale devices

    Science.gov (United States)

    Signorello, G.; Schraff, M.; Zellekens, P.; Drechsler, U.; Bürge, M.; Steinauer, H. R.; Heller, R.; Tschudy, M.; Riel, H.

    2017-05-01

    We present an automatic measurement platform that enables the characterization of nanodevices by electrical transport and optical spectroscopy as a function of the uniaxial stress. We provide insights into and detailed descriptions of the mechanical device, the substrate design and fabrication, and the instrument control software, which is provided under open-source license. The capability of the platform is demonstrated by characterizing the piezo-resistance of an InAs nanowire device using a combination of electrical transport and Raman spectroscopy. The advantages of this measurement platform are highlighted by comparison with state-of-the-art piezo-resistance measurements in InAs nanowires. We envision that the systematic application of this methodology will provide new insights into the physics of nanoscale devices and novel materials for electronics, and thus contribute to the assessment of the potential of strain as a technology booster for nanoscale electronics.

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

    Science.gov (United States)

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

    2017-04-01

    The GEOtop hydrological scientific package is an integrated hydrological model that simulates the heat and water budgets at and below the soil surface. It describes the three-dimensional water flow in the soil and the energy exchange with the atmosphere, considering the radiative and turbulent fluxes. Furthermore, it reproduces the highly non-linear interactions between the water and energy balance during soil freezing and thawing, and simulates the temporal evolution of snow cover, soil temperature and moisture. The core components of the package were presented in the 2.0 version (Endrizzi et al, 2014), which was released as Free Software Open-source project. However, despite the high scientific quality of the project, a modern software engineering approach was still missing. Such weakness hindered its scientific potential and its use both as a standalone package and, more importantly, in an integrate way with other hydrological software tools. In this contribution we present our recent software re-engineering efforts to create a robust and stable scientific software package open to the hydrological community, easily usable by researchers and experts, and interoperable with other packages. The activity takes as a starting point the 2.0 version, scientifically tested and published. This version, together with several test cases based on recent published or available GEOtop applications (Cordano and Rigon, 2013, WRR, Kollet et al, 2016, WRR) provides the baseline code and a certain number of referenced results as benchmark. Comparison and scientific validation can then be performed for each software re-engineering activity performed on the package. To keep track of any single change the package is published on its own github repository geotopmodel.github.io/geotop/ under GPL v3.0 license. A Continuous Integration mechanism by means of Travis-CI has been enabled on the github repository on master and main development branches. The usage of CMake configuration tool

  6. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment

    Science.gov (United States)

    Tosco, Paolo; Balle, Thomas; Shiri, Fereshteh

    2011-08-01

    An open-source, cross-platform software aimed at conformer generation and unsupervised rigid-body molecular alignment is presented. Different algorithms have been implemented to perform single and multi-conformation superimpositions on one or more templates. Alignments can be accomplished by matching pharmacophores, heavy atoms or a combination of the two. All methods have been successfully validated on eight comprehensive datasets previously gathered by Sutherland and co-workers. High computational performance has been attained through efficient parallelization of the code. The unsupervised nature of the alignment algorithms, together with its scriptable interface, make Open3DALIGN an ideal component of high-throughput, automated cheminformatics workflows.

  7. The effect of competition from open source software on the quality of proprietary software in the presence of network externalities

    Directory of Open Access Journals (Sweden)

    Mingqing Xing

    2015-05-01

    Full Text Available Purpose: A growing number of open source software emerges in many segments of the software market. In addition, software products usually exhibit network externalities. The purpose of this paper is to study the impact of open source software on the quality choices of proprietary software vendors when the market presents positive network externalities. Design/methodology: To analyze how open source software affects the optimal quality of proprietary software, this paper constructs two vertical differentiation models: the basic model considers proprietary software monopolizing the market, and its extended one considers proprietary software competing with open source substitute. Findings: This paper mainly finds that the presence of open source software does not necessarily lead to the quality of proprietary software decreases (or increases. The network externalities and compatibility between open source and proprietary software may change the impact of open source software on the quality of proprietary software and may affect the quality choices of proprietary software vendors. Originality/value: The main contribution of this paper is to examine the effect of open source software on the quality choices for proprietary software vendors in software markets exhibiting positive network externalities.

  8. Model Driven Architecture (MDA: Integration and Model Reuse for Open Source eLearning Platforms

    Directory of Open Access Journals (Sweden)

    Blasius Lofi Dewanto

    2005-02-01

    Full Text Available Open Source (OS community offers numerous eLearning platforms of both types: Learning Management Systems (LMS and Learning Content Systems (LCS. General purpose OS intermediaries such as SourceForge, ObjectWeb, Apache or specialized intermediaries like CampusSource reduce the cost to locate such eLearning platforms. Still, it is impossible to directly compare the functionalities of those OS software products without performing detailed testing on each product. Some articles available from eLearning Wikipedia show comparisons between eLearning platforms which can help, but at the end they barely serve as documentation which are becoming out of date quickly (1. The absence of integration activities between OS eLearning platforms - which are sometimes quite similar in terms of functionalities and implementation technologies - is sometimes critical since most of the OS projects possess small financial and human resources. This paper shows a possible solution for these barriers of OS eLearning platforms. We propose the Model Driven Architecture (MDA concept to capture functionalities and to identify similarities between available OS eLearning platforms. This contribution evolved from a fruitful discussion at the 2nd CampusSource Developer Conference at the University of Muenster (27th August 2004.Die Open Source-Community bietet zahlreiche eLearning-Plattformen an: Learning Management-Systeme (LMS sowie Learning Content-Systeme (LCS. Allgemeine Open-Source-Mediatoren, wie SourceForge, ObjectWeb, Apache und der eLearning-spezifische Mediator CampusSource ermöglichen eine einfache Suche nach eLearning-Softwareprodukten. Ein Vergleich unterschiedlicher Plattformen in Bezug auf ihre Funktionalitäten ist jedoch aufwändig. Beiträge aus der “eLearning Wikipedia” können kaum als Entscheidungsgrundlage genutzt werden, da sie schnell veraltet sind (1. Zudem fehlen derzeit Aktivitäten zur Integration von Open Source-eLearning-Plattformen, die oft

  9. Modular Open-Source Software for Item Factor Analysis

    Science.gov (United States)

    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…

  10. Modular Open-Source Software for Item Factor Analysis

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    Ardal, Christine; Alstadsæter, Annette; Røttingen, John-Arne

    2011-09-28

    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. 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. 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. 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.

  13. Open Source software and social networks: disruptive alternatives for medical imaging.

    Science.gov (United States)

    Ratib, Osman; Rosset, Antoine; Heuberger, Joris

    2011-05-01

    In recent decades several major changes in computer and communication technology have pushed the limits of imaging informatics and PACS beyond the traditional system architecture providing new perspectives and innovative approach to a traditionally conservative medical community. Disruptive technologies such as the world-wide-web, wireless networking, Open Source software and recent emergence of cyber communities and social networks have imposed an accelerated pace and major quantum leaps in the progress of computer and technology infrastructure applicable to medical imaging applications. This paper reviews the impact and potential benefits of two major trends in consumer market software development and how they will influence the future of medical imaging informatics. Open Source software is emerging as an attractive and cost effective alternative to traditional commercial software developments and collaborative social networks provide a new model of communication that is better suited to the needs of the medical community. Evidence shows that successful Open Source software tools have penetrated the medical market and have proven to be more robust and cost effective than their commercial counterparts. Developed by developers that are themselves part of the user community, these tools are usually better adapted to the user's need and are more robust than traditional software programs being developed and tested by a large number of contributing users. This context allows a much faster and more appropriate development and evolution of the software platforms. Similarly, communication technology has opened up to the general public in a way that has changed the social behavior and habits adding a new dimension to the way people communicate and interact with each other. The new paradigms have also slowly penetrated the professional market and ultimately the medical community. Secure social networks allowing groups of people to easily communicate and exchange information

  14. Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology

    Science.gov (United States)

    Siegle, Joshua H.; Cuevas López, Aarón; Patel, Yogi A.; Abramov, Kirill; Ohayon, Shay; Voigts, Jakob

    2017-08-01

    Objective. Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. Approach. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard ‘open-loop’ visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. Main results. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. Significance. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.

  15. Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology.

    Science.gov (United States)

    Siegle, Joshua H; López, Aarón Cuevas; Patel, Yogi A; Abramov, Kirill; Ohayon, Shay; Voigts, Jakob

    2017-02-07

    Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.

  16. Open Source Software Development with Your Mother Language : Intercultural Collaboration Experiment 2002

    DEFF Research Database (Denmark)

    Nomura, Saeko; Ishida, Saeko; Jensen, Mika Yasuoka;

    2002-01-01

    Open Source Software Development with Your Mother Language: Intercultural Collaboration Experiment 2002,” 10th International Conference on Human – Computer Interaction (HCII2003), June 2003, Crete, Greece.......”Open Source Software Development with Your Mother Language: Intercultural Collaboration Experiment 2002,” 10th International Conference on Human – Computer Interaction (HCII2003), June 2003, Crete, Greece....

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

    Science.gov (United States)

    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)

  18. PaDEL-DDPredictor: open-source software for PD-PK-T prediction.

    Science.gov (United States)

    He, Yuye; Liew, Chin Yee; Sharma, Nitin; Woo, Sze Kwang; Chau, Yi Ting; Yap, Chun Wei

    2013-03-15

    ADMET (absorption, distribution, metabolism, excretion, and toxicity)-related failure of drug candidates is a major issue for the pharmaceutical industry today. Prediction of PD-PK-T properties using in silico tools has become very important in pharmaceutical research to reduce cost and enhance efficiency. PaDEL-DDPredictor is an in silico tool for rapid prediction of PD-PK-T properties of compounds from their chemical structures. It is free and open-source software that, has both graphical user interface and command line interface, can work on all major platforms (Windows, Linux, and MacOS) and supports more than 90 different molecular file formats. The software can be downloaded from http://padel.nus.edu.sg/software/padelddpredictor.

  19. An Investigation of an Open-Source Software Development Environment in a Software Engineering Graduate Course

    OpenAIRE

    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 revealed that while the OSSD learning environment motivated students to engage in real-world projects, tensions were found between the students’ self-pro...

  20. ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

    Science.gov (United States)

    Dickson, B M; Cornett, E M; Ramjan, Z; Rothbart, S B

    2016-01-01

    Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools.

  1. Sustainability and social responsibility reporting in open source software

    Directory of Open Access Journals (Sweden)

    Maria Isabel Alonso de Magdaleno

    2015-03-01

    Full Text Available Digital commons have held the interest of the research community in recent years. However, institutional recognition has not been fully awarded mainly due to the absence of a comprehensive reporting framework. The objective of our research is to identify indicators in order to measure open source projects performance. Motivation that led us to carry out this analysis was the fact that, despite the many benefits attributed to open sourcing, no information about it was disclosed on annual reports. We are based on previous literature about creating institutions to governing the commons. One of the key goals is institutional reporting to members of the community, so we believe that a reporting model based on social responsibility framework is clearly suitable for this purpose. Social responsibility and sustainability are about enabling organizations to incorporate creation of social, environmental and economic value into core strategy and operations; their reporting is key to create value for organizations, their stakeholders and society as a whole. To reach our goal, we asked a panel of open source experts their opinion about the key success factors and other relevant variables for the purpose of recommend a methodology to calculate specific indicators to be disclosed on social responsibility reports.

  2. Coordination Implications of Software Coupling in Open Source Projects

    NARCIS (Netherlands)

    Amrit, Chintan; Hillegersberg, van Jos; Ågerfalk, Pär

    2010-01-01

    The effect of software coupling on the quality of software has been studied quite widely since the seminal paper on software modularity by Parnas [1]. However, the effect of the increase in software coupling on the coordination of the developers has not been researched as much. In commercial softwar

  3. Open Source Software Movement:A Challenging Opportunity for the Development of China's Software Industry

    Institute of Scientific and Technical Information of China (English)

    LI Mingzhi; ZHENG Jie

    2004-01-01

    The software industries in developing countries are facing enormous challenges in order to grow amid fierce competition of import from the software makers in developed countries. Open source software (OSS) movement, which is a particular phenomenon in the software industries, seems to be a challenging opportunity for the developing countries that wants to move their own software industries up the value chain. This paper, using China as an example, identifies the issues that need to be addressed for the software industry, as well as the special characteristics of software products that need to be dealt with carefully. It proposes promoting OSS as a strategy the Chinese government should adopt to grow the software industry and the speciftc actions that should be taken.

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

    Science.gov (United States)

    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.

  5. NeuroPG: Open source software for optical pattern generation and data acquisition

    Directory of Open Access Journals (Sweden)

    Benjamin W. Avants

    2015-03-01

    Full Text Available Patterned illumination using a digital micromirror device (DMD is a powerful tool for optogenetics. Compared to a scanning laser, DMDs are inexpensive and can easily create complex illumination patterns. Combining these complex spatiotemporal illumination patterns with optogenetics allows DMD-equipped microscopes to probe neural circuits by selectively manipulating the activity of many individual cells or many subcellular regions at the same time. To use DMDs to study neural activity, scientists must develop specialized software to coordinate optical stimulation patterns with the acquisition of electrophysiological and fluorescence data. To meet this growing need we have developed an open source optical pattern generation software for neuroscience - NeuroPG - that combines, DMD control, sample visualization, and data acquisition in one application. Built on a MATLAB platform, NeuroPG can also process, analyze, and visualize data. The software is designed specifically for the Mightex Polygon400; however, as an open source package, NeuroPG can be modified to incorporate any data acquisition, imaging, or illumination equipment that is compatible with MATLAB’s Data Acquisition and Image Acquisition toolboxes.

  6. Implementing an integrative multi-agent clinical decision support system with open source software.

    Science.gov (United States)

    Sayyad Shirabad, Jelber; Wilk, Szymon; Michalowski, Wojtek; Farion, Ken

    2012-02-01

    Clinical decision making is a complex multi-stage process. Decision support can play an important role at each stage of this process. At present, the majority of clinical decision support systems have been focused on supporting only certain stages. In this paper we present the design and implementation of MET3-a prototype multi-agent system providing an integrative decision support that spans over the entire decision making process. The system helps physicians with data collection, diagnosis formulation, treatment planning and finding supporting evidence. MET3 integrates with external hospital information systems via HL7 messages and runs on various computing platforms available at the point of care (e.g., tablet computers, mobile phones). Building MET3 required sophisticated and reliable software technologies. In the past decade the open source software movement has produced mature, stable, industrial strength software systems with a large user base. Therefore, one of the decisions that should be considered before developing or acquiring a decision support system is whether or not one could use open source technologies instead of proprietary ones. We believe MET3 shows that the answer to this question is positive.

  7. An Embedded Systems Course for Engineering Students Using Open-Source Platforms in Wireless Scenarios

    Science.gov (United States)

    Rodriguez-Sanchez, M. C.; Torrado-Carvajal, Angel; Vaquero, Joaquin; Borromeo, Susana; Hernandez-Tamames, Juan A.

    2016-01-01

    This paper presents a case study analyzing the advantages and disadvantages of using project-based learning (PBL) combined with collaborative learning (CL) and industry best practices, integrated with information communication technologies, open-source software, and open-source hardware tools, in a specialized microcontroller and embedded systems…

  8. Coordination Implications of Software Coupling in Open Source Projects

    NARCIS (Netherlands)

    Amrit, Chintan Amrit; van Hillegersberg, Jos; Ågerfalk, Pär

    2010-01-01

    The effect of software coupling on the quality of software has been studied quite widely since the seminal paper on software modularity by Parnas [1]. However, the effect of the increase in software coupling on the coordination of the developers has not been researched as much. In commercial

  9. An Open-Source Tool Set Enabling Analog-Digital-Software Co-Design

    Directory of Open Access Journals (Sweden)

    Michelle Collins

    2016-02-01

    Full Text Available This paper presents an analog-digital hardware-software co-design environment for simulating and programming reconfigurable systems. The tool simulates, designs, as well as enables experimental measurements after compiling to configurable systems in the same integrated design tool framework. High level software in Scilab/Xcos (open-source programs similar to MATLAB/Simulink that converts the high-level block description by the user to blif format (sci2blif, which acts as an input to the modified VPR tool, including the code v p r 2 s w c s , encoding the specific platform through specific architecture files, resulting in a targetable switch list on the resulting configurable analog–digital system. The resulting tool uses an analog and mixed-signal library of components, enabling users and future researchers access to the basic analog operations/computations that are possible.

  10. THE BERKELEY DATA ANALYSIS SYSTEM (BDAS): AN OPEN SOURCE PLATFORM FOR BIG DATA ANALYTICS

    Science.gov (United States)

    2017-09-01

    THE BERKELEY DATA ANALYSIS SYSTEM (BDAS): AN OPEN SOURCE PLATFORM FOR BIG DATA ANALYTICS UNIVERSITY OF CALIFORNIA, BERKELEY...COMMAND NOTICE AND SIGNATURE PAGE Using Government drawings, specifications, or other data included in this document for any purpose other than...2017 4. TITLE AND SUBTITLE THE BERKELEY DATA ANALYSIS SYSTEM (BDAS): AN OPEN SOURCE PLATFORM FOR BIG DATA ANALYTICS 5a. CONTRACT NUMBER FA8750-12-2

  11. CustusX: an open-source research platform for image-guided therapy.

    Science.gov (United States)

    Askeland, Christian; Solberg, Ole Vegard; Bakeng, Janne Beate Lervik; Reinertsen, Ingerid; Tangen, Geir Arne; Hofstad, Erlend Fagertun; Iversen, Daniel Høyer; Våpenstad, Cecilie; Selbekk, Tormod; Langø, Thomas; Hernes, Toril A Nagelhus; Olav Leira, Håkon; Unsgård, Geirmund; Lindseth, Frank

    2016-04-01

    CustusX is an image-guided therapy (IGT) research platform dedicated to intraoperative navigation and ultrasound imaging. In this paper, we present CustusX as a robust, accurate, and extensible platform with full access to data and algorithms and show examples of application in technological and clinical IGT research. CustusX has been developed continuously for more than 15 years based on requirements from clinical and technological researchers within the framework of a well-defined software quality process. The platform was designed as a layered architecture with plugins based on the CTK/OSGi framework, a superbuild that manages dependencies and features supporting the IGT workflow. We describe the use of the system in several different clinical settings and characterize major aspects of the system such as accuracy, frame rate, and latency. The validation experiments show a navigation system accuracy of [Formula: see text]1.1 mm, a frame rate of 20 fps, and latency of 285 ms for a typical setup. The current platform is extensible, user-friendly and has a streamlined architecture and quality process. CustusX has successfully been used for IGT research in neurosurgery, laparoscopic surgery, vascular surgery, and bronchoscopy. CustusX is now a mature research platform for intraoperative navigation and ultrasound imaging and is ready for use by the IGT research community. CustusX is open-source and freely available at http://www.custusx.org.

  12. Industrial Software Rejuvenation Using Open-Source Parsers

    NARCIS (Netherlands)

    Mooij, A.J.; Joy, M.M.; Eggen, G.; Janson, P.; Radulescu, A.

    2016-01-01

    Software maintenance consumes an increasing proportion of industrial software engineering budgets. Over time the technical debt grows, until it becomes unavoidable to rejuvenate the legacy software to a new design, while preserving the valuable domain logic. In this paper, we explore the feasibility

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

    Science.gov (United States)

    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,…

  14. Investigating the effects of different factors on development of open source enterprise resources planning software packages

    Directory of Open Access Journals (Sweden)

    Mehdi Ghorbaninia

    2014-08-01

    Full Text Available This paper investigates the effects of different factors on development of open source enterprise resources planning software packages. The study designs a questionnaire in Likert scale and distributes it among 210 experts in the field of open source software package development. Cronbach alpha has been calculated as 0.93, which is well above the minimum acceptable level. Using Pearson correlation as well as stepwise regression analysis, the study determines three most important factors including fundamental issues, during and after implementation of open source software development. The study also determines a positive and strong relationship between fundamental factors and after implementation factors (r=0.9006, Sig. = 0.000.

  15. Open-Source as a strategy for operational software - the case of Enki

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  17. Automatic Selection of Open Source Multimedia Softwares Using Error Back-Propagation Neural Network

    Directory of Open Access Journals (Sweden)

    Deepika

    2015-07-01

    Full Text Available Open source opens a new era to provide license of the software for the user at free of cost which is advantage over paid licensed software. In Multimedia applications there are many versions of software are available and there is a problem for the user to select compatible software for their own system. Most of the time while surfing for software a huge list of software opens in response. The selection of particular software which is pretty suitable for the system from a real big list is the biggest challenge that is faced by the users. This work has been done that focuses on the existing open source software that are widely used and to design an automatic system for selection of particular open source software according to the compatibility of users own system. In this work, error back-propagation based neural network is designed in MATLAB for automatic selection of open source software. The system provides the open source software name after taking the information from user. Regression coefficient of 0.93877 is obtained and the results shown are up to the mark and can be utilized for the fast and effective software search.

  18. Open source software and low cost sensors for teaching UAV science

    Science.gov (United States)

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

    2016-12-01

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

  19. The Case for Open Source Software: The Interactional Discourse Lab

    Science.gov (United States)

    Choi, Seongsook

    2016-01-01

    Computational techniques and software applications for the quantitative content analysis of texts are now well established, and many qualitative data software applications enable the manipulation of input variables and the visualization of complex relations between them via interactive and informative graphical interfaces. Although advances in…

  20. The Case for Open Source Software: The Interactional Discourse Lab

    Science.gov (United States)

    Choi, Seongsook

    2016-01-01

    Computational techniques and software applications for the quantitative content analysis of texts are now well established, and many qualitative data software applications enable the manipulation of input variables and the visualization of complex relations between them via interactive and informative graphical interfaces. Although advances in…

  1. Falcon: a highly flexible open-source software for closed-loop neuroscience

    Science.gov (United States)

    Ciliberti, Davide; Kloosterman, Fabian

    2017-08-01

    Objective. Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. Approach. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. Main results. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Significance. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those

  2. Falcon: a highly flexible open-source software for closed-loop neuroscience.

    Science.gov (United States)

    Ciliberti, Davide; Kloosterman, Fabian

    2017-05-26

    Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real

  3. The potential role of open source software in overcoming digital poverty

    CSIR Research Space (South Africa)

    Kinyondo, J

    2012-09-01

    Full Text Available Developing countries, such as Tanzania, are characterized by digital poverty and a lack of information and communication technology (ICT) acceptance. The use of open source software (OSS) has been proposed as a potential strategy for addressing ICT...

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

    Science.gov (United States)

    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. Image Harvest: an open-source platform for high-throughput plant image processing and analysis.

    Science.gov (United States)

    Knecht, Avi C; Campbell, Malachy T; Caprez, Adam; Swanson, David R; Walia, Harkamal

    2016-05-01

    High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets.

  6. NeuroVR: an open source virtual reality platform for clinical psychology and behavioral neurosciences.

    Science.gov (United States)

    Riva, Giuseppe; Gaggioli, Andrea; Villani, Daniela; Preziosa, Alessandra; Morganti, Francesca; Corsi, Riccardo; Faletti, Gianluca; Vezzadini, Luca

    2007-01-01

    In the past decade, the use of virtual reality for clinical and research applications has become more widespread. However, the diffusion of this approach is still limited by three main issues: poor usability, lack of technical expertise among clinical professionals, and high costs. To address these challenges, we introduce NeuroVR (http://www.neurovr.org--http://www.neurotiv.org), a cost-free virtual reality platform based on open-source software, that allows non-expert users to adapt the content of a pre-designed virtual environment to meet the specific needs of the clinical or experimental setting. Using the NeuroVR Editor, the user can choose the appropriate psychological stimuli/stressors from a database of objects (both 2D and 3D) and videos, and easily place them into the virtual environment. The edited scene can then be visualized in the NeuroVR Player using either immersive or non-immersive displays. Currently, the NeuroVR library includes different virtual scenes (apartment, office, square, supermarket, park, classroom, etc.), covering two of the most studied clinical applications of VR: specific phobias and eating disorders. The NeuroVR Editor is based on Blender (http://www.blender.org), the open source, cross-platform suite of tools for 3D creation, and is available as a completely free resource. An interesting feature of the NeuroVR Editor is the possibility to add new objects to the database. This feature allows the therapist to enhance the patient's feeling of familiarity and intimacy with the virtual scene, i.e., by using photos or movies of objects/people that are part of the patient's daily life, thereby improving the efficacy of the exposure. The NeuroVR platform runs on standard personal computers with Microsoft Windows; the only requirement for the hardware is related to the graphics card, which must support OpenGL.

  7. Critical Aspects of Modern Open Source SoftwareTechnology to Support Emerging Demands

    CERN Document Server

    Farooq, Umer; Shabbir, Usman; Nazir, Sohail; 10.5120/3330-4580

    2011-01-01

    Software has gained immense importance in our everyday lifeand is handling each and every aspect of today's technologicalworld. The idea of software at initial phase was implemented bya very precise minority of individual and now it's everywherewhether one's personal life or an organization .Financiallystrong organization and people who can purchase this bounty oftechnological era can fulfill their desires efficiently. For sure it's not a generalized case that one is financially strong and caneasily afford the desired software. There are numerous userswho cannot do so. Open source software has a way out for theseusers it provides them the same facilities and functionalities asin their equivalent software irrespective of any financialpressure. So the financially constrained personals ororganization can make use of open source software forachievement of their desired tasks. In this research paper ananalysis of open source software has been presented byproviding a brief comparison of Ubuntu as an emerging highqu...

  8. OsiriX: an open-source software for navigating in multidimensional DICOM images.

    Science.gov (United States)

    Rosset, Antoine; Spadola, Luca; Ratib, Osman

    2004-09-01

    A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

  9. cPath: open source software for collecting, storing, and querying biological pathways

    Directory of Open Access Journals (Sweden)

    Gross Benjamin E

    2006-11-01

    Full Text Available Abstract Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

  10. WormGender - Open-Source Software for Automatic Caenorhabditis elegans Sex Ratio Measurement.

    Directory of Open Access Journals (Sweden)

    Marta K Labocha

    Full Text Available Fast and quantitative analysis of animal phenotypes is one of the major challenges of current biology. Here we report the WormGender open-source software, which is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i automatic recognition and counting of adult hermaphrodites and males, ii a manual inspection feature that enables manual correction of errors, and iii flexibility to use new training images to optimize the software for different imaging conditions. We evaluated the performance of our software by comparing manual and automated assessment of sex ratio. Our data showed that the WormGender software provided overall accurate sex ratio measurements. We further demonstrated the usage of WormGender by quantifying the high incidence of male (him phenotype in 27 mutant strains. Mutants of nine genes (brc-1, C30G12.6, cep-1, coh-3, him-3, him-5, him-8, skr-1, unc-86 showed significant him phenotype. The WormGender is written in Java and can be installed and run on both Windows and Mac platforms. The source code is freely available together with a user manual and sample data at http://www.QuantWorm.org/. The source code and sample data are also available at http://dx.doi.org/10.6084/m9.figshare.1541248.

  11. Open Source Software for Mapping Human Impacts on Marine Ecosystems with an Additive Model

    Directory of Open Access Journals (Sweden)

    Andy Stock

    2016-06-01

    Full Text Available This paper describes an easy-to-use open source software tool implementing a commonly used additive model (Halpern et al., 'Science', 2008 for mapping human impacts on marine ecosystems. The tool has been used to map the potential for cumulative human impacts in Arctic marine waters and can support future human impact mapping projects by 1 making the model easier to use; 2 making updates of model results straightforward when better input data become available; 3 storing input data and information about processing steps in a defined format and thus facilitating data sharing and reproduction of modeling results; 4 supporting basic visualization of model inputs and outputs without the need for advanced technical skills. The tool, called EcoImpactMapper, was implemented in Java and is thus platform-independent. A tutorial, example data, the tool and the source code are available online.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-04-01

    The Free and Open Source Software (FOSS) movement promotes community engagement in software development, as well as provides access to a range of sophisticated technologies that would be prohibitively expensive if obtained commercially. However, as geoinformatics and eResearch tools and services become more dispersed, it becomes more complicated to identify and interface between the many required components. Virtual Laboratories (VLs, also known as Science Gateways) simplify the management and coordination of these components by providing a platform linking many, if not all, of the steps in particular scientific processes. These enable scientists to focus on their science, rather than the underlying supporting technologies. We describe a modular, open source, VL infrastructure that can be reconfigured to create VLs for a wide range of disciplines. Development of this infrastructure has been led by CSIRO in collaboration with Geoscience Australia and the National Computational Infrastructure (NCI) with support from the National eResearch Collaboration Tools and Resources (NeCTAR) and the Australian National Data Service (ANDS). Initially, the infrastructure was developed to support the Virtual Geophysical Laboratory (VGL), and has subsequently been repurposed to create the Virtual Hazards Impact and Risk Laboratory (VHIRL) and the reconfigured Australian National Virtual Geophysics Laboratory (ANVGL). During each step of development, new capabilities and services have been added and/or enhanced. We plan on continuing to follow this model using a shared, community code base. The VL platform facilitates transparent and reproducible science by providing access to both the data and methodologies used during scientific investigations. This is further enhanced by the ability to set up and run investigations using computational resources accessed through the VL. Data is accessed using registries pointing to catalogues within public data repositories (notably including the

  14. Integrating open-source software applications to build molecular dynamics systems.

    Science.gov (United States)

    Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

    2014-04-05

    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. Copyright © 2014 Wiley Periodicals, Inc.

  15. Evaluation of open source data mining software packages

    Science.gov (United States)

    Bonnie Ruefenacht; Greg Liknes; Andrew J. Lister; Haans Fisk; Dan Wendt

    2009-01-01

    Since 2001, the USDA Forest Service (USFS) has used classification and regression-tree technology to map USFS Forest Inventory and Analysis (FIA) biomass, forest type, forest type groups, and National Forest vegetation. This prior work used Cubist/See5 software for the analyses. The objective of this project, sponsored by the Remote Sensing Steering Committee (RSSC),...

  16. A Business Case Study of Open Source Software

    Science.gov (United States)

    2001-07-01

    softlinux.com.br www.softlinux.com.br Investigacion y Desarrollo Agora www.id-agora.com SOT Finnish Software Engineering www.sot.com Iplabs www.iplabs.ru...College, Air University, June 11, 1999, http://ceu.fi.udc.es/GPUL/ articulos /varios/US_DoD_and_OSS.txt. 48. Slackware, www.slackware.com. 49. Slater, Derek

  17. Closed-loop, multichannel experimentation using the open-source NeuroRighter electrophysiology platform

    Directory of Open Access Journals (Sweden)

    Jonathan Paul Newman

    2013-01-01

    Full Text Available Single neuron feedback control techniques, such as voltage clamp and dynamic clamp, have enabled numerous advances in our understanding of ion channels, electrochemical signaling, and neural dynamics. Although commercially available multichannel recording and stimulation systems are commonly used for studying neural processing at the network level, they provide little native support for real-time feedback. We developed the open-source NeuroRighter multichannel electrophysiology hardware and software platform for closed-loop multichannel control with a focus on accessibility and low cost. NeuroRighter allows 64 channels of stimulation and recording for around US $10,000, along with the ability to integrate with other software and hardware. Here, we present substantial enhancements to the NeuroRighter platform, including a redesigned desktop application, a new stimulation subsystem allowing arbitrary stimulation patterns, low-latency data servers for accessing data streams, and a new application programming interface (API for creating closed-loop protocols that can be inserted into NeuroRighter as plugin programs. This greatly simplifies the design of sophisticated real-time experiments without sacrificing the power and speed of a compiled programming language. Here we present a detailed description of NeuroRighter as a stand alone application, its plugin API, and an extensive set of case studies that highlight the system's abilities for conducting closed-loop, multichannel interfacing experiments.

  18. Shaping Software Engineering Curricula Using Open Source Communities: A Case Study

    Science.gov (United States)

    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…

  19. Expanding Human Capabilities through the Adoption and Utilization of Free, Libre, and Open Source Software

    Science.gov (United States)

    Simpson, James Daniel

    2014-01-01

    Free, libre, and open source software (FLOSS) is software that is collaboratively developed. FLOSS provides end-users with the source code and the freedom to adapt or modify a piece of software to fit their needs (Deek & McHugh, 2008; Stallman, 2010). FLOSS has a 30 year history that dates to the open hacker community at the Massachusetts…

  20. Expanding Human Capabilities through the Adoption and Utilization of Free, Libre, and Open Source Software

    Science.gov (United States)

    Simpson, James Daniel

    2014-01-01

    Free, libre, and open source software (FLOSS) is software that is collaboratively developed. FLOSS provides end-users with the source code and the freedom to adapt or modify a piece of software to fit their needs (Deek & McHugh, 2008; Stallman, 2010). FLOSS has a 30 year history that dates to the open hacker community at the Massachusetts…

  1. Shaping Software Engineering Curricula Using Open Source Communities: A Case Study

    Science.gov (United States)

    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. DUNE as an Example of Sustainable Open Source Scientific Software Development

    OpenAIRE

    Blatt, Makus

    2013-01-01

    In this paper we describe how DUNE, an open source scientific software framework, is developed. Having a sustainable software framework for the solution of partial differential equations is the main driver of DUNE's development. We take a look how DUNE strives to stay sustainable software.

  3. Bug-Fixing and Code-Writing: The Private Provision of Open Source Software

    DEFF Research Database (Denmark)

    Bitzer, Jürgen; Schröder, Philipp

    2002-01-01

    Open source software (OSS) is a public good. A self-interested individual would consider providing such software, if the benefits he gained from having it justified the cost of programming. Nevertheless each agent is tempted to free ride and wait for others to develop the software instead. This p...... their programming skills; the startup (and collapse) of an OSS project displays bandwagon dynamics....

  4. Technical Evaluation Report 24: Open Source Software: an alternative to costly Learning Management Systems

    Directory of Open Access Journals (Sweden)

    Jim Depow

    2003-10-01

    Full Text Available This is the first in a series of two reports discussing the use of open source software (OSS and free software (FS in online education as an alternative to expensive proprietary software. It details the steps taken in a Canadian community college to download and install the Linux Operating System in order to support an OSS/ FS learning management system (LMS.

  5. Open Source Scanning Probe Microscopy Control Software Package Gxsm

    Energy Technology Data Exchange (ETDEWEB)

    Zahl P.; Wagner, T.; Moller, R.; Klust, A.

    2009-08-10

    Gxsm is a full featured and modern scanning probe microscopy (SPM) software. It can be used for powerful multidimensional image/data processing, analysis, and visualization. Connected toan instrument, it is operating many different avors of SPM, e.g., scanning tunneling microscopy(STM) and atomic force microscopy (AFM) or in general two-dimensional multi channel data acquisition instruments. The Gxsm core can handle different data types, e.g., integer and oating point numbers. An easily extendable plug-in architecture provides many image analysis and manipulation functions. A digital signal processor (DSP) subsystem runs the feedback loop, generates the scanning signals and acquires the data during SPM measurements. The programmable Gxsm vector probe engine performs virtually any thinkable spectroscopy and manipulation task, such as scanning tunneling spectroscopy (STS) or tip formation. The Gxsm software is released under the GNU general public license (GPL) and can be obtained via the Internet.

  6. Survivability as a Tool for Evaluating Open Source Software

    Science.gov (United States)

    2015-06-01

    technology has expanded rapidly in recent years, largely due to the advancing complexity of military systems. The F-22 Raptor , which demonstrated initial...manner in order to feed OSS survivability analyses? 4. How could an adversary destroy a system or force a mission failure by manipulating software embedded...Malicious code initiates programmed flight path What is the intent of the malicious code? What impact does initiation have on the UAV’s behavior ? 3. Code

  7. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

    Science.gov (United States)

    Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

    2012-10-01

    The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

  8. VALUATION OF OPEN SOURCE SOFTWARE: HOW DO YOU PUT A VALUE ON FREE?

    Directory of Open Access Journals (Sweden)

    Jesús García-García

    2013-04-01

    Full Text Available The aim of this study is to assess the financial reporting framework applied to open source software. Open sourcing software developments means sharing technology and resources with communities worldwide to help eliminate the digital divide, create economic opportunity, and support equal access to technology. Therefore, a methodological approach is needed to assess properly the performance and the value generation potential and to put such measure into organizational reports. International financial reporting framework is checked over conditions to allow value recognition of open sourced assets. Linux kernel development value is estimated to reflect worth of open source developments despite absence of book value due to inexistence of a single cost source. Several attempts to estimate a valuation of open source software have been performed previously. However, this study is the first to judge suitability of accounting framework to report on this value. The main finding is that open sourced assets do not fully accomplish conditions to be included in financial reports. We seek to stimulate academic and professional debate about the pursuit of valuation of a large and efficient ecosystem of software innovation, freely available to society.

  9. Ebooks without Vendors: Using Open Source Software to Create and Share Meaningful Ebook Collections

    Directory of Open Access Journals (Sweden)

    Matt Weaver

    2014-07-01

    Full Text Available The Community Cookbook project began with wondering how to take local cookbooks in the library’s collection and create a recipe database. The final website is both a recipe website and collection of ebook versions of local cookbooks. This article will discuss the use of open source software at every stage in the project, which proves that an open source publishing model is possible for any library.

  10. Dynamic online surveys and experiments with the free open-source software dynQuest.

    Science.gov (United States)

    Rademacher, Jens D M; Lippke, Sonia

    2007-08-01

    With computers and the World Wide Web widely available, collecting data through Web browsers is an attractive method utilized by the social sciences. In this article, conducting PC- and Web-based trials with the software package dynQuest is described. The software manages dynamic questionnaire-based trials over the Internet or on single computers, possibly as randomized control trials (RCT), if two or more groups are involved. The choice of follow-up questions can depend on previous responses, as needed for matched interventions. Data are collected in a simple text-based database that can be imported easily into other programs for postprocessing and statistical analysis. The software consists of platform-independent scripts written in the programming language PERL that use the common gateway interface between Web browser and server for submission of data through HTML forms. Advantages of dynQuest are parsimony, simplicity in use and installation, transparency, and reliability. The program is available as open-source freeware from the authors.

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

    Science.gov (United States)

    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.

  12. Open Source Software in Teaching Physics: A Case Study on Vector Algebra and Visual Representations

    Science.gov (United States)

    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…

  13. A study on the Open Source Digital Library Software's: Special Reference to DSpace, EPrints and Greenstone

    Science.gov (United States)

    Tramboo, Shahkar; Humma, Humma; M Shafi, S.; Gul, Sumeer

    2012-12-01

    The richness in knowledge has changed access methods for all stake holders in retrieving key knowledge and relevant information. This paper presents a study of three open source digital library management software used to assimilate and disseminate information to world audience. The methodology followed involves online survey and study of related software documentation and associated technical manuals.

  14. FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data

    NARCIS (Netherlands)

    Oostenveld, R.; Fries, P.; Maris, E.; Schoffelen, J.M.

    2011-01-01

    This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimenta

  15. Enhancing Software Engineering Education through Open Source Projects: Four Years of Students' Perspectives

    NARCIS (Netherlands)

    Papadopoulos, P.M.; Stamelos, I.G.; Meiszner, A.

    2015-01-01

    This paper presents the results after four years of running of an instructional method that utilizes free/libre open source software (FLOSS) projects as tools for teaching software engineering in formal education. In the last four academic years, a total of 408 juniors majoring in Informatics (in a

  16. STATISTICAL ANALYSIS ON SOFTWARE METRICS AFFECTING MODULARITY IN OPEN SOURCE SOFTWARE

    Directory of Open Access Journals (Sweden)

    Andi Wahju Rahardjo Emanuel

    2011-06-01

    Full Text Available Modularity has been identified by many researchers as one of the success factors of Open Source Software (OSS Projects. This modularity trait are influenced by some aspects of software metrics such as size, complexity, cohesion, and coupling. In this research, we analyze the software metrics such as Size Metrics (NCLOC, Lines, and Statements, Complexity Metrics (McCabe's Cyclomatic Complexity, Cohesion Metrics (LCOM4, and Coupling Metrics (RFC, Afferent coupling and Efferent coupling of 59 Java-based OSS Projects from Sourceforge.net. By assuming that the number of downloads can be used as the indication of success of these projects, the OSS Projects being selected are the projects which have been downloaded more than 100,000 times. The software metrics reflecting the modularity of these projects are collected using SONAR tool and then statistically analyzed using scatter graph, Pearson rproduct-moment correlation, and least-square-fit linear approximation. It can be shown that there areonly three independent metrics reflecting modularity which are NCLOC, LCOM4, and Afferent Coupling, whereas there is also one inconclusive result regarding Efferent Coupling.

  17. Interactive multicentre teleconferences using open source software in a team of thoracic surgeons.

    Science.gov (United States)

    Ito, Kazuhiro; Shimada, Junichi; Katoh, Daishiro; Nishimura, Motohiro; Yanada, Masashi; Okada, Satoru; Ishihara, Shunta; Ichise, Kaori

    2012-12-01

    Real-time consultation between a team of thoracic surgeons is important for the management of difficult cases. We established a system for interactive teleconsultation between multiple sites, based on open-source software. The graphical desktop-sharing system VNC (virtual network computing) was used for remotely controlling another computer. An image-processing package (OsiriX) was installed on the server to share the medical images. We set up a voice communication system using Voice Chatter, a free, cross-platform voice communication application. Four hospitals participated in the trials. One was connected by gigabit ethernet, one by WiMAX and one by ADSL. Surgeons at three of the sites found that it was comfortable to view images and consult with each other using the teleconferencing system. However, it was not comfortable using the client that connected via WiMAX, because of dropped frames. Apart from the WiMAX connection, the VNC-based screen-sharing system transferred the clinical images efficiently and in real time. We found the screen-sharing software VNC to be a good application for medical image interpretation, especially for a team of thoracic surgeons using multislice CT scans.

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

    Science.gov (United States)

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

    2016-12-01

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

  19. Inequalities in Open Source Software Development: Analysis of Contributor's Commits in Apache Software Foundation Projects.

    Science.gov (United States)

    Chełkowski, Tadeusz; Gloor, Peter; Jemielniak, Dariusz

    2016-01-01

    While researchers are becoming increasingly interested in studying OSS phenomenon, there is still a small number of studies analyzing larger samples of projects investigating the structure of activities among OSS developers. The significant amount of information that has been gathered in the publicly available open-source software repositories and mailing-list archives offers an opportunity to analyze projects structures and participant involvement. In this article, using on commits data from 263 Apache projects repositories (nearly all), we show that although OSS development is often described as collaborative, but it in fact predominantly relies on radically solitary input and individual, non-collaborative contributions. We also show, in the first published study of this magnitude, that the engagement of contributors is based on a power-law distribution.

  20. The Impact of Entry and Competition by Open Source Software on Innovation Activity

    DEFF Research Database (Denmark)

    Schröder, Philipp J.H.; Bitzer, Jürgen

    2006-01-01

    This chapter presents the stylized facts of open source software innovation and provides empirical evidence on the impact of increased competition by OSS on the innovative activity in the software industry. Furthermore, we introduce a simple formal model that captures the innovation impact of OSS...... entry by examining a change in market structure from monopoly to duopoly under the assumption that software producers compete in technology rather than price or quantities. The chapter identifies a pro-innovative effect of OSS competition....

  1. APERO, AN OPEN SOURCE BUNDLE ADJUSMENT SOFTWARE FOR AUTOMATIC CALIBRATION AND ORIENTATION OF SET OF IMAGES

    OpenAIRE

    M. Pierrot Deseilligny; I. Clery

    2012-01-01

    IGN has developed a set of photogrammetric tools, APERO and MICMAC, for computing 3D models from set of images. This software, developed initially for its internal needs are now delivered as open source code. This paper focuses on the presentation of APERO the orientation software. Compared to some other free software initiatives, it is probably more complex but also more complete, its targeted user is rather professionals (architects, archaeologist, geomophologist) than people. APERO uses bo...

  2. UCVM: Open Source Software for Understanding and Delivering 3D Velocity Models

    Science.gov (United States)

    Gill, D.; Small, P.; Maechling, P. J.; Jordan, T. H.; Shaw, J. H.; Plesch, A.; Chen, P.; Lee, E. J.; Taborda, R.; Olsen, K. B.; Callaghan, S.

    2014-12-01

    Physics-based ground motion simulations can calculate the propagation of earthquake waves through 3D velocity models of the Earth. The Southern California Earthquake Center (SCEC) has developed the Unified Community Velocity Model (UCVM) framework to help researchers build structured or unstructured velocity meshes from 3D velocity models for use in wave propagation simulations. The UCVM software framework makes it easy to extract P and S wave propagation speeds and other material properties from 3D velocity models by providing a common interface through which researchers can query earth models for a given location and depth. Currently, the platform supports multiple California models, including SCEC CVM-S4 and CVM-H 11.9.1, and has been designed to support models from any region on earth. UCVM is currently being use to generate velocity meshes for many SCEC wave propagation codes, including AWP-ODC-SGT and Hercules. In this presentation, we describe improvements to the UCVM software. The current version, UCVM 14.3.0, released in March of 2014, supports the newest Southern California velocity model, CVM-S4.26, which was derived from 26 full-3D tomographic iterations using CVM-S4 as the starting model (Lee et al., this meeting), and the Broadband 1D velocity model used in the CyberShake 14.2 study. We have ported UCVM to multiple Linux distributions and OS X. Also included in this release is the ability to add small-scale stochastic heterogeneities to extract Cartesian meshes for use in high-frequency ground motion simulations. This tool was built using the C language open-source FFT library, FFTW. The stochastic parameters (Hurst exponent, correlation length, and the horizontal/vertical aspect ratio) can be customized by the user. UCVM v14.3.0 also provides visualization scripts for constructing cross-sections, horizontal slices, basin depths, and Vs30 maps. The interface allows researchers to visually review velocity models . Also, UCVM v14.3.0 can extract

  3. An Organizational-Technical Concept to Deal with Open Source Software License Terms

    Directory of Open Access Journals (Sweden)

    Sergius Dyck

    2016-06-01

    Full Text Available Open source software (OSS released under various license terms is widely used as third party libraries in today's software projects. To ensure open source compliance within an organization, a strategic approach to OSS management is needed. As basis for such an approach, we introduce an organizational-technical concept for dealing with the various OSS licenses by using procedural instructions and build automation software. The concept includes the careful consideration of OSS license conditions. The results obtained from this consideration and additional necessary commitments are documented in a so-called license playbook. We introduce procedure instructions enabling a consistent approach for software development using OSS libraries. The procedure instructions are described in a way such that they can be implemented for example for Java projects using the popular build automation tool Apache Maven and the software repository tool Nexus. We give guidance on how to realize such an implementation on basis of automation tools in practice.

  4. Open source EMR software: profiling, insights and hands-on analysis.

    Science.gov (United States)

    Kiah, M L M; Haiqi, Ahmed; Zaidan, B B; Zaidan, A A

    2014-11-01

    The use of open source software in health informatics is increasingly advocated by authors in the literature. Although there is no clear evidence of the superiority of the current open source applications in the healthcare field, the number of available open source applications online is growing and they are gaining greater prominence. This repertoire of open source options is of a great value for any future-planner interested in adopting an electronic medical/health record system, whether selecting an existent application or building a new one. The following questions arise. How do the available open source options compare to each other with respect to functionality, usability and security? Can an implementer of an open source application find sufficient support both as a user and as a developer, and to what extent? Does the available literature provide adequate answers to such questions? This review attempts to shed some light on these aspects. The objective of this study is to provide more comprehensive guidance from an implementer perspective toward the available alternatives of open source healthcare software, particularly in the field of electronic medical/health records. The design of this study is twofold. In the first part, we profile the published literature on a sample of existent and active open source software in the healthcare area. The purpose of this part is to provide a summary of the available guides and studies relative to the sampled systems, and to identify any gaps in the published literature with respect to our research questions. In the second part, we investigate those alternative systems relative to a set of metrics, by actually installing the software and reporting a hands-on experience of the installation process, usability, as well as other factors. The literature covers many aspects of open source software implementation and utilization in healthcare practice. Roughly, those aspects could be distilled into a basic taxonomy, making the

  5. The Gaggle: An open-source software system for integrating bioinformatics software and data sources

    Directory of Open Access Journals (Sweden)

    Bonneau Richard

    2006-03-01

    Full Text Available Abstract Background Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing. Results In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools. Conclusion We have integrated diverse databases (for example, KEGG, BioCyc, String and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer. Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions, functional associations (operon, chromosomal

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

    Science.gov (United States)

    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

  7. Comparative Study on Innovation Incentives for Commercial Open Source Software under Different Licenses

    Directory of Open Access Journals (Sweden)

    Mingqing Xing

    2013-02-01

    Full Text Available This study compares technological innovation incentives for commercial open source software under two typical licenses (the GNU General Public License and the Berkeley Software Distribution License, i.e., GPL and BSD. In the case of private optimum, the incentive towards software features (resp. usability innovation is always higher (resp. lower under BSD than under GPL. Contrast to the private optimum, the social planner expects more investment in software feature under both BSD and GPL, but less (resp. equivalent investment in software usability under BSD (resp. GPL.

  8. TRACC: an open source software for processing sap flux data from thermal dissipation probes

    Science.gov (United States)

    Eric J. Ward; Jean-Christophe Domec; John King; Ge Sun; Steve McNulty; Asko Noormets

    2017-01-01

    Key message TRACC is an open-source software for standardizing the cleaning, conversion, and calibration of sap flux density data from thermal dissipation probes, which addresses issues of nighttime transpiration and water storage. Abstract Thermal dissipation probes (TDPs) have become a widely used method of monitoring plant water use in recent years. The use of TDPs...

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

    Science.gov (United States)

    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…

  10. Exploring the impact of socio-technical core-periphery structures in open source software development

    NARCIS (Netherlands)

    Amrit, Chintan; Hillegersberg, van Jos

    2010-01-01

    In this paper we apply the social network concept of core-periphery structure to the socio-technical structure of a software development team. We propose a socio-technical pattern that can be used to locate emerging coordination problems in Open Source projects. With the help of our tool and method

  11. Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

    Science.gov (United States)

    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…

  12. Images of innovation in discourses of free and open source software

    NARCIS (Netherlands)

    Dafermos, G.; Van Eeten, M.J.G.

    2014-01-01

    In this study, we examine the relationship between innovation and free/open source software (FOSS) based on the views of contributors to FOSS projects, using Q methodology as a method of discourse analysis to make visible the positions held by FOSS contributors and identify the discourses encountere

  13. Tensor calculus with open-source software: the SageManifolds project

    CERN Document Server

    Gourgoulhon, Eric; Mancini, Marco

    2014-01-01

    The SageManifolds project aims at extending the mathematics software system Sage towards differential geometry and tensor calculus. As Sage itself, it 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 category pattern, and present a concrete example of use.

  14. PyPedal, an open source software package for pedigree analysis

    Science.gov (United States)

    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...

  15. Learning and Best Practices for Learning in Open-Source Software Communities

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  17. Identifying Business Barriers and Enablers for the Adoption of Open Source Software

    DEFF Research Database (Denmark)

    Holck, Jesper; Holm Larsen, Michael; Pedersen, Mogens Kuhn

    2004-01-01

    The main research interest in Open Source Software (OSS) has been in answering the questions of why individuals and organizations without economic compensation contribute to OSS projects and how these projects are organized. In this paper we instead focus on managerial decisions for acquisition...

  18. Learning and Best Practices for Learning in Open-Source Software Communities

    Science.gov (United States)

    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…

  19. Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

    Science.gov (United States)

    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…

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

    Directory of Open Access Journals (Sweden)

    Shuichi Kajihata

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  2. Demo abstract: Flexhouse-2-an open source building automation platform with a focus on flexible control

    DEFF Research Database (Denmark)

    Gehrke, Oliver; Kosek, Anna Magdalena; Svendsen, Mathias

    2014-01-01

    in or on buildings, and most of these resources will not be communicating directly with the smart grid; in order to allow internal coordination and optimization of resource use at building level, a building automation platform will act as an intermediary. Such a platform must be easy to adapt to the multitude......, an open-source implementation of a building automation system which has been designed with a strong focus on enabling the integration of the building into a smart power system and dedicated support for the requirements of an R&D environment. We will demonstrate the need for such a platform, discuss...

  3. Advancing global marine biogeography research with open-source GIS software and cloud-computing

    Science.gov (United States)

    Fujioka, Ei; Vanden Berghe, Edward; Donnelly, Ben; Castillo, Julio; Cleary, Jesse; Holmes, Chris; McKnight, Sean; Halpin, patrick

    2012-01-01

    Across many scientific domains, the ability to aggregate disparate datasets enables more meaningful global analyses. Within marine biology, the Census of Marine Life served as the catalyst for such a global data aggregation effort. Under the Census framework, the Ocean Biogeographic Information System was established to coordinate an unprecedented aggregation of global marine biogeography data. The OBIS data system now contains 31.3 million observations, freely accessible through a geospatial portal. The challenges of storing, querying, disseminating, and mapping a global data collection of this complexity and magnitude are significant. In the face of declining performance and expanding feature requests, a redevelopment of the OBIS data system was undertaken. Following an Open Source philosophy, the OBIS technology stack was rebuilt using PostgreSQL, PostGIS, GeoServer and OpenLayers. This approach has markedly improved the performance and online user experience while maintaining a standards-compliant and interoperable framework. Due to the distributed nature of the project and increasing needs for storage, scalability and deployment flexibility, the entire hardware and software stack was built on a Cloud Computing environment. The flexibility of the platform, combined with the power of the application stack, enabled rapid re-development of the OBIS infrastructure, and ensured complete standards-compliance.

  4. Tools of creation of urban geographic information systems based on software and open source

    Directory of Open Access Journals (Sweden)

    Володимир Пилипович Ткаченко

    2015-06-01

    Full Text Available Conceptual principles of the creation of Urban Geographic Information System (UGIS tools based on software products with open source are considered. Organizational and technical structure of UGIS, the basic provisions of its conceptual architecture, tool software modules functions and their means of implementation are provided. Rational organization of municipal information resources for functional UGIS subsystem creations is proposed, and the examples of its implementation are provided

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

    Science.gov (United States)

    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

  6. LabKey Server: An open source platform for scientific data integration, analysis and collaboration

    Directory of Open Access Journals (Sweden)

    Lum Karl

    2011-03-01

    Full Text Available Abstract Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i Submitting specimens requests across collaborating organizations (ii Graphically defining new experimental data types, metadata and wizards for data collection (iii Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v Interacting dynamically with external data sources (vi Tracking study participants and cohorts over time (vii Developing custom interfaces using client libraries (viii Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36

  7. Bug-Fixing and Code-Writing: The Private Provision of Open Source Software

    DEFF Research Database (Denmark)

    Bitzer, Jürgen; Schröder, Philipp

    2002-01-01

    Open source software (OSS) is a public good. A self-interested individual would consider providing such software, if the benefits he gained from having it justified the cost of programming. Nevertheless each agent is tempted to free ride and wait for others to develop the software instead....... This problem is modelled as a war of attrition with complete information, job signaling, repeated contribution to the public good and uncertainty in programming. The resulting game does not feature any delay: software will be provided swiftly, by young, low-cost individuals who gain considerably by signaling...

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

    Science.gov (United States)

    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.

  9. Simulation of neutron multiplicity measurements using Geant4. Open source software for nuclear arms control

    Energy Technology Data Exchange (ETDEWEB)

    Kuett, Moritz

    2016-07-07

    Nuclear arms control, including nuclear safeguards and verification technologies for nuclear disarmament typically use software as part of many different technological applications. This thesis proposes to use three open source criteria for such software, allowing users and developers to have free access to a program, have access to the full source code and be able to publish modifications for the program. This proposition is presented and analyzed in detail, together with the description of the development of ''Open Neutron Multiplicity Simulation'', an open source software tool to simulate neutron multiplicity measurements. The description includes physical background of the method, details of the developed program and a comprehensive set of validation calculations.

  10. For fun and profit a history of the free and open source software revolution

    CERN Document Server

    Tozzi, Christopher

    2017-01-01

    In the 1980s, there was a revolution with far-reaching consequences -- a revolution to restore software freedom. In the early 1980s, after decades of making source code available with programs, most programmers ceased sharing code freely. A band of revolutionaries, self-described "hackers," challenged this new norm by building operating systems with source code that could be freely shared. In For Fun and Profit, Christopher Tozzi offers an account of the free and open source software (FOSS) revolution, from its origins as an obscure, marginal effort by a small group of programmers to the widespread commercial use of open source software today. Tozzi explains FOSS's historical trajectory, shaped by eccentric personalities -- including Richard Stallman and Linus Torvalds -- and driven both by ideology and pragmatism, by fun and profit. Tozzi examines hacker culture and its influence on the Unix operating system, the reaction to Unix's commercialization, and the history of early Linux development. He describes ...

  11. The Role of Free/Libre and Open Source Software in Learning Health Systems.

    Science.gov (United States)

    Paton, C; Karopka, T

    2017-08-01

    Objective: To give an overview of the role of Free/Libre and Open Source Software (FLOSS) in the context of secondary use of patient data to enable Learning Health Systems (LHSs). Methods: We conducted an environmental scan of the academic and grey literature utilising the MedFLOSS database of open source systems in healthcare to inform a discussion of the role of open source in developing LHSs that reuse patient data for research and quality improvement. Results: A wide range of FLOSS is identified that contributes to the information technology (IT) infrastructure of LHSs including operating systems, databases, frameworks, interoperability software, and mobile and web apps. The recent literature around the development and use of key clinical data management tools is also reviewed. Conclusions: FLOSS already plays a critical role in modern health IT infrastructure for the collection, storage, and analysis of patient data. The nature of FLOSS systems to be collaborative, modular, and modifiable may make open source approaches appropriate for building the digital infrastructure for a LHS. Georg Thieme Verlag KG Stuttgart.

  12. Open Source in Education

    Science.gov (United States)

    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…

  13. srsLTE: An Open-Source Platform for LTE Evolution and Experimentation

    OpenAIRE

    2016-01-01

    Testbeds are essential for experimental evaluation as well as for product development. In the context of LTE networks, existing testbed platforms are limited either in functionality and/or extensibility or are too complex to modify and customise. In this work we present srsLTE, an open-source platform for LTE experimentation designed for maximum modularity and code reuse and fully compliant with LTE Release 8. We show the potential of the srsLTE library by extending the baseline code to allow...

  14. Building a Snow Data Management System using Open Source Software (and IDL)

    Science.gov (United States)

    Goodale, C. E.; Mattmann, C. A.; Ramirez, P.; Hart, A. F.; Painter, T.; Zimdars, P. A.; Bryant, A.; Brodzik, M.; Skiles, M.; Seidel, F. C.; Rittger, K. E.

    2012-12-01

    At NASA's Jet Propulsion Laboratory free and open source software is used everyday to support a wide range of projects, from planetary to climate to research and development. In this abstract I will discuss the key role that open source software has played in building a robust science data processing pipeline for snow hydrology research, and how the system is also able to leverage programs written in IDL, making JPL's Snow Data System a hybrid of open source and proprietary software. Main Points: - The Design of the Snow Data System (illustrate how the collection of sub-systems are combined to create a complete data processing pipeline) - Discuss the Challenges of moving from a single algorithm on a laptop, to running 100's of parallel algorithms on a cluster of servers (lesson's learned) - Code changes - Software license related challenges - Storage Requirements - System Evolution (from data archiving, to data processing, to data on a map, to near-real-time products and maps) - Road map for the next 6 months (including how easily we re-used the snowDS code base to support the Airborne Snow Observatory Mission) Software in Use and their Software Licenses: IDL - Used for pre and post processing of data. Licensed under a proprietary software license held by Excelis. Apache OODT - Used for data management and workflow processing. Licensed under the Apache License Version 2. GDAL - Geospatial Data processing library used for data re-projection currently. Licensed under the X/MIT license. GeoServer - WMS Server. Licensed under the General Public License Version 2.0 Leaflet.js - Javascript web mapping library. Licensed under the Berkeley Software Distribution License. Python - Glue code and miscellaneous data processing support. Licensed under the Python Software Foundation License. Perl - Script wrapper for running the SCAG algorithm. Licensed under the General Public License Version 3. PHP - Front-end web application programming. Licensed under the PHP License Version

  15. Improvement of Open Source Software Usability: An Empirical Evaluation from Developers' Perspective

    Directory of Open Access Journals (Sweden)

    Arif Raza

    2010-01-01

    Full Text Available User satisfaction has always been important for software success whether it is Open Source Software (OSS or closed proprietary software. Even though we do not presume that OSS always has poor usability, as there are examples of good usable open source software, it would still be agreed that OSS usability has room for further improvement. This paper presents an empirical investigation to study the impact of some key factors on OSS usability from developers' points of view. This is one of the series of four studies that we are conducting regarding improvement of OSS usability from OSS developers, users, contributors, and industry perspectives. The research model of this empirical investigation studies and establishes the relationship between the key usability factors from developers' perspective and OSS usability. A data set of 106 OSS developers from 18 open source projects of varied size has been used to study the research model. The results of this study provide empirical evidence that the studied key factors play a significant role in improving OSS usability.

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

    Directory of Open Access Journals (Sweden)

    Sivas Deniz

    2016-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  18. BioSig: the free and open source software library for biomedical signal processing.

    Science.gov (United States)

    Vidaurre, Carmen; Sander, Tilmann H; Schlögl, Alois

    2011-01-01

    BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals.

  19. The Image-Guided Surgery ToolKit IGSTK: an open source C++ software toolkit

    Science.gov (United States)

    Cheng, Peng; Ibanez, Luis; Gobbi, David; Gary, Kevin; Aylward, Stephen; Jomier, Julien; Enquobahrie, Andinet; Zhang, Hui; Kim, Hee-su; Blake, M. Brian; Cleary, Kevin

    2007-03-01

    The Image-Guided Surgery Toolkit (IGSTK) is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. The focus of the toolkit is on robustness using a state machine architecture. This paper presents an overview of the project based on a recent book which can be downloaded from igstk.org. The paper includes an introduction to open source projects, a discussion of our software development process and the best practices that were developed, and an overview of requirements. The paper also presents the architecture framework and main components. This presentation is followed by a discussion of the state machine model that was incorporated and the associated rationale. The paper concludes with an example application.

  20. Development of an open source software module for enhanced visualization during MR-guided interstitial gynecologic brachytherapy.

    Science.gov (United States)

    Chen, Xiaojun; Egger, Jan

    2014-01-01

    In 2010, gynecologic malignancies were the 4th leading cause of death in U.S. women and for patients with extensive primary or recurrent disease, treatment with interstitial brachytherapy may be an option. However, brachytherapy requires precise insertion of hollow catheters with introducers into the tumor in order to eradicate the cancer. In this study, a software solution to assist interstitial gynecologic brachytherapy has been investigated and the software has been realized as an own module under (3D) Slicer, which is a free open source software platform for (translational) biomedical research. The developed research module allows on-time processing of intra-operative magnetic resonance imaging (iMRI) data over a direct DICOM connection to a MR scanner. Afterwards follows a multi-stage registration of CAD models of the medical brachytherapy devices (template, obturator) to the patient's MR images, enabling the virtual placement of interstitial needles to assist the physician during the intervention.

  1. Crawling The Web for Libre: Selecting, Integrating, Extending and Releasing Open Source Software

    Science.gov (United States)

    Truslove, I.; Duerr, R. E.; Wilcox, H.; Savoie, M.; Lopez, L.; Brandt, M.

    2012-12-01

    Libre is a project developed by the National Snow and Ice Data Center (NSIDC). Libre is devoted to liberating science data from its traditional constraints of publication, location, and findability. Libre embraces and builds on the notion of making knowledge freely available, and both Creative Commons licensed content and Open Source Software are crucial building blocks for, as well as required deliverable outcomes of the project. One important aspect of the Libre project is to discover cryospheric data published on the internet without prior knowledge of the location or even existence of that data. Inspired by well-known search engines and their underlying web crawling technologies, Libre has explored tools and technologies required to build a search engine tailored to allow users to easily discover geospatial data related to the polar regions. After careful consideration, the Libre team decided to base its web crawling work on the Apache Nutch project (http://nutch.apache.org). Nutch is "an open source web-search software project" written in Java, with good documentation, a significant user base, and an active development community. Nutch was installed and configured to search for the types of data of interest, and the team created plugins to customize the default Nutch behavior to better find and categorize these data feeds. This presentation recounts the Libre team's experiences selecting, using, and extending Nutch, and working with the Nutch user and developer community. We will outline the technical and organizational challenges faced in order to release the project's software as Open Source, and detail the steps actually taken. We distill these experiences into a set of heuristics and recommendations for using, contributing to, and releasing Open Source Software.

  2. Technical Evaluation Report 25: Open Source Software: Two learning management systems

    Directory of Open Access Journals (Sweden)

    Jim Depow

    2003-10-01

    Full Text Available This report is the second in a two-part series about open source (OSS and free software (FS systems in online education. These are rapidly emerging as alternatives to costly proprietary learning management systems (LMS and content management systems (CMS. This report reviews two LMS systems and one CMS system, all developed on the OSS/ FS principle and available to users free of charge.

  3. MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics

    DEFF Research Database (Denmark)

    Mortensen, Peter; Gouw, Joost W; Olsen, Jesper V

    2010-01-01

    Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environment...... on precursor ion intensities, including element labels (e.g., (15)N), residue labels (e.g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net ....

  4. Anser EMT: the first open-source electromagnetic tracking platform for image-guided interventions.

    Science.gov (United States)

    Jaeger, Herman Alexander; Franz, Alfred Michael; O'Donoghue, Kilian; Seitel, Alexander; Trauzettel, Fabian; Maier-Hein, Lena; Cantillon-Murphy, Pádraig

    2017-06-01

    Electromagnetic tracking is the gold standard for instrument tracking and navigation in the clinical setting without line of sight. Whilst clinical platforms exist for interventional bronchoscopy and neurosurgical navigation, the limited flexibility and high costs of electromagnetic tracking (EMT) systems for research investigations mitigate against a better understanding of the technology's characterisation and limitations. The Anser project provides an open-source implementation for EMT with particular application to image-guided interventions. This work provides implementation schematics for our previously reported EMT system which relies on low-cost acquisition and demodulation techniques using both National Instruments and Arduino hardware alongside MATLAB support code. The system performance is objectively compared to other commercial tracking platforms using the Hummel assessment protocol. Positional accuracy of 1.14 mm and angular rotation accuracy of [Formula: see text] are reported. Like other EMT platforms, Anser is susceptible to tracking errors due to eddy current and ferromagnetic distortion. The system is compatible with commercially available EMT sensors as well as the Open Network Interface for image-guided therapy (OpenIGTLink) for easy communication with visualisation and medical imaging toolkits such as MITK and 3D Slicer. By providing an open-source platform for research investigations, we believe that novel and collaborative approaches can overcome the limitations of current EMT technology.

  5. Drug discovery applications for KNIME: an open source data mining platform.

    Science.gov (United States)

    Mazanetz, Michael P; Marmon, Robert J; Reisser, Catherine B T; Morao, Inaki

    2012-01-01

    Technological advances in high-throughput screening methods, combinatorial chemistry and the design of virtual libraries have evolved in the pursuit of challenging drug targets. Over the last two decades a vast amount of data has been generated within these fields and as a consequence data mining methods have been developed to extract key pieces of information from these large data pools. Much of this data is now available in the public domain. This has been helpful in the arena of drug discovery for both academic groups and for small to medium sized enterprises which previously would not have had access to such data resources. Commercial data mining software is sometimes prohibitively expensive and the alternate open source data mining software is gaining momentum in both academia and in industrial applications as the costs of research and development continue to rise. KNIME, the Konstanz Information Miner, has emerged as a leader in open source data mining tools. KNIME provides an integrated solution for the data mining requirements across the drug discovery pipeline through a visual assembly of data workflows drawing from an extensive repository of tools. This review will examine KNIME as an open source data mining tool and its applications in drug discovery.

  6. Open source posturography.

    Science.gov (United States)

    Rey-Martinez, Jorge; Pérez-Fernández, Nicolás

    2016-12-01

    The proposed validation goal of 0.9 in intra-class correlation coefficient was reached with the results of this study. With the obtained results we consider that the developed software (RombergLab) is a validated balance assessment software. The reliability of this software is dependent of the used force platform technical specifications. Develop and validate a posturography software and share its source code in open source terms. Prospective non-randomized validation study: 20 consecutive adults underwent two balance assessment tests, six condition posturography was performed using a clinical approved software and force platform and the same conditions were measured using the new developed open source software using a low cost force platform. Intra-class correlation index of the sway area obtained from the center of pressure variations in both devices for the six conditions was the main variable used for validation. Excellent concordance between RombergLab and clinical approved force platform was obtained (intra-class correlation coefficient =0.94). A Bland and Altman graphic concordance plot was also obtained. The source code used to develop RombergLab was published in open source terms.

  7. Open-source mobile digital platform for clinical trial data collection in low-resource settings

    Science.gov (United States)

    van Dam, Joris; Omondi Onyango, Kevin; Midamba, Brian; Groosman, Nele; Hooper, Norman; Spector, Jonathan; Pillai, Goonaseelan (Colin); Ogutu, Bernhards

    2017-01-01

    Background Governments, universities and pan-African research networks are building durable infrastructure and capabilities for biomedical research in Africa. This offers the opportunity to adopt from the outset innovative approaches and technologies that would be challenging to retrofit into fully established research infrastructures such as those regularly found in high-income countries. In this context we piloted the use of a novel mobile digital health platform, designed specifically for low-resource environments, to support high-quality data collection in a clinical research study. Objective Our primary aim was to assess the feasibility of a using a mobile digital platform for clinical trial data collection in a low-resource setting. Secondarily, we sought to explore the potential benefits of such an approach. Methods The investigative site was a research institute in Nairobi, Kenya. We integrated an open-source platform for mobile data collection commonly used in the developing world with an open-source, standard platform for electronic data capture in clinical trials. The integration was developed using common data standards (Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model), maximising the potential to extend the approach to other platforms. The system was deployed in a pharmacokinetic study involving healthy human volunteers. Results The electronic data collection platform successfully supported conduct of the study. Multidisciplinary users reported high levels of satisfaction with the mobile application and highlighted substantial advantages when compared with traditional paper record systems. The new system also demonstrated a potential for expediting data quality review. Discussion and Conclusions This pilot study demonstrated the feasibility of using a mobile digital platform for clinical research data collection in low-resource settings. Sustainable scientific capabilities and infrastructure are essential to attract and

  8. Release Process on Quality Improvement in Open Source Software Project Management

    Directory of Open Access Journals (Sweden)

    S. Chandra Kumar Mangalam

    2012-01-01

    Full Text Available Problem statement: The Software Industry has changed and developed as a consequence of the impact of Open Source Software (OSS since 1990s. Over a period of time, OSS has evolved in an integrated manner and most of the participants in OSS activity are volunteers. Approach: This coordination form of development has produced a considerable quantity of software; and often, the development method has been viewed as an unorganized and unstructured method of development. Few existing researches deal with the Open Source Software phenomenon from a quality perception point of view and studies where enhancements are possible in the development process. Results: Release Process in OSS plays a key role in most of the OSS projects. As this process is related to the evolution of a quality software from the community of OSS developers, this research attempts to explore the process practices which are employed by OSS developers and examines the problems associated with the development process. The scope of the study is mainly confined to process management in OSS. “Prototype development and iterative development process” approaches were adapted as a methodology. Conclusion/Recommendations: The major finding and conclusion drawn is ‘lack of coordination among developers’ who are geographically isolated. Hence, the study suggests the need for coordination among developers to line up their development process for achieving the goal of the software release process.

  9. Is There Such a Thing as Free Software? The Pros and Cons of Open-Source Software

    Science.gov (United States)

    Trappler, Thomas J.

    2009-01-01

    Today's higher education environment is marked by heightened accountability and decreased budgets. In such an environment, no higher education institution can afford to ignore alternative approaches that could result in more effective and less costly solutions. Open-source software (OSS) can serve as a viable alternative to traditional proprietary…

  10. GNSS-SDR, un ricevitore software completamente open-source pronto per GALILEO

    Directory of Open Access Journals (Sweden)

    Mara Branzanti

    2014-05-01

    Full Text Available With the advent of new in-orbit satellites, the landscape of GNSS is going to change rapidly and thereceiver architectures must continuously be able to exploit the full potential of the forthcoming scenarios. For such reasons, the SDR (Software Defined Receiver philosophy have a great response in the GNSS applications.Here, the first open source SDR software (GNSS-SDR ready for the Galileo constellation is presented, together with its participation in the Google Summer of Code.

  11. Takin: An open-source software for experiment planning, visualisation, and data analysis

    Science.gov (United States)

    Weber, Tobias; Georgii, Robert; Böni, Peter

    Due to their non-trivial resolution function, measurements on triple-axis spectrometers require extra care from the experimentalist in order to obtain optimal results and to avoid unwanted spurious artefacts. We present a free and open-source software system that aims to ease many of the tasks encountered during the planning phase, in the execution and in data treatment of experiments performed on neutron triple-axis spectrometers. The software is currently in use and has been successfully tested at the MLZ, but can be configured to work with other triple-axis instruments and instrument control systems.

  12. GNSS-SDR, un ricevitore software completamente open-source pronto per GALILEO

    OpenAIRE

    Mara Branzanti

    2014-01-01

    With the advent of new in-orbit satellites, the landscape of GNSS is going to change rapidly and thereceiver architectures must continuously be able to exploit the full potential of the forthcoming scenarios. For such reasons, the SDR (Software Defined Receiver) philosophy have a great response in the GNSS applications.Here, the first open source SDR software (GNSS-SDR) ready for the Galileo constellation is presented, together with its participation in the Google Summer of Code.

  13. Auscope: Australian Earth Science Information Infrastructure using Free and Open Source Software

    Science.gov (United States)

    Woodcock, R.; Cox, S. J.; Fraser, R.; Wyborn, L. A.

    2013-12-01

    Since 2005 the Australian Government has supported a series of initiatives providing researchers with access to major research facilities and information networks necessary for world-class research. Starting with the National Collaborative Research Infrastructure Strategy (NCRIS) the Australian earth science community established an integrated national geoscience infrastructure system called AuScope. AuScope is now in operation, providing a number of components to assist in understanding the structure and evolution of the Australian continent. These include the acquisition of subsurface imaging , earth composition and age analysis, a virtual drill core library, geological process simulation, and a high resolution geospatial reference framework. To draw together information from across the earth science community in academia, industry and government, AuScope includes a nationally distributed information infrastructure. Free and Open Source Software (FOSS) has been a significant enabler in building the AuScope community and providing a range of interoperable services for accessing data and scientific software. A number of FOSS components have been created, adopted or upgraded to create a coherent, OGC compliant Spatial Information Services Stack (SISS). SISS is now deployed at all Australian Geological Surveys, many Universities and the CSIRO. Comprising a set of OGC catalogue and data services, and augmented with new vocabulary and identifier services, the SISS provides a comprehensive package for organisations to contribute their data to the AuScope network. This packaging and a variety of software testing and documentation activities enabled greater trust and notably reduced barriers to adoption. FOSS selection was important, not only for technical capability and robustness, but also for appropriate licensing and community models to ensure sustainability of the infrastructure in the long term. Government agencies were sensitive to these issues and Au

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

    Science.gov (United States)

    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

  15. An Enterprise Perspective on Customer Value Propositions for Open Source Software

    Directory of Open Access Journals (Sweden)

    Aparna Shanker

    2012-12-01

    Full Text Available Research on open source software (OSS has examined value creation primarily from the perspective of the individuals and suppliers that create the software. The perspective of enterprise users who use and pay for OSS has been largely neglected so far. Understanding what paying customers want and how to create products and services they value is the cornerstone of any business model. Therefore, research on what enterprise users value in OSS is of paramount importance to OSS solution suppliers; it can be used to create a new customer base and sustain an existing one. This study examines the value of OSS as perceived by enterprise customers. Through an analysis of three literature streams (firm participation in open source software, business models, and customer value, a model on customer value creation was developed. Interviews were conducted with nine decision makers from enterprises that use OSS in operational projects. The key findings of this research are that: i the maturity of the software determines the degree to which customers value their relationship with the supplier; ii customers value differentiating functionality and costs savings; and iii switching costs with OSS depend on the size, complexity, and dependencies of the software itself. This research identifies the points of value that the suppliers of OSS should focus on, and it points to the need for marketing strategies that can demonstrate this value to enterprise customers.

  16. The EDRN knowledge environment: an open source, scalable informatics platform for biological sciences research

    Science.gov (United States)

    Crichton, Daniel; Mahabal, Ashish; Anton, Kristen; Cinquini, Luca; Colbert, Maureen; Djorgovski, S. George; Kincaid, Heather; Kelly, Sean; Liu, David

    2017-05-01

    We describe here the Early Detection Research Network (EDRN) for Cancer's knowledge environment. It is an open source platform built by NASA's Jet Propulsion Laboratory with contributions from the California Institute of Technology, and Giesel School of Medicine at Dartmouth. It uses tools like Apache OODT, Plone, and Solr, and borrows heavily from JPL's Planetary Data System's ontological infrastructure. It has accumulated data on hundreds of thousands of biospecemens and serves over 1300 registered users across the National Cancer Institute (NCI). The scalable computing infrastructure is built such that we are being able to reach out to other agencies, provide homogeneous access, and provide seamless analytics support and bioinformatics tools through community engagement.

  17. Cell_motility: a cross-platform, open source application for the study of cell motion paths

    Directory of Open Access Journals (Sweden)

    Gevaert Kris

    2006-06-01

    Full Text Available Abstract Background Migration is an important aspect of cellular behaviour and is therefore widely studied in cell biology. Numerous components are known to participate in this process in a highly dynamic manner. In order to obtain a better insight in cell migration, mutants or drugs are used and their motive phenotype is then linked with the disturbing factors. One of the typical approaches to study motion paths of individual cells relies on fitting mean square displacements to a persistent random walk function. Since the numerous calculations involved often rely on diverse commercial software packages, the analysis can be expensive, labour-intensive and error-prone work. Additionally, due to the nature of algorithms employed the calculations involved are not readily reproducible without access to the exact software package(s used. Results We here present the cell_motility software, an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data. The application features an intuitive graphical user interface as well as full user and developer documentation and both source and binary files can be freely downloaded from the project website at http://genesis.UGent.be/cell_motility . Conclusion In providing a free, open source software solution for the automated processing of cell motion data, we aim to achieve two important goals: labs can greatly simplify their data analysis pipeline as switching between different computational software packages becomes obsolete (thus reducing the chances for human error during data manipulation and transfer and secondly, to provide scientists in the field with a freely available common platform to perform their analyses, enabling more efficient

  18. An economic perspective on software licenses--open source, maintainers and user-developers

    DEFF Research Database (Denmark)

    Edwards, Kasper

    2005-01-01

    This paper presents a model for understanding behaviour of agents using and/or contributing to open source software. The model illustrates behaviour of agents under three licenses regimes: 1) The GPL, The BSD and 3) The Microsoft EULA. The latter license is not an open source license...... benefit. Agents are divided into firms and individuals, which can be either maintainer or user-developers. A maintainer is an agent responsible for releasing new versions of a program and a user-developer is an agent who use but may also become a developer. It is observed through the model that the three...... licenses induce different incentives and dynamics for maintainer and user-developer and the paper explains, from an economic standpoint, the mechanisms that ensure programs are developed and maintained under the three license regimes....

  19. A Quantitative Study of Social Organization in Open Source Software Communities

    CERN Document Server

    Zanetti, Marcelo Serrano; Scholtes, Ingo; Tessone, Claudio Juan; Schweitzer, Frank

    2012-01-01

    The success of open source projects crucially depends on the voluntary contributions of a sufficiently large community of users. Apart from the mere size of the community, interesting questions arise when looking at the evolution of structural features of collaborations between community members. In this article, we discuss several network analytic proxies that can be used to quantify different aspects of the social organisation in social collaboration networks. We particularly focus on measures that can be related to the cohesiveness of the communities, the distribution of responsibilities and the resilience against turnover of community members. We present a comparative analysis on a large-scale dataset that covers the full history of collaborations between users of 14 major open source software communities. Our analysis covers both aggregate and time-evolving measures and highlights differences in the social organisation across communities. We argue that our results are a promising step towards the definit...

  20. UCVM: An Open Source Software Package for Querying and Visualizing 3D Velocity Models

    Science.gov (United States)

    Gill, D.; Small, P.; Maechling, P. J.; Jordan, T. H.; Shaw, J. H.; Plesch, A.; Chen, P.; Lee, E. J.; Taborda, R.; Olsen, K. B.; Callaghan, S.

    2015-12-01

    Three-dimensional (3D) seismic velocity models provide foundational data for ground motion simulations that calculate the propagation of earthquake waves through the Earth. The Southern California Earthquake Center (SCEC) has developed the Unified Community Velocity Model (UCVM) package for both Linux and OS X. This unique framework provides a cohesive way for querying and visualizing 3D models. UCVM v14.3.0, supports many Southern California velocity models including CVM-S4, CVM-H 11.9.1, and CVM-S4.26. The last model was derived from 26 full-3D tomographic iterations on CVM-S4. Recently, UCVM has been used to deliver a prototype of a new 3D model of central California (CCA) also based on full-3D tomographic inversions. UCVM was used to provide initial plots of this model and will be used to deliver CCA to users when the model is publicly released. Visualizing models is also possible with UCVM. Integrated within the platform are plotting utilities that can generate 2D cross-sections, horizontal slices, and basin depth maps. UCVM can also export models in NetCDF format for easy import into IDV and ParaView. UCVM has also been prototyped to export models that are compatible with IRIS' new Earth Model Collaboration (EMC) visualization utility. This capability allows for user-specified horizontal slices and cross-sections to be plotted in the same 3D Earth space. UCVM was designed to help a wide variety of researchers. It is currently being use to generate velocity meshes for many SCEC wave propagation codes, including AWP-ODC-SGT and Hercules. It is also used to provide the initial input to SCEC's CyberShake platform. For those interested in specific data points, the software framework makes it easy to extract P and S wave propagation speeds and other material properties from 3D velocity models by providing a common interface through which researchers can query earth models for a given location and depth. Also included in the last release was the ability to add small

  1. Getting Open Source Right for Big Data Analytics: Software Sharing, Governance, Collaboration and Most of All, Fun!

    Science.gov (United States)

    Mattmann, C. A.

    2013-12-01

    A wave of open source big data analytic infrastructure is currently shaping government, private sector, and academia. Projects are consuming, adapting, and contributing back to various ecosystems of software e.g., the Apache Hadoop project and its ecosystem of related efforts including Hive, HBase, Pig, Oozie, Ambari, Knox, Tez and Yarn, to name a few; the Berkeley AMPLab stack which includes Spark, Shark, Mesos, Tachyon, BlinkDB, MLBase, and other emerging efforts; MapR and its related stack of technologies, offerings from commercial companies building products around these tools e.g., Hortonworks Data Platform (HDP), Cloudera's CDH project, etc. Though the technologies all offer different capabilities including low latency support/in-memory, versus record oriented file I/O, high availability, support for the Map Reduce programming paradigm or other dataflow/workflow constructs, there is a common thread that binds these products - they are all released under an open source license e.g., Apache2, MIT, BSD, GPL/LGPL, etc.; all thrive in various ecosystems, such as Apache, or Berkeley AMPLab; all are developed collaboratively, and all technologies provide plug in architecture models and methodologies for allowing others to contribute, and participate via various community models. This talk will cover the open source aspects and governance aspects of the aforementioned Big Data ecosystems and point out the differences, subtleties, and implications of those differences. The discussion will be by example, using several national deployments and Big Data initiatives stemming from the Administration including DARPA's XDATA program; NASA's CMAC program; NSF's EarthCube and geosciences BigData projects. Lessons learned from these efforts in terms of the open source aspects of these technologies will help guide the AGU community in their use, deployment and understanding.

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

    Science.gov (United States)

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

    2015-12-01

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

  3. radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar.

    Science.gov (United States)

    Taylor, Philip D; Brzustowski, John M; Matkovich, Carolyn; Peckford, Michael L; Wilson, Dave

    2010-10-26

    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. 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. Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets.

  4. Developing an Open Source, Reusable Platform for Distributed Collaborative Information Management in the Early Detection Research Network

    Science.gov (United States)

    Hart, Andrew F.; Verma, Rishi; Mattmann, Chris A.; Crichton, Daniel J.; Kelly, Sean; Kincaid, Heather; Hughes, Steven; Ramirez, Paul; Goodale, Cameron; Anton, Kristen; hide

    2012-01-01

    For the past decade, the NASA Jet Propulsion Laboratory, in collaboration with Dartmouth University has served as the center for informatics for the Early Detection Research Network (EDRN). The EDRN is a multi-institution research effort funded by the U.S. National Cancer Institute (NCI) and tasked with identifying and validating biomarkers for the early detection of cancer. As the distributed network has grown, increasingly formal processes have been developed for the acquisition, curation, storage, and dissemination of heterogeneous research information assets, and an informatics infrastructure has emerged. In this paper we discuss the evolution of EDRN informatics, its success as a mechanism for distributed information integration, and the potential sustainability and reuse benefits of emerging efforts to make the platform components themselves open source. We describe our experience transitioning a large closed-source software system to a community driven, open source project at the Apache Software Foundation, and point to lessons learned that will guide our present efforts to promote the reuse of the EDRN informatics infrastructure by a broader community.

  5. IDENTIFICATION AND QUANTIFICATION OF FACTORS AFFECTING REUSABILITY OF OPEN SOURCE SOFTWARE IN REUSE-INTENSIVE SOFTWARE DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Aized Amin Soof

    2017-02-01

    Full Text Available Open Source Software (OSS is one of the emerging areas in software engineering. Reuse of OSS is employed in reuse-intensive software development such as Component Based Software Development and Software Product Lines. OSS is gaining the interest of the software development community due to its enormous benefits. The context of this study is the identification and quantification of factors affecting reusability of OSS in reuse-intensive software development. The use of OSS in the systematic reuse of software, such as in Software Product Lines (SPLs is a new phenomenon. Therefore, the aim of this study is to identify and quantify the factors affecting the reusability of OSS in reuse-intensive software development, especially for SPLs. In this study, a mixed methods based approach is employed to identify the factors affecting the reusability of OSS. Interviews are conducted with experts in this field as the qualitative part, followed by a survey, experiments and a statistical analysis. The factors identified during the interviews are ranked by software engineers in a survey. Experiment is conducted to assess the reusability of open source packages. The factors are validated by conducting a statistical analysis of the results of the experiments. A set of nine factors were identified as a result of the qualitative study. A model was formed on the basis of the findings of interviews and a survey. It includes five factors. These were statistically analyzed by applying the model to 77 open source packages. A set of nine factors were identified as affecting reusability of OSS in a reuse-intensive development environment. Five of them were validated at the code level. The statistical results show a positive correlation between reusability and the identified factors.

  6. The State of Open Source Electronic Health Record Projects: A Software Anthropology Study.

    Science.gov (United States)

    Alsaffar, Mona; Yellowlees, Peter; Odor, Alberto; Hogarth, Michael

    2017-02-24

    Electronic health records (EHR) are a key tool in managing and storing patients' information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers' motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects. This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers. This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were "certified" EHRs. Health care F/OSS developers were also surveyed using an online survey. At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7% (26/101) of EHR F/OSS developers are, or have been

  7. The State of Open Source Electronic Health Record Projects: A Software Anthropology Study

    Science.gov (United States)

    2017-01-01

    Background Electronic health records (EHR) are a key tool in managing and storing patients’ information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers’ motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects. Objective This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers. Methods This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were “certified” EHRs. Health care F/OSS developers were also surveyed using an online survey. Results At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7% (26

  8. A Tour of Big Data, Open Source Data Management Technologies from the Apache Software Foundation

    Science.gov (United States)

    Mattmann, C. A.

    2012-12-01

    The Apache Software Foundation, a non-profit foundation charged with dissemination of open source software for the public good, provides a suite of data management technologies for distributed archiving, data ingestion, data dissemination, processing, triage and a host of other functionalities that are becoming critical in the Big Data regime. Apache is the world's largest open source software organization, boasting over 3000 developers from around the world all contributing to some of the most pervasive technologies in use today, from the HTTPD web server that powers a majority of Internet web sites to the Hadoop technology that is now projected at over a $1B dollar industry. Apache data management technologies are emerging as de facto off-the-shelf components for searching, distributing, processing and archiving key science data sets both geophysical, space and planetary based, all the way to biomedicine. In this talk, I will give a virtual tour of the Apache Software Foundation, its meritocracy and governance structure, and also its key big data technologies that organizations can take advantage of today and use to save cost, schedule, and resources in implementing their Big Data needs. I'll illustrate the Apache technologies in the context of several national priority projects, including the U.S. National Climate Assessment (NCA), and in the International Square Kilometre Array (SKA) project that are stretching the boundaries of volume, velocity, complexity, and other key Big Data dimensions.

  9. Lessons in modern digital field geology: Open source software, 3D techniques, and the new world of digital mapping

    Science.gov (United States)

    Pavlis, Terry; Hurtado, Jose; Langford, Richard; Serpa, Laura

    2014-05-01

    Although many geologists refuse to admit it, it is time to put paper-based geologic mapping into the historical archives and move to the full potential of digital mapping techniques. For our group, flat map digital geologic mapping is now a routine operation in both research and instruction. Several software options are available, and basic proficiency with the software can be learned in a few hours of instruction and practice. The first practical field GIS software, ArcPad, remains a viable, stable option on Windows-based systems. However, the vendor seems to be moving away from ArcPad in favor of mobile software solutions that are difficult to implement without GIS specialists. Thus, we have pursued a second software option based on the open source program QGIS. Our QGIS system uses the same shapefile-centric data structure as our ArcPad system, including similar pop-up data entry forms and generic graphics for easy data management in the field. The advantage of QGIS is that the same software runs on virtually all common platforms except iOS, although the Android version remains unstable as of this writing. A third software option we are experimenting with for flat map-based field work is Fieldmove, a derivative of the 3D-capable program Move developed by Midland Valley. Our initial experiments with Fieldmove are positive, particularly with the new, inexpensive (problem. As spatial databases evolve these 3D models should be readily importable into the database.

  10. A multi-purpose open-source triggering platform for magnetic resonance.

    Science.gov (United States)

    Ruytenberg, T; Webb, A G; Beenakker, J W M

    2014-10-01

    Many MR scans need to be synchronised with external events such as the cardiac or respiratory cycles. For common physiological functions commercial trigger equipment exists, but for more experimental inputs these are not available. This paper describes the design of a multi-purpose open-source trigger platform for MR systems. The heart of the system is an open-source Arduino Due microcontroller. This microcontroller samples an analogue input and digitally processes these data to determine the trigger. The output of the microcontroller is programmed to mimic a physiological signal which is fed into the electrocardiogram (ECG) or pulse oximeter port of MR scanner. The microcontroller is connected to a Bluetooth dongle that allows wireless monitoring and control outside the scanner room. This device can be programmed to generate a trigger based on various types of input. As one example, this paper describes how it can be used as an acoustic cardiac triggering unit. For this, a plastic stethoscope is connected to a microphone which is used as an input for the system. This test setup was used to acquire retrospectively-triggered cardiac scans in ten volunteers. Analysis showed that this platform produces a reliable trigger (>99% triggers are correct) with a small average 8 ms variation between the exact trigger points.

  11. Adopting Open-Source Software Applications in U. S. Higher Education: A Cross-Disciplinary Review of the Literature

    Science.gov (United States)

    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…

  12. Application of Open Source Software by the Lunar Mapping and Modeling Project

    Science.gov (United States)

    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. A glass slipper? For cash-strapped organizations with EMR dreams, open-source software may be a perfect fit.

    Science.gov (United States)

    Hagland, Mark

    2009-08-01

    Open-source EMR software is a potential, and relatively economical, option for hospital organizations that can't afford proprietary commercial EMR software, or whose leaders want a non-commercial option. While access to VistA's source code is free, any hospital organization seeking to implement commercialized VistA will need assistance from one of the vendors supporting that software. Implementing open-source is a bit closer to self-development than to implementing proprietary, commercial EMR software. CCHIT recently announced it will introduce new channels for certification of open-source EMR software, addressing the concerns of those in healthcare who want to pursue the open-source option while also applying for funding under ARRA-HITECH.

  14. VOLTTRON: An Open-Source Software Platform of the Future

    Energy Technology Data Exchange (ETDEWEB)

    Katipamula, Srinivas; Haack, Jereme; Hernandez, George; Akyol, Bora; Hagerman, Joseph

    2016-12-01

    Buildings consume over 30% of the total primary energy consumed worldwide and contribute to a third of the world greenhouse gas (GHG) emissions. In the US, buildings consume over 40% of total energy and contribute to almost 38% in GHG emissions. In addition, buildings in the US consume over 75% of electricity generated. The need to mitigate climate change is driving efforts to make the US generation cleaner, which has given new impetus for improving the operating efficiency of buildings at scale and increasing the hosting capacity of distributed renewable generation. Because these renewable generation technologies are variable in nature, they create significant short- and long-term imbalance between supply and demand.

  15. High Resolution Topography of Polar Regions from Commercial Satellite Imagery, Petascale Computing and Open Source Software

    Science.gov (United States)

    Morin, Paul; Porter, Claire; Cloutier, Michael; Howat, Ian; Noh, Myoung-Jong; Willis, Michael; Kramer, WIlliam; Bauer, Greg; Bates, Brian; Williamson, Cathleen

    2017-04-01

    Surface topography is among the most fundamental data sets for geosciences, essential for disciplines ranging from glaciology to geodynamics. Two new projects are using sub-meter, commercial imagery licensed by the National Geospatial-Intelligence Agency and open source photogrammetry software to produce a time-tagged 2m posting elevation model of the Arctic and an 8m posting reference elevation model for the Antarctic. When complete, this publically available data will be at higher resolution than any elevation models that cover the entirety of the Western United States. These two polar projects are made possible due to three equally important factors: 1) open-source photogrammetry software, 2) petascale computing, and 3) sub-meter imagery licensed to the United States Government. Our talk will detail the technical challenges of using automated photogrammetry software; the rapid workflow evolution to allow DEM production; the task of deploying the workflow on one of the world's largest supercomputers; the trials of moving massive amounts of data, and the management strategies the team needed to solve in order to meet deadlines. Finally, we will discuss the implications of this type of collaboration for future multi-team use of leadership-class systems such as Blue Waters, and for further elevation mapping.

  16. A Survey of Usability Practices in Free/Libre/Open Source Software

    Science.gov (United States)

    Paul, Celeste Lyn

    A review of case studies about usability in eight Free/Libre/Open Source Software (FLOSS) projects showed that an important issue regarding a usability initiative in the project was the lack of user research. User research is a key component in the user-centered design (UCD) process and a necessary step for creating usable products. Reasons why FLOSS projects suffered from a lack of user research included poor or unclear project leadership, cultural differences between developer and designers, and a lack of usability engineers. By identifying these critical issues, the FLOSS usability community can begin addressing problems in the efficacy of usability activities and work towards creating more usable FLOSS products.

  17. CalVR: an advanced open source virtual reality software framework

    Science.gov (United States)

    Schulze, Jürgen P.; Prudhomme, Andrew; Weber, Philip; DeFanti, Thomas A.

    2013-03-01

    We developed CalVR because none of the existing virtual reality software frameworks offered everything we needed, such as cluster-awareness, multi-GPU capability, Linux compatibility, multi-user support, collaborative session support, or custom menu widgets. CalVR combines features from multiple existing VR frameworks into an open-source system, which we use in our laboratory on a daily basis, and for which dozens of VR applications have already been written at UCSD but also other research laboratories world-wide. In this paper, we describe the philosophy behind CalVR, its standard and unique features and functions, its programming interface, and its inner workings.

  18. Reproducible Matrix Deposition for MALDI MSI Based on Open-Source Software and Hardware.

    Science.gov (United States)

    Stoeckli, Markus; Staab, Dieter

    2015-06-01

    The new open-source software and hardware matrix deposition device named iMatrixSpray was optimized and specified for homogeneity, reproducibility, and sensitivity in MS imaging experiments. The results confirm the design claims, with the device delivering uniform coatings with a constant quality from experiment to experiment. The robustness in combination with the open design allows developing and sharing of matrix deposition and sample preparation protocols between labs. This tool therefore enables researchers to enter the field of MALDI MSI without previous experience in matrix coating.

  19. APERO, AN OPEN SOURCE BUNDLE ADJUSMENT SOFTWARE FOR AUTOMATIC CALIBRATION AND ORIENTATION OF SET OF IMAGES

    Directory of Open Access Journals (Sweden)

    M. Pierrot Deseilligny

    2012-09-01

    Full Text Available IGN has developed a set of photogrammetric tools, APERO and MICMAC, for computing 3D models from set of images. This software, developed initially for its internal needs are now delivered as open source code. This paper focuses on the presentation of APERO the orientation software. Compared to some other free software initiatives, it is probably more complex but also more complete, its targeted user is rather professionals (architects, archaeologist, geomophologist than people. APERO uses both computer vision approach for estimation of initial solution and photogrammetry for a rigorous compensation of the total error; it has a large library of parametric model of distortion allowing a precise modelization of all the kind of pinhole camera we know, including several model of fish-eye; there is also several tools for geo-referencing the result. The results are illustrated on various application, including the data-set of 3D-Arch workshop.

  20. Categorizing Bugs with Social Networks: A Case Study on Four Open Source Software Communities

    CERN Document Server

    Zanetti, Marcelo Serrano; Tessone, Claudio Juan; Schweitzer, Frank

    2013-01-01

    Efficient bug triaging procedures are an important precondition for successful collaborative software engineering projects. Triaging bugs can become a laborious task particularly in open source software (OSS) projects with a large base of comparably inexperienced part-time contributors. In this paper, we propose an efficient and practical method to identify valid bug reports which a) refer to an actual software bug, b) are not duplicates and c) contain enough information to be processed right away. Our classification is based on nine measures to quantify the social embeddedness of bug reporters in the collaboration network. We demonstrate its applicability in a case study, using a comprehensive data set of more than 700,000 bug reports obtained from the Bugzilla installation of four major OSS communities, for a period of more than ten years. For those projects that exhibit the lowest fraction of valid bug reports, we find that the bug reporters' position in the collaboration network is a strong indicator for ...

  1. Apero, AN Open Source Bundle Adjusment Software for Automatic Calibration and Orientation of Set of Images

    Science.gov (United States)

    Pierrot Deseilligny, M.; Clery, I.

    2011-09-01

    IGN has developed a set of photogrammetric tools, APERO and MICMAC, for computing 3D models from set of images. This software, developed initially for its internal needs are now delivered as open source code. This paper focuses on the presentation of APERO the orientation software. Compared to some other free software initiatives, it is probably more complex but also more complete, its targeted user is rather professionals (architects, archaeologist, geomophologist) than people. APERO uses both computer vision approach for estimation of initial solution and photogrammetry for a rigorous compensation of the total error; it has a large library of parametric model of distortion allowing a precise modelization of all the kind of pinhole camera we know, including several model of fish-eye; there is also several tools for geo-referencing the result. The results are illustrated on various application, including the data-set of 3D-Arch workshop.

  2. Towards easing the configuration and new team member accommodation for open source software based portals

    Science.gov (United States)

    Fu, L.; West, P.; Zednik, S.; Fox, P. A.

    2013-12-01

    For simple portals such as vocabulary based services, which contain small amounts of data and require only hyper-textual representation, it is often an overkill to adopt the whole software stack of database, middleware and front end, or to use a general Web development framework as the starting point of development. Directly combining open source software is a much more favorable approach. However, our experience with the Coastal and Marine Spatial Planning Vocabulary (CMSPV) service portal shows that there are still issues such as system configuration and accommodating a new team member that need to be handled carefully. In this contribution, we share our experience in the context of the CMSPV portal, and focus on the tools and mechanisms we've developed to ease the configuration job and the incorporation process of new project members. We discuss the configuration issues that arise when we don't have complete control over how the software in use is configured and need to follow existing configuration styles that may not be well documented, especially when multiple pieces of such software need to work together as a combined system. As for the CMSPV portal, it is built on two pieces of open source software that are still under rapid development: a Fuseki data server and Epimorphics Linked Data API (ELDA) front end. Both lack mature documentation and tutorials. We developed comparison and labeling tools to ease the problem of system configuration. Another problem that slowed down the project is that project members came and went during the development process, so new members needed to start with a partially configured system and incomplete documentation left by old members. We developed documentation/tutorial maintenance mechanisms based on our comparison and labeling tools to make it easier for the new members to be incorporated into the project. These tools and mechanisms also provided benefit to other projects that reused the software components from the CMSPV

  3. Free and Open Source Software underpinning the European Forest Data Centre

    Science.gov (United States)

    Rodriguez Aseretto, Dario; Di Leo, Margherita; de Rigo, Daniele; Corti, Paolo; McInerney, Daniel; Camia, Andrea; San-Miguel-Ayanz, Jesús

    2013-04-01

    forest data and information (see also [18]). A set of web-based tools allow accessing the information located in EFDAC. The following applications - running on GNU/Linux platforms - are the core elements of EFDAC: In (a.1) a metadata client allows users to search for EFDAC related spatial datasets while (a.2) is a customized web map service that allows the user to visualize, navigate and query available maps and derived geo-datasets on several forest-related topics. The database system currently relies on ORACLE and PostgreSQL [24] with PostGIS [25]. EFFIS (a.3) [26-33] is a comprehensive system covering the full cycle of forest-fire management. The system supports forest-fire prevention and fighting in Europe, North Africa and Middle East countries through the provision of timely and reliable information on forest-fires [29,30,32]. Within EFFIS, UMN Mapserver [34] is used for the management and publication of the fire behavior forecast and the other fire-related layers in a wide range of formats including INSPIRE and Open Geospatial Consortium (OGC) standards such as: Transdisciplinary modelling research. The EFDAC portal [39] provides data and information which rely on coordinated research [40-50] on wide-scale transdisciplinary modelling for environment (WSTMe) [51]. This contributed to advanced computational modelling approaches such as morphological spatial pattern analysis (MSPA) [52-54] and geospatial semantic array programming (GeoSemAP) [51,55]. FOSS is here essential. For example, GeoSemAP is based on a semantically-enhanced [56,57] joint use of geospatial and array programming [58] tools (c) where semantic transparency also implies FOSS use. References Hahn, R. W., Bessen, J., Evans, D. S., Lessig, L., Smith, B. L., 2009. Government Policy Toward Open Source Software. Hahn, R. W. (Ed.). ISBN: 0-8157-3393-3 http://dx.doi.org/10.2139/ssrn Free Software Foundation, 2012. What is free software? http://www.gnu.org/philosophy/free-sw.html (revision 1.118 archived at

  4. Open source platform for collaborative construction of wearable sensor datasets for human motion analysis and an application for gait analysis.

    Science.gov (United States)

    Llamas, César; González, Manuel A; Hernández, Carmen; Vegas, Jesús

    2016-10-01

    Nearly every practical improvement in modeling human motion is well founded in a properly designed collection of data or datasets. These datasets must be made publicly available for the community could validate and accept them. It is reasonable to concede that a collective, guided enterprise could serve to devise solid and substantial datasets, as a result of a collaborative effort, in the same sense as the open software community does. In this way datasets could be complemented, extended and expanded in size with, for example, more individuals, samples and human actions. For this to be possible some commitments must be made by the collaborators, being one of them sharing the same data acquisition platform. In this paper, we offer an affordable open source hardware and software platform based on inertial wearable sensors in a way that several groups could cooperate in the construction of datasets through common software suitable for collaboration. Some experimental results about the throughput of the overall system are reported showing the feasibility of acquiring data from up to 6 sensors with a sampling frequency no less than 118Hz. Also, a proof-of-concept dataset is provided comprising sampled data from 12 subjects suitable for gait analysis.

  5. IBIS: an OR ready open-source platform for image-guided neurosurgery.

    Science.gov (United States)

    Drouin, Simon; Kochanowska, Anna; Kersten-Oertel, Marta; Gerard, Ian J; Zelmann, Rina; De Nigris, Dante; Bériault, Silvain; Arbel, Tal; Sirhan, Denis; Sadikot, Abbas F; Hall, Jeffery A; Sinclair, David S; Petrecca, Kevin; DelMaestro, Rolando F; Collins, D Louis

    2017-03-01

    Navigation systems commonly used in neurosurgery suffer from two main drawbacks: (1) their accuracy degrades over the course of the operation and (2) they require the surgeon to mentally map images from the monitor to the patient. In this paper, we introduce the Intraoperative Brain Imaging System (IBIS), an open-source image-guided neurosurgery research platform that implements a novel workflow where navigation accuracy is improved using tracked intraoperative ultrasound (iUS) and the visualization of navigation information is facilitated through the use of augmented reality (AR). The IBIS platform allows a surgeon to capture tracked iUS images and use them to automatically update preoperative patient models and plans through fast GPU-based reconstruction and registration methods. Navigation, resection and iUS-based brain shift correction can all be performed using an AR view. IBIS has an intuitive graphical user interface for the calibration of a US probe, a surgical pointer as well as video devices used for AR (e.g., a surgical microscope). The components of IBIS have been validated in the laboratory and evaluated in the operating room. Image-to-patient registration accuracy is on the order of [Formula: see text] and can be improved with iUS to a median target registration error of 2.54 mm. The accuracy of the US probe calibration is between 0.49 and 0.82 mm. The average reprojection error of the AR system is [Formula: see text]. The system has been used in the operating room for various types of surgery, including brain tumor resection, vascular neurosurgery, spine surgery and DBS electrode implantation. The IBIS platform is a validated system that allows researchers to quickly bring the results of their work into the operating room for evaluation. It is the first open-source navigation system to provide a complete solution for AR visualization.

  6. Open Source Software & Digital Libraries%开放源码软件与数字图书馆

    Institute of Scientific and Technical Information of China (English)

    黄玉梅

    2002-01-01

    The paper introduces Open Source Software(OSS)and its similarity to the library,discusses the benefits of and the problems in using OSS in the digital library, and lists the impact of OSS on librarians.

  7. VIVO Open Source Software: Connecting Facilities to Promote Discovery and Further Research.

    Science.gov (United States)

    Gross, M. B.; Rowan, L. R.; Mayernik, M. S.; Daniels, M. D.; Stott, D.; Allison, J.; Maull, K. E.; Krafft, D. B.; Khan, H.

    2016-12-01

    EarthCollab (http://earthcube.org/group/earthcollab), a National Science Foundation (NSF) EarthCube Building Block project, has adapted an open source semantic web application, VIVO, for use within the earth science domain. EarthCollab is a partnership between UNAVCO, an NSF facility supporting research through geodetic services, the Earth Observing Laboratory (EOL) at the National Center for Atmospheric Research (NCAR), and Cornell University, where VIVO was created to highlight the scholarly output of researchers at universities. Two public sites have been released: Connect UNAVCO (connect.unavco.org) and Arctic Data Connects (vivo.eol.ucar.edu). The core VIVO software and ontology have been extended to work better with concepts necessary for capturing work within UNAVCO's and EOL's province such as principal investigators for continuous GPS/GNSS stations at UNAVCO and keywords describing cruise datasets at EOL. The sites increase discoverability of large and diverse data archives by linking data with people, research, and field projects. Disambiguation is a major challenge when using VIVO and open data when "anyone can say anything about anything." Concepts and controlled vocabularies help to build consistent and easily searchable connections within VIVO. We use aspects of subject heading services such as FAST and LOC, as well as AGU and GSA fields of research and subject areas to reveal connections, especially with VIVO instances at other institutions. VIVO works effectively with persistent IDs and the projects strive to utilize publication and data DOIs, ORCIDs for people, and ISNI and GRID for organizations. ORCID, an open source project, is very useful for disambiguation and unlike other identifier systems for people developed by publishers, makes public data available via an API. VIVO utilizes Solr and Freemarker, which are open source search engine and templating technologies, respectively. Additionally, a handful of popular open source libraries and

  8. Contribution to Asterisk Open Source Project

    OpenAIRE

    González Martín, Sergio

    2009-01-01

    With this final master thesis we are going to contribute to the Asterisk open source project. Asterisk is an open source project that started with the main objective of develop an IP telephony platform, completely based on Software (so not hardware dependent) and under an open license like GPL. This project was started on 1999 by the software engineer Mark Spencer at Digium. The main motivation of that open source project was that the telecommunications sector is lack of open solutions, and m...

  9. Open source non-invasive prenatal testing platform and its performance in a public health laboratory.

    Science.gov (United States)

    Johansen, Peter; Richter, Stine R; Balslev-Harder, Marie; Miltoft, Caroline B; Tabor, Ann; Duno, Morten; Kjaergaard, Susanne

    2016-06-01

    The objective of this study was to introduce non-invasive prenatal testing (NIPT) for fetal autosomal trisomies and gender in a Danish public health setting, using semi-conductor sequencing and published open source scripts for analysis. Plasma-derived DNA from a total of 375 pregnant women (divided into three datasets) was whole-genome sequenced on the Ion Proton™ platform and analyzed using a pipeline based on WISECONDOR for fetal autosomal aneuploidy detection and SeqFF for fetal DNA fraction estimation. We furthermore validated a fetal sex determination analysis. The pipeline correctly detected 27/27 trisomy 21, 4/4 trisomy 18, and 3/3 trisomy 13 fetuses. Neither false negatives nor false positives (chromosomes 13, 18, and 21) were observed in our validation dataset. Fetal sex was identified correctly in all but one triploid fetus (172/173). SeqFF showed a strong correlation (R(2)  = 0.72) to Y-chromosomal content of the male fetus samples. We have implemented NIPT into Danish health care using published open source scripts for autosomal aneuploidy detection and fetal DNA fraction estimation showing excellent false negative and false positive rates. SeqFF provides a good estimation of fetal DNA fraction. This coupled with an analysis of fetal sex that provides a complete NIPT workflow, which may easily be adapted for implementation in other public health laboratories. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.

  10. Social.Water--Open Source Citizen Science Software for CrowdHydrology

    Science.gov (United States)

    Fienen, M. N.; Lowry, C.

    2013-12-01

    CrowdHydrology is a crowd-sourced citizen science project in which passersby near streams are encouraged to read a gage and send an SMS (text) message with the water level to a number indicated on a sign. The project was initially started using free services such as Google Voice, Gmail, and Google Maps to acquire and present the data on the internet. Social.Water is open-source software, using Python and JavaScript, that automates the acquisition, categorization, and presentation of the data. Open-source objectives pervade both the project and the software as the code is hosted at Github, only free scripting codes are used, and any person or organization can install a gage and join the CrowdHydrology network. In the first year, 10 sites were deployed in upstate New York, USA. In the second year, expansion to 44 sites throughout the upper Midwest USA was achieved. Comparison with official USGS and academic measurements have shown low error rates. Citizen participation varies greatly from site to site, so surveys or other social information is sought for insight into why some sites experience higher rates of participation than others.

  11. An open source software project for obstetrical procedure scheduling and occupancy analysis.

    Science.gov (United States)

    Isken, Mark W; Ward, Timothy J; Littig, Steven J

    2011-03-01

    Increases in the rate of births via cesarean section and induced labor have led to challenging scheduling and capacity planning problems for hospital inpatient obstetrical units. We present occupancy and patient scheduling models to help address these challenges. These patient flow models can be used to explore the relationship between procedure scheduling practices and the resulting occupancy on inpatient obstetrical units such as labor and delivery and postpartum. The models capture numerous important characteristics of inpatient obstetrical patient flow such as time of day and day of week dependent arrivals and length of stay, multiple patient types and clinical interventions, and multiple patient care units with inter-unit patient transfers. We have used these models in several projects at different hospitals involving design of procedure scheduling templates and analysis of inpatient obstetrical capacity. In the development of these models, we made heavy use of open source software tools and have released the entire project as a free and open source model and software toolkit.

  12. Clinical records anonymisation and text extraction (CRATE): an open-source software system.

    Science.gov (United States)

    Cardinal, Rudolf N

    2017-04-26

    Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.

  13. PASSIM – an open source software system for managing information in biomedical studies

    Directory of Open Access Journals (Sweden)

    Neogi Sudeshna

    2007-02-01

    Full Text Available Abstract Background One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS. Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management. Results We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project. Conclusion The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.

  14. Campus Monitoring System for Annamalai University by Open Source Software and Modern Surveying Application

    Directory of Open Access Journals (Sweden)

    K.R. VENKATESH

    2016-06-01

    Full Text Available In urban planning management, the third dimension is becoming a necessity. Using 3D GIS model offers a flexible, interactive system while providing one of the best visual interpretation of data, which supports planning and decision processes for the planner. GIS-based maps and visualizations greatly assist in understanding information about the location. Since, interpretation of 3D data is cost effective using open source software than any other to do analysis. In this study, across multiple domains, 3D models were utilized to understand and document the state of the art. An effort has been taken to overcome this problem and to develop the Campus Monitoring System. In particular, a campus map was proposed which covers four main aspects: Geo referencing, 2D smart campus map, vertical laser measurements by spike application and 3D visualization with attribute data. Finally, the results, problems and limitations of the achieved products were investigated in order to evaluate and confirm the reliability and convenience of open source software.

  15. Web-Based Data Visualization and Analysis using HydroShare and the Open Source Tethys Platform

    Science.gov (United States)

    Ames, D. P.; Li, Z.; Qiao, X.; Tarboton, D. G.; Idaszak, R.; Horsburgh, J. S.; Merwade, V.; Miles, B.; Swain, N. R.; Lineberger, R.; Rice, E.

    2015-12-01

    HydroShare is a collaborative environment developed to make it easy for the hydrology community to share and publish data, models, and analytical tools. HydroShare is deployed at http://www.hydroshare.org/ with capabilities for uploading and publishing any type of hydrologic digital data as a Library of Congress-BagIt formatted digital "resource" object. Examples of supported hydrologic data resources include: geographic rasters, NetCDF multi-dimensional data, time series, model programs, and model instances. To support web-based visualization and analysis of these digital objects, we have deployed an instance of the open source Tethys Platform web app hosting system at http://apps.hydroshare.org/. Tethys is a web development platform that provides web application developers with a Python-based programming environment for building and hosting hydrologic "web apps" - loosely defined as single purpose, task-oriented, user-friendly, web-accessible applications. Tethys Platform includes an open source GIS software suite comprised of GeoServer, PostGIS, 52-North, GRASS, R, OpenLayers, HighCharts, and other useful tools to support custom web app development. This presentation will introduce the Web App resource type in HydroShare and its custom metadata elements - illustrating how we used HydroShare itself as a catalog for web apps. The approach uses loose coupling and web services to link HydroShare resources with web apps in a scalable way that can expand to third party web apps. Example Tethys-based web app resources presently available in HydroShare will be highlighted.

  16. ANALISIS FAKTOR-FAKTOR YANG MEMPENGARUHI PERILAKU PENGGUNA UNTUK MENDORONG PENGGUNAAN OPEN SOURCE SOFTWARE DAN IMPLIKASI MANAJERIALNYA

    OpenAIRE

    Erry Ricardo Nurzal; E. Gumbira Sa’id; Heny K Daryanto; Hartoyo Hartoyo

    2011-01-01

    This study has two objectives namely (1) To measure the acceptance of Open Source Software, (2) To determine whether OSS quality, OSS availability, personal innovativeness, gender, income, social influence, cultural affinity and type of university influence users using or not using Open Source Software.Data used in this research were primary data. The data collected were data from informatic engineering or computer science students using OSS in Bogor Agricultural University, Bandung Institu...

  17. An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Kühne Titus

    2010-07-01

    Full Text Available Abstract Background In magnetic resonance (MR imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. Results After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. Conclusions MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet.

  18. Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

    Science.gov (United States)

    Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

    2015-12-01

    Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical

  19. Metronome LKM: An open source virtual keyboard driver to measure experiment software latencies.

    Science.gov (United States)

    Garaizar, Pablo; Vadillo, Miguel A

    2017-09-15

    Experiment software is often used to measure reaction times gathered with keyboards or other input devices. In previous studies, the accuracy and precision of time stamps has been assessed through several means: (a) generating accurate square wave signals from an external device connected to the parallel port of the computer running the experiment software, (b) triggering the typematic repeat feature of some keyboards to get an evenly separated series of keypress events, or (c) using a solenoid handled by a microcontroller to press the input device (keyboard, mouse button, touch screen) that will be used in the experimental setup. Despite the advantages of these approaches in some contexts, none of them can isolate the measurement error caused by the experiment software itself. Metronome LKM provides a virtual keyboard to assess an experiment's software. Using this open source driver, researchers can generate keypress events using high-resolution timers and compare the time stamps collected by the experiment software with those gathered by Metronome LKM (with nanosecond resolution). Our software is highly configurable (in terms of keys pressed, intervals, SysRq activation) and runs on 2.6-4.8 Linux kernels.

  20. Cross-Participants : fostering design-use mediation in an Open Source Software community

    CERN Document Server

    Barcellini, Flore; Burkhardt, Jean-Marie

    2007-01-01

    Motivation - This research aims at investigating emerging roles and forms of participation fostering design-use mediation during the Open Source Software design process Research approach - We compare online interactions for a successful "pushed-by-users" design process with unsuccessful previous proposals. The methodology developed, articulate structural analyses of the discussions (organization of discussions, participation) to actions to the code and documentation made by participants to the project. We focus on the useroriented and the developer-oriented mailing-lists of the Python project. Findings/Design - We find that key-participants, the cross-participants, foster the design process and act as boundary spanners between the users and the developers' communities. Research limitations/Implications - These findings can be reinforced developing software to automate the structural analysis of discussions and actions to the code and documentation. Further analyses, supported by these tools, will be necessary...

  1. Aristotle vs. Ringelmann: A response to Scholtes et al. on Superlinear Production in Open Source Software

    CERN Document Server

    Maillart, Thomas

    2016-01-01

    On December 19, 2015, Scholtes et al.'s work was published online in the Journal of Empirical Software Engineering, in which they challenged the exciting findings that we (with another co-author) presented in 2014, showing that open source software production exhibits superlinear productive bursts. We presented our findings as the first quantification of Aristotle's famous adage: The whole is more than the sum of its parts. In contrast, Scholtes et al. referred to Maximilien Ringelmann, a French agricultural engineer (1861-1931) who discovered the tendency for individual members of a group to become increasingly less productive as the size of their group increases. Since Ringelmann, the topic of collective intelligence has interested numbers of researchers in social sciences, as well as practitioners in management aiming at improving the performance of their team. And indeed, in most research and practice case studies, the Ringelmann effect has been found to hold. Our results challenge common wisdom, precisel...

  2. 基于开源软件《数学教学论》网络学习平台的设计与实现%Design and Realization of Mathematics Teaching Theory Network Learning Platform Based on Open Source Software

    Institute of Scientific and Technical Information of China (English)

    林锋锋; 张君敏; 钟平; 张磊

    2013-01-01

    Mathematics Teaching Theory is one of important compulsory course for the Mathematics Normal College Students. The article analyzes the present situation of Mathematics Teaching Theory at first,and aims at the shortage of teaching and the need of Building up a Network Learning Platform.In order to constructivism As a main guide,Network Learning Platform of mathematics teaching theory has been designed by Open Source Software,which realizes course content management, Network learning, exam online, question response interaction, BBS, etc. Students can get what they need online in dependence to make up the short of traditional teaching to optimize the teaching effect.%《数学教学论》是数学专业师范生一门重要必修课程。该文首先分析阐述了该课程教学的现状,针对传统教学的诸多不足以及建立网络学习平台的必要性,基于建构主义理论为主要的理论指导,采用开源软件设计了《数学教学论》网络学习平台,实现了课程内容管理、网络学习、在线考试、问答互动、论坛等交互功能。学生通过该网络学习平台进行自主学习,与传统教学相互结合,实现教学效果的最优化。

  3. Laser scanner data processing and 3D modeling using a free and open source software

    Energy Technology Data Exchange (ETDEWEB)

    Gabriele, Fatuzzo [Dept. of Industrial and Mechanical Engineering, University of Catania (Italy); Michele, Mangiameli, E-mail: amichele.mangiameli@dica.unict.it; Giuseppe, Mussumeci; Salvatore, Zito [Dept. of Civil Engineering and Architecture, University of Catania (Italy)

    2015-03-10

    The laser scanning is a technology that allows in a short time to run the relief geometric objects with a high level of detail and completeness, based on the signal emitted by the laser and the corresponding return signal. When the incident laser radiation hits the object to detect, then the radiation is reflected. The purpose is to build a three-dimensional digital model that allows to reconstruct the reality of the object and to conduct studies regarding the design, restoration and/or conservation. When the laser scanner is equipped with a digital camera, the result of the measurement process is a set of points in XYZ coordinates showing a high density and accuracy with radiometric and RGB tones. In this case, the set of measured points is called “point cloud” and allows the reconstruction of the Digital Surface Model. Even the post-processing is usually performed by closed source software, which is characterized by Copyright restricting the free use, free and open source software can increase the performance by far. Indeed, this latter can be freely used providing the possibility to display and even custom the source code. The experience started at the Faculty of Engineering in Catania is aimed at finding a valuable free and open source tool, MeshLab (Italian Software for data processing), to be compared with a reference closed source software for data processing, i.e. RapidForm. In this work, we compare the results obtained with MeshLab and Rapidform through the planning of the survey and the acquisition of the point cloud of a morphologically complex statue.

  4. TIDE TOOL: Open-Source Sea-Level Monitoring Software for Tsunami Warning Systems

    Science.gov (United States)

    Weinstein, S. A.; Kong, L. S.; Becker, N. C.; Wang, D.

    2012-12-01

    A tsunami warning center (TWC) typically decides to issue a tsunami warning bulletin when initial estimates of earthquake source parameters suggest it may be capable of generating a tsunami. A TWC, however, relies on sea-level data to provide prima facie evidence for the existence or non-existence of destructive tsunami waves and to constrain tsunami wave height forecast models. In the aftermath of the 2004 Sumatra disaster, the International Tsunami Information Center asked the Pacific Tsunami Warning Center (PTWC) to develop a platform-independent, easy-to-use software package to give nascent TWCs the ability to process WMO Global Telecommunications System (GTS) sea-level messages and to analyze the resulting sea-level curves (marigrams). In response PTWC developed TIDE TOOL that has since steadily grown in sophistication to become PTWC's operational sea-level processing system. TIDE TOOL has two main parts: a decoder that reads GTS sea-level message logs, and a graphical user interface (GUI) written in the open-source platform-independent graphical toolkit scripting language Tcl/Tk. This GUI consists of dynamic map-based clients that allow the user to select and analyze a single station or groups of stations by displaying their marigams in strip-chart or screen-tiled forms. TIDE TOOL also includes detail maps of each station to show each station's geographical context and reverse tsunami travel time contours to each station. TIDE TOOL can also be coupled to the GEOWARE™ TTT program to plot tsunami travel times and to indicate the expected tsunami arrival time on the marigrams. Because sea-level messages are structured in a rich variety of formats TIDE TOOL includes a metadata file, COMP_META, that contains all of the information needed by TIDE TOOL to decode sea-level data as well as basic information such as the geographical coordinates of each station. TIDE TOOL can therefore continuously decode theses sea-level messages in real-time and display the time

  5. FloWave.US: validated, open-source, and flexible software for ultrasound blood flow analysis.

    Science.gov (United States)

    Coolbaugh, Crystal L; Bush, Emily C; Caskey, Charles F; Damon, Bruce M; Towse, Theodore F

    2016-10-01

    Automated software improves the accuracy and reliability of blood velocity, vessel diameter, blood flow, and shear rate ultrasound measurements, but existing software offers limited flexibility to customize and validate analyses. We developed FloWave.US-open-source software to automate ultrasound blood flow analysis-and demonstrated the validity of its blood velocity (aggregate relative error, 4.32%) and vessel diameter (0.31%) measures with a skeletal muscle ultrasound flow phantom. Compared with a commercial, manual analysis software program, FloWave.US produced equivalent in vivo cardiac cycle time-averaged mean (TAMean) velocities at rest and following a 10-s muscle contraction (mean bias blood flow data was 9.8 times faster than the manual method. Finally, a case study of a lower extremity muscle contraction experiment highlighted the ability of FloWave.US to measure small fluctuations in TAMean velocity, vessel diameter, and mean blood flow at specific time points in the cardiac cycle. In summary, the collective features of our newly designed software-accuracy, reliability, reduced processing time, cost-effectiveness, and flexibility-offer advantages over existing proprietary options. Further, public distribution of FloWave.US allows researchers to easily access and customize code to adapt ultrasound blood flow analysis to a variety of vascular physiology applications.

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

    Science.gov (United States)

    Lin, Yu-Wei; Zini, Enrico

    2008-01-01

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

  7. Building an open-source simulation platform of acoustic radiation force-based breast elastography.

    Science.gov (United States)

    Wang, Yu; Peng, Bo; Jiang, Jingfeng

    2017-03-07

    summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments.

  8. Building an open-source simulation platform of acoustic radiation force-based breast elastography

    Science.gov (United States)

    Wang, Yu; Peng, Bo; Jiang, Jingfeng

    2017-03-01

    . In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments.

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

    Science.gov (United States)

    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

  10. Assessment of open source software for CBCT in detecting additional mental foramina

    Directory of Open Access Journals (Sweden)

    Oséas Santos Junior

    2013-04-01

    Full Text Available The purpose of this study was to evaluate which post-processing imaging protocol would be better to analyze the additional mental foramen (AMF in preoperative planning with cone-beam computed tomography (CBCT exams, and to test reproducibility of measurements, using open source software (OsiriX. The software was used to detect the cases of AMF from among 58 exams for dental implant planning in edentulous mandible areas-three cases were found. The case images were submitted to qualitative analysis using 2D orthogonal MPR, 3D-MPR and 3D volume rendering protocols by two oral and maxillofacial radiologists. Quantitative analysis used the 3D-MPR protocol; the closed polygon tool measured the mental foramen (MF and the AMF areas; the length tool measured the distance between foramina. The measurements were performed independently by the examiners, at two different times. Intra- and interexaminer agreement was assessed using the intraclass correlation coefficient. The panoramic view did not show the MF and the AMF clearly. The AMF could be detected in the parasagittal view. 2D Orthogonal MPR was effective to observe the AMF in some cases. The 3D-MPR and 3D view protocols were the most effective to locate and analyze the AMF. In conclusion, a 3D view improves visualization when anatomical points are not clearly visible. 3D-MPR was considered a more effective post-processing imaging protocol to observe foramina relationships. The high reproducibility of measurements for anatomical MF variations was established using specific tools featured in open source software for CBCT. OsiriX is realistic and recommended for preoperative planning.

  11. MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses.

    Science.gov (United States)

    Bokhart, Mark T; Nazari, Milad; Garrard, Kenneth P; Muddiman, David C

    2017-09-20

    A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstract ᅟ.

  12. AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter

    Science.gov (United States)

    Mingasson, Tom; Duval, Tanguy; Stikov, Nikola; Cohen-Adad, Julien

    2017-01-01

    HIGHLIGHTS AxonPacking: Open-source software for simulating white matter microstructure.Validation on a theoretical disk packing problem.Reproducible and stable for various densities and diameter distributions.Can be used to study interplay between myelin/fiber density and restricted fraction. Quantitative Magnetic Resonance Imaging (MRI) can provide parameters that describe white matter microstructure, such as the fiber volume fraction (FVF), the myelin volume fraction (MVF) or the axon volume fraction (AVF) via the fraction of restricted water (fr). While already being used for clinical application, the complex interplay between these parameters requires thorough validation via simulations. These simulations required a realistic, controlled and adaptable model of the white matter axons with the surrounding myelin sheath. While there already exist useful algorithms to perform this task, none of them combine optimisation of axon packing, presence of myelin sheath and availability as free and open source software. Here, we introduce a novel disk packing algorithm that addresses these issues. The performance of the algorithm is tested in term of reproducibility over 50 runs, resulting density, and stability over iterations. This tool was then used to derive multiple values of FVF and to study the impact of this parameter on fr and MVF in light of the known microstructure based on histology sample. The standard deviation of the axon density over runs was lower than 10−3 and the expected hexagonal packing for monodisperse disks was obtained with a density close to the optimal density (obtained: 0.892, theoretical: 0.907). Using an FVF ranging within [0.58, 0.82] and a mean inter-axon gap ranging within [0.1, 1.1] μm, MVF ranged within [0.32, 0.44] and fr ranged within [0.39, 0.71], which is consistent with the histology. The proposed algorithm is implemented in the open-source software AxonPacking (https://github.com/neuropoly/axonpacking) and can be useful for

  13. AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter.

    Science.gov (United States)

    Mingasson, Tom; Duval, Tanguy; Stikov, Nikola; Cohen-Adad, Julien

    2017-01-01

    HIGHLIGHTS AxonPacking: Open-source software for simulating white matter microstructure.Validation on a theoretical disk packing problem.Reproducible and stable for various densities and diameter distributions.Can be used to study interplay between myelin/fiber density and restricted fraction. Quantitative Magnetic Resonance Imaging (MRI) can provide parameters that describe white matter microstructure, such as the fiber volume fraction (FVF), the myelin volume fraction (MVF) or the axon volume fraction (AVF) via the fraction of restricted water (fr). While already being used for clinical application, the complex interplay between these parameters requires thorough validation via simulations. These simulations required a realistic, controlled and adaptable model of the white matter axons with the surrounding myelin sheath. While there already exist useful algorithms to perform this task, none of them combine optimisation of axon packing, presence of myelin sheath and availability as free and open source software. Here, we introduce a novel disk packing algorithm that addresses these issues. The performance of the algorithm is tested in term of reproducibility over 50 runs, resulting density, and stability over iterations. This tool was then used to derive multiple values of FVF and to study the impact of this parameter on fr and MVF in light of the known microstructure based on histology sample. The standard deviation of the axon density over runs was lower than 10(-3) and the expected hexagonal packing for monodisperse disks was obtained with a density close to the optimal density (obtained: 0.892, theoretical: 0.907). Using an FVF ranging within [0.58, 0.82] and a mean inter-axon gap ranging within [0.1, 1.1] μm, MVF ranged within [0.32, 0.44] and fr ranged within [0.39, 0.71], which is consistent with the histology. The proposed algorithm is implemented in the open-source software AxonPacking (https://github.com/neuropoly/axonpacking) and can be useful for

  14. The Use of Open Source Software for Open Architecture System on CNC Milling Machine

    Directory of Open Access Journals (Sweden)

    Dalmasius Ganjar Subagio

    2012-03-01

    Full Text Available Computer numerical control (CNC milling machine system cannot be separated from the software required to follow the provisions of the Open Architecture capabilities that have portability, extend ability, interoperability, and scalability. When a prescribed period of a CNC milling machine has passed and the manufacturer decided to discontinue it, then the user will have problems for maintaining the performance of the machine. This paper aims to show that the using of open source software (OSS is the way out to maintain engine performance. With the use of OSS, users no longer depend on the software built by the manufacturer because OSS is open and can be developed independently. In this paper, USBCNC V.3.42 is used as an alternative OSS. The test result shows that the work piece is in match with the desired pattern. The test result shows that the performance of machines using OSS has similar performance with the machine using software from the manufacturer. 

  15. Development of an Open Source Image-Based Flow Modeling Software - SimVascular

    Science.gov (United States)

    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.

  16. An open source cryostage and software analysis method for detection of antifreeze activity

    DEFF Research Database (Denmark)

    Lørup Buch, Johannes; Ramløv, H

    2016-01-01

    The aim of this study is to provide the reader with a simple setup that can detect antifreeze proteins (AFP) by inhibition of ice recrystallisation in very small sample sizes. This includes an open source cryostage, a method for preparing and loading samples as well as a software analysis method....... The entire setup was tested using hyperactive AFP from the cerambycid beetle, Rhagium mordax. Samples containing AFP were compared to buffer samples, and the results are visualised as crystal radius evolution over time and in absolute change over 30 min. Statistical analysis showed that samples containing...... AFP could reliably be told apart from controls after only two minutes of recrystallisation. The goal of providing a fast, cheap and easy method for detecting antifreeze proteins in solution was met, and further development of the system can be followed at https://github.com/pechano/cryostage....

  17. Real-time analysis of mechanical and electrical resonances with open source sound card software

    CERN Document Server

    Makan, Gergely; Gingl, Zoltán

    2013-01-01

    We present an easily reproducible, open-source, sound card based experimental set-up to support transfer function measurement. Our system is able to visualize signals of mechanical and electrical resonances and their spectra in real time. We give a brief description of the system, and show some examples of electrical and mechanical resonance experiments that are supported by the system. The theoretical background, experimental set-up, component selection and digital signal processing are all discussed, and more detailed information (building instructions, software download) is provided on a dedicated web page (http://www.noise.inf.u-szeged.hu/edudev/RealTimeAnalysisOfResonances/) The experimental set-up can support undergraduate and graduate education of students of physics, physics education and engineering by means of experimental demonstrations and laboratory exercises. The very low cost, high efficiency and transparent system provides a scalable experimental environment that can be easily built in several...

  18. A Stigmergy Collaboration Approach in the Open Source Software Developer Community

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Xiaohui [ORNL; Pullum, Laura L [ORNL; Treadwell, Jim N [ORNL; Potok, Thomas E [ORNL

    2009-01-01

    The communication model of some self-organized online communities is significantly different from the traditional social network based community. It is problematic to use social network analysis to analyze the collaboration structure and emergent behaviors in these communities because these communities lack peer-to-peer connections. Stigmergy theory provides an explanation of the collaboration model of these communities. In this research, we present a stigmergy approach for building an agent-based simulation to simulate the collaboration model in the open source software (OSS) developer community. We used a group of actors who collaborate on OSS projects through forums as our frame of reference and investigated how the choices actors make in contributing their work on the projects determines the global status of the whole OSS project. In our simulation, the forum posts serve as the digital pheromone and the modified Pierre-Paul Grasse pheromone model is used for computing the developer agents behavior selection probability.

  19. Comparative analysis of colorimetric staining in skin using open-source software

    Science.gov (United States)

    Billings, Paul C; Sanzari, Jenine K.; Kennedy, Ann R.; Cengel, Keith A.; Seykora, John T.

    2015-01-01

    Colorimetric staining techniques such as immunohistochemistry (IHC), immunofluorescence (IF) and histochemistry (HC) provide useful information regarding the localization and relative amount of a molecule/substance in skin. We have developed a novel, straightforward method to assess colorimetric staining by combining features from two open-source software programs. As a proof of principle, we demonstrate the utility of this approach by analyzing changes in skin melanin deposition during the radiation-induced tanning response of Yucatan mini-pigs. This method includes a visualization step to validate the accuracy of color selection before quantitation to ensure accuracy. The data show that this method is robust and will provide a means to obtain accurate comparative analyses of staining in IHC/IF/HC samples. PMID:25393687

  20. Karyotyping human and mouse cells using probes from single-sorted chromosomes and open source software.

    Science.gov (United States)

    Potapova, Tamara A; Unruh, Jay R; Box, Andrew C; Bradford, William D; Seidel, Christopher W; Slaughter, Brian D; Sivagnanam, Shamilene; Wu, Yuping; Li, Rong

    2015-12-01

    Multispectral karyotyping analyzes all chromosomes in a single cell by labeling them with chromosome-specific probes conjugated to unique combinations of fluorophores. Currently available multispectral karyotyping systems require the purchase of specialized equipment and reagents. However, conventional laser scanning confocal microscopes that are capable of separating multiple overlapping emission spectra through spectral imaging and linear unmixing can be utilized for classifying chromosomes painted with multicolor probes. Here, we generated multicolor chromosome paints from single-sorted human and mouse chromosomes and developed the Karyotype Identification via Spectral Separation (KISS) analysis package, a set of freely available open source ImageJ tools for spectral unmixing and karyotyping. Chromosome spreads painted with our multispectral probe sets can be imaged on widely available spectral laser scanning confocal microscopes and analyzed using our ImageJ tools. Together, our probes and software enable academic labs with access to a laser-scanning spectral microscope to perform multicolor karyotyping in a cost-effective manner.

  1. Comparative analysis of colorimetric staining in skin using open-source software.

    Science.gov (United States)

    Billings, Paul C; Sanzari, Jenine K; Kennedy, Ann R; Cengel, Keith A; Seykora, John T

    2015-02-01

    Colorimetric staining techniques such as immunohistochemistry (IHC), immunofluorescence (IF) and histochemistry (HC) provide useful information regarding the localization and relative amount of a molecule/substance in skin. We have developed a novel, straightforward method to assess colorimetric staining by combining features from two open-source software programs. As a proof of principle, we demonstrate the utility of this approach by analysing changes in skin melanin deposition during the radiation-induced tanning response of Yucatan mini-pigs. This method includes a visualization step to validate the accuracy of colour selection before quantitation to ensure accuracy. The data show that this method is robust and will provide a means to obtain accurate comparative analyses of staining in IHC/IF/HC samples.

  2. An open source cryostage and software analysis method for detection of antifreeze activity.

    Science.gov (United States)

    Buch, J L; Ramløv, H

    2016-06-01

    The aim of this study is to provide the reader with a simple setup that can detect antifreeze proteins (AFP) by inhibition of ice recrystallisation in very small sample sizes. This includes an open source cryostage, a method for preparing and loading samples as well as a software analysis method. The entire setup was tested using hyperactive AFP from the cerambycid beetle, Rhagium mordax. Samples containing AFP were compared to buffer samples, and the results are visualised as crystal radius evolution over time and in absolute change over 30 min. Statistical analysis showed that samples containing AFP could reliably be told apart from controls after only two minutes of recrystallisation. The goal of providing a fast, cheap and easy method for detecting antifreeze proteins in solution was met, and further development of the system can be followed at https://github.com/pechano/cryostage.

  3. Open Source Opens Doors: Repurposing Library Software to Facilitate Faculty Research and Collaboration

    Directory of Open Access Journals (Sweden)

    Sandra L. Stump

    2013-10-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE Asked to convert a faculty-created Microsoft Word document of biblical references found within popular films into a searchable database for scholars, the Albright College library staff helped create a multi-access database called Bible in the Reel World. The database relied on student workers for inputting data, used MARC standard formatting for future portability, and encouraged interactive feedback, enabling scholars to submit comments and suggest additional films and references. Using the open source integrated library system Koha, MarcEdit software, and free record exporting from IMDb, library staff created a fully-searchable database for researchers and scholars to examine the use of scripture in popular film.

  4. The role of on-line communication in open source software development

    DEFF Research Database (Denmark)

    Vujovic, S.; Ulhøi, John Parm

    2004-01-01

    allow parallel development and dynamic online exchanges during the overall innovation process. In conceptualizing online computer-based innovation process in the form of Open Source Software, the paper will borrow from theory on networks and communities of practice, which take into account social...... concludes that online computer-based innovation fundamentally challenges the contemporary way of communication, cooperation and coordination during innovation and product developments. Moreover, it challenges the traditional business model in that it forces the actors involved to move the focus away from......Online computer technologies provide an effective means for communication, cooperation and coordination. In this paper we address the extent innovation based upon non-proprietary knowledge offers the participating actors an interesting alternative for product development. Such an alternative would...

  5. Technical Evaluation Report 43: Open Source Software: Fully featured vs. "the devil you know"?

    Directory of Open Access Journals (Sweden)

    Michael Hotrum

    2005-03-01

    Full Text Available 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 development. The current findings were compared with DE students’ reactions to a similar LMS product, ATutor, also rated highly in the independent OSS evaluation. In comparing an ATutor course website with a simple HTML-based version of the same site, the ten students voted unanimously to retain the simpler site. This result is consistent with previous evaluation findings in the current series of reports, and indicates that increasing integration of product features does not necessarily improve a product’s ease of use or educational effectiveness.

  6. Open-source hardware and software and web application for gamma dose rate network operation.

    Science.gov (United States)

    Luff, R; Zähringer, M; Harms, W; Bleher, M; Prommer, B; Stöhlker, U

    2014-08-01

    The German Federal Office for Radiation Protection operates a network of about 1800 gamma dose rate stations as a part of the national emergency preparedness plan. Each of the six network centres is capable of operating the network alone. Most of the used hardware and software have been developed in-house under open-source license. Short development cycles and close cooperation between developers and users ensure robustness, transparency and fast maintenance procedures, thus avoiding unnecessary complex solutions. This also reduces the overall costs of the network operation. An easy-to-expand web interface has been developed to make the complete system available to other interested network operators in order to increase cooperation between different countries. The interface is also regularly in use for education during scholarships of trainees supported, e.g. by the 'International Atomic Energy Agency' to operate a local area dose rate monitoring test network.

  7. The role of on-line communication in open source software development

    DEFF Research Database (Denmark)

    Vujovic, S.; Ulhøi, John Parm

    2004-01-01

    the innovation itself and upstream in the value chain to identifying new supporting services. In closing the paper addresses motivations of companies to integrate this alternative and non-proprietary way of product development into their proprietary business model. We do this by presenting an example....... concludes that online computer-based innovation fundamentally challenges the contemporary way of communication, cooperation and coordination during innovation and product developments. Moreover, it challenges the traditional business model in that it forces the actors involved to move the focus away from...... allow parallel development and dynamic online exchanges during the overall innovation process. In conceptualizing online computer-based innovation process in the form of Open Source Software, the paper will borrow from theory on networks and communities of practice, which take into account social...

  8. Real-time analysis of mechanical and electrical resonances with open-source sound card software

    Science.gov (United States)

    Makan, G.; Kopasz, K.; Gingl, Z.

    2014-01-01

    We present an easily reproducible, open-source, sound card based experimental set-up to support transfer function measurement. Our system is able to visualize the signals of mechanical and electrical resonances and their spectra in real time. We give a brief description of the system, and show some examples of electrical and mechanical resonance experiments that are supported by the system. The theoretical background, experimental set-up, component selection and digital signal processing are all discussed, and more detailed information (building instructions, software download) is provided on a dedicated web page (www.noise.inf.u-szeged.hu/edudev/RealTimeAnalysisOfResonances/). The experimental set-up can support the undergraduate and graduate education of students of physics, physics education and engineering by means of experimental demonstrations and laboratory exercises. The very low cost, high efficiency and transparent system provides a scalable experimental environment that can be easily built in several instances.

  9. Robotics-assisted mass spectrometry assay platform enabled by open-source electronics.

    Science.gov (United States)

    Chiu, Shih-Hao; Urban, Pawel L

    2015-02-15

    Mass spectrometry (MS) is an important analytical technique with numerous applications in clinical analysis, biochemistry, environmental analysis, geology and physics. Its success builds on the ability of MS to determine molecular weights of analytes, and elucidate their structures. However, sample handling prior to MS requires a lot of attention and labor. In this work we were aiming to automate processing samples for MS so that analyses could be conducted without much supervision of experienced analysts. The goal of this study was to develop a robotics and information technology-oriented platform that could control the whole analysis process including sample delivery, reaction-based assay, data acquisition, and interaction with the analyst. The proposed platform incorporates a robotic arm for handling sample vials delivered to the laboratory, and several auxiliary devices which facilitate and secure the analysis process. They include: multi-relay board, infrared sensors, photo-interrupters, gyroscopes, force sensors, fingerprint scanner, barcode scanner, touch screen panel, and internet interface. The control of all the building blocks is achieved through implementation of open-source electronics (Arduino), and enabled by custom-written programs in C language. The advantages of the proposed system include: low cost, simplicity, small size, as well as facile automation of sample delivery and processing without the intervention of the analyst. It is envisaged that this simple robotic system may be the forerunner of automated laboratories dedicated to mass spectrometric analysis of biological samples.

  10. Open-source platform to benchmark fingerprints for ligand-based virtual screening.

    Science.gov (United States)

    Riniker, Sereina; Landrum, Gregory A

    2013-05-30

    : Similarity-search methods using molecular fingerprints are an important tool for ligand-based virtual screening. A huge variety of fingerprints exist and their performance, usually assessed in retrospective benchmarking studies using data sets with known actives and known or assumed inactives, depends largely on the validation data sets used and the similarity measure used. Comparing new methods to existing ones in any systematic way is rather difficult due to the lack of standard data sets and evaluation procedures. Here, we present a standard platform for the benchmarking of 2D fingerprints. The open-source platform contains all source code, structural data for the actives and inactives used (drawn from three publicly available collections of data sets), and lists of randomly selected query molecules to be used for statistically valid comparisons of methods. This allows the exact reproduction and comparison of results for future studies. The results for 12 standard fingerprints together with two simple baseline fingerprints assessed by seven evaluation methods are shown together with the correlations between methods. High correlations were found between the 12 fingerprints and a careful statistical analysis showed that only the two baseline fingerprints were different from the others in a statistically significant way. High correlations were also found between six of the seven evaluation methods, indicating that despite their seeming differences, many of these methods are similar to each other.

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

    Science.gov (United States)

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

    2015-12-01

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

  12. On Open- source Multi-robot simulators

    CSIR Research Space (South Africa)

    Namoshe, M

    2008-07-01

    Full Text Available Open source software simulators play a major role in robotics design and research as platforms for developing, testing and improving architectures, concepts and algorithms for cooperative/multi-robot systems. Simulation environment enables control...

  13. Open Source Business Solutions

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2008-01-01

    Full Text Available This analyses the Open source movement. Open source development process and management is seen different from the classical point of view. This focuses on characteristics and software market tendencies for the main Open source initiatives. It also points out the labor market future evolution for the software developers.

  14. Distance education course on spatial multi-hazard risk assessment, using Open Source software

    Science.gov (United States)

    van Westen, C. J.; Frigerio, S.

    2009-04-01

    As part of the capacity building activities of the United Nations University - ITC School on Disaster Geo-Information Management (UNU-ITC DGIM) the International Institute for Geoinformation Science and Earth Observation (ITC) has developed a distance education course on the application of Geographic Information Systems for multi-hazard risk assessment. This course is designed for academic staff, as well as for professionals working in (non-) governmental organizations where knowledge of disaster risk management is essential. The course guides the participants through the entire process of risk assessment, on the basis of a case study of a city exposed to multiple hazards, in a developing country. The courses consists of eight modules, each with a guide book explaining the theoretical background, and guiding the participants through spatial data requirements for risk assessment, hazard assessment procedures, generation of elements at risk databases, vulnerability assessment, qualitative and quantitative risk assessment methods, risk evaluation and risk reduction. Linked to the theory is a large set of exercises, with exercise descriptions, answer sheets, demos and GIS data. The exercises deal with four different types of hazards: earthquakes, flooding, technological hazards, and landslides. One important consideration in designing the course is that people from developing countries should not be restricted in using it due to financial burdens for software acquisition. Therefore the aim was to use Open Source software as a basis. The GIS exercises are written for the ILWIS software. All exercises have also been integrated into a WebGIS, using the Open source software CartoWeb (based on GNU License). It is modular and customizable thanks to its object-oriented architecture and based on a hierarchical structure (to manage and organize every package of information of every step required in risk assessment). Different switches for every component of the risk assessment

  15. STARS 2.0: 2nd-generation open-source archiving and query software

    Science.gov (United States)

    Winegar, Tom

    2008-07-01

    The Subaru Telescope is in process of developing an open-source alternative to the 1st-generation software and databases (STARS 1) used for archiving and query. For STARS 2, we have chosen PHP and Python for scripting and MySQL as the database software. We have collected feedback from staff and observers, and used this feedback to significantly improve the design and functionality of our future archiving and query software. Archiving - We identified two weaknesses in 1st-generation STARS archiving software: a complex and inflexible table structure and uncoordinated system administration for our business model: taking pictures from the summit and archiving them in both Hawaii and Japan. We adopted a simplified and normalized table structure with passive keyword collection, and we are designing an archive-to-archive file transfer system that automatically reports real-time status and error conditions and permits error recovery. Query - We identified several weaknesses in 1st-generation STARS query software: inflexible query tools, poor sharing of calibration data, and no automatic file transfer mechanisms to observers. We are developing improved query tools and sharing of calibration data, and multi-protocol unassisted file transfer mechanisms for observers. In the process, we have redefined a 'query': from an invisible search result that can only transfer once in-house right now, with little status and error reporting and no error recovery - to a stored search result that can be monitored, transferred to different locations with multiple protocols, reporting status and error conditions and permitting recovery from errors.

  16. LISIRD 2: Applying Standards and Open Source Software in Exploring and Serving Scientific Data

    Science.gov (United States)

    Wilson, A.; Lindholm, D. M.; Ware Dewolfe, A.; Lindholm, C.; Pankratz, C. K.; Snow, M.; Woods, T. N.

    2009-12-01

    The LASP Interactive Solar IRradiance Datacenter (LISIRD), http://lasp.colorado.edu/lisird, seeks to provide exploration of and access to solar irradiance data, models and other related data. These irradiance datasets, from the SME, UARS, TIMED, and SORCE missions, are primarily a function of time and often also wavelength. Their measurements are typically made on a scale of seconds and derived products are provided at daily cadence. The first version of the LISIRD site was built using non standard, proprietary software. The non standard application structure and tight coupling to a variety of dataset representations made changes arduous and maintenance difficult. Eventually the software vender decided to no longer support a critical software component, further decreasing the viability of the site. In LISIRD 2, through the application of the Java EE standard coupled with open source software to fetch and plot the data, the functionality of the original site is being improved while the code structure is being streamlined and simplified. With a relatively minimal effort, the new site can access and serve a greater variety of datasets in an easier fashion, and produce responsive, interactive plots of datasets overlaid and/or linked in time. And it does so using a significantly smaller code base that is, at the same time, much more flexible and extensible. In particular, LISIRD 2 heavily leverages powerful, flexible functionality provided by the Time Series Data Server (TSDS). The OPeNDAP compliant TSDS supports requests for any data that are function of time. It can support scalar, vector, and spectra data types. Through the use of the Unidata NetCDF-Java library and NcML, the TSDS supports multiple input and output formats and is easily extended to support more. It also supports a variety of filters that can be chained and applied to the data on the server before being delivered. TSDS thinning capabilities make it easy for the clients to request appropriate data

  17. Real Space Multigrid (RMG) Open Source Software Suite for Multi-Petaflops Electronic Structure Calculations

    Science.gov (United States)

    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.

  18. Comparison of 3D reconstruction of mandible for pre-operative planning using commercial and open-source software

    Science.gov (United States)

    Abdullah, Johari Yap; Omar, Marzuki; Pritam, Helmi Mohd Hadi; Husein, Adam; Rajion, Zainul Ahmad

    2016-12-01

    3D printing of mandible is important for pre-operative planning, diagnostic purposes, as well as for education and training. Currently, the processing of CT data is routinely performed with commercial software which increases the cost of operation and patient management for a small clinical setting. Usage of open-source software as an alternative to commercial software for 3D reconstruction of the mandible from CT data is scarce. The aim of this study is to compare two methods of 3D reconstruction of the mandible using commercial Materialise Mimics software and open-source Medical Imaging Interaction Toolkit (MITK) software. Head CT images with a slice thickness of 1 mm and a matrix of 512x512 pixels each were retrieved from the server located at the Radiology Department of Hospital Universiti Sains Malaysia. The CT data were analysed and the 3D models of mandible were reconstructed using both commercial Materialise Mimics and open-source MITK software. Both virtual 3D models were saved in STL format and exported to 3matic and MeshLab software for morphometric and image analyses. Both models were compared using Wilcoxon Signed Rank Test and Hausdorff Distance. No significant differences were obtained between the 3D models of the mandible produced using Mimics and MITK software. The 3D model of the mandible produced using MITK open-source software is comparable to the commercial MIMICS software. Therefore, open-source software could be used in clinical setting for pre-operative planning to minimise the operational cost.

  19. Open Source Based Sensor Platform for Mobile Environmental Monitoring and Data Acquisition

    Science.gov (United States)

    Schima, Robert; Goblirsch, Tobias; Misterek, René; Salbach, Christoph; Schlink, Uwe; Francyk, Bogdan; Dietrich, Peter; Bumberger, Jan

    2016-04-01

    data processing, data provision and data visualization. The smart phone app allows the configuration of the mobile sensor devices and provides some built-in functions such as simple data visualization or data transmission via e-mail whereas the web service provides the visualization of the data and tools for data processing. In an initial field experiment, a methane monitoring based on our sensor integration platform was performed in the city area of Leipzig (Germany) in late June 2015. The study has shown that an urban monitoring can be conducted based on open source components. Moreover, the system enabled the detection of hot spots and methane emission sources. In September 2015, a larger scaled city monitoring based on the mobile monitoring platform was performed by five independently driving cyclists through the city center of Leipzig (Germany). As a result we were able to instantly show a heat and humidity map of the inner city center as well as an exposure map for each cyclist. This emphasizes the feasibility and high potential of open source based monitoring approaches for future research in the field of urban area monitoring in general, citizen science or the validation of remote sensing data.

  20. Development and evaluation of an open source software tool for deidentification of pathology reports

    Directory of Open Access Journals (Sweden)

    Mahaadevan Rajeshwarri

    2006-03-01

    Full Text Available Abstract Background Electronic medical records, including pathology reports, are often used for research purposes. Currently, there are few programs freely available to remove identifiers while leaving the remainder of the pathology report text intact. Our goal was to produce an open source, Health Insurance Portability and Accountability Act (HIPAA compliant, deidentification tool tailored for pathology reports. We designed a three-step process for removing potential identifiers. The first step is to look for identifiers known to be associated with the patient, such as name, medical record number, pathology accession number, etc. Next, a series of pattern matches look for predictable patterns likely to represent identifying data; such as dates, accession numbers and addresses as well as patient, institution and physician names. Finally, individual words are compared with a database of proper names and geographic locations. Pathology reports from three institutions were used to design and test the algorithms. The software was improved iteratively on training sets until it exhibited good performance. 1800 new pathology reports were then processed. Each report was reviewed manually before and after deidentification to catalog all identifiers and note those that were not removed. Results 1254 (69.7 % of 1800 pathology reports contained identifiers in the body of the report. 3439 (98.3% of 3499 unique identifiers in the test set were removed. Only 19 HIPAA-specified identifiers (mainly consult accession numbers and misspelled names were missed. Of 41 non-HIPAA identifiers missed, the majority were partial institutional addresses and ages. Outside consultation case reports typically contain numerous identifiers and were the most challenging to deidentify comprehensively. There was variation in performance among reports from the three institutions, highlighting the need for site-specific customization, which is easily accomplished with our tool

  1. Facilitating Real-time Triage of Astronomical Data with Open Source Software

    Science.gov (United States)

    Khudikyan, S.; Mattmann, C. A.; Cinquini, L.; Hart, A. F.; Thompson, D. R.; Wagstaff, K.; Burke-Spolaor, S.; Tingay, S.; Wayth, R.; Deller, A.; Majid, W.; Lazio, J.; Jones, D. L.

    2013-12-01

    Relatively bright, millisecond-duration pulses of radio-frequency energy have been discovered recently at the Parkes radio telescope in Australia. These Fast Radio Bursts (FRBs) have properties consistent with extragalactic origin, and they may represent the discovery of a completely new class of astronomical objects. Models for the generation of these events are poorly constrained, in part because the Parkes radio telescope can locate the direction of the pulses to about 15 arcminute (60 arcminutes = 1 degree) precision. The Very Long Baseline Array (VLBA) is a network of 10 telescopes distributed across the United States. If it were to detect such a pulse, it could provide exceptionally precise localization of the pulse's direction (to better than a nanoradian), thus allowing possible identification of the celestial object from which the pulse originated. The challenge is that the data rate from the VLBA antennas can be as large as 20 Gb/s, and the VLBA was not designed to store the data from the individual antennas for any significant length of time. The VLBA Fast Radio Transients (V-FASTR) experiment has developed a real-time, scalable data 'triage' system that makes use of algorithms capable of discovering meaningful signals, and open source code stewarded at the Apache Software Foundation. This system is designed to identify potential FRBs during real-time processing of the VLBA data stream, save only the relevant bits for further (off-line) processing, and curate the data products. As such, the V-FASTR experiment exemplifies the software design for a distributed sensor network that generates data at rates requiring real-time or near-real-time processing. Building flexible portals and applications has become vital with the constantly expanding astronomical data. The V-FASTR collaborative review portal is built using the Apache OODT Balance framework due to the ease at which it integrates with the flexible search capabilities of Apache Solr. We utilize Apache

  2. ADFNE: Open source software for discrete fracture network engineering, two and three dimensional applications

    Science.gov (United States)

    Fadakar Alghalandis, Younes

    2017-05-01

    Rapidly growing topic, the discrete fracture network engineering (DFNE), has already attracted many talents from diverse disciplines in academia and industry around the world to challenge difficult problems related to mining, geothermal, civil, oil and gas, water and many other projects. Although, there are few commercial software capable of providing some useful functionalities fundamental for DFNE, their costs, closed code (black box) distributions and hence limited programmability and tractability encouraged us to respond to this rising demand with a new solution. This paper introduces an open source comprehensive software package for stochastic modeling of fracture networks in two- and three-dimension in discrete formulation. Functionalities included are geometric modeling (e.g., complex polygonal fracture faces, and utilizing directional statistics), simulations, characterizations (e.g., intersection, clustering and connectivity analyses) and applications (e.g., fluid flow). The package is completely written in Matlab scripting language. Significant efforts have been made to bring maximum flexibility to the functions in order to solve problems in both two- and three-dimensions in an easy and united way that is suitable for beginners, advanced and experienced users.

  3. SiGN-SSM: open source parallel software for estimating gene networks with state space models.

    Science.gov (United States)

    Tamada, Yoshinori; Yamaguchi, Rui; Imoto, Seiya; Hirose, Osamu; Yoshida, Ryo; Nagasaki, Masao; Miyano, Satoru

    2011-04-15

    SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles. SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site. tamada@ims.u-tokyo.ac.jp.

  4. Seismic reflection imaging of underground cavities using open-source software

    Energy Technology Data Exchange (ETDEWEB)

    Mellors, R J

    2011-12-20

    The Comprehensive Nuclear Test Ban Treaty (CTBT) includes provisions for an on-site inspection (OSI), which allows the use of specific techniques to detect underground anomalies including cavities and rubble zones. One permitted technique is active seismic surveys such as seismic refraction or reflection. The purpose of this report is to conduct some simple modeling to evaluate the potential use of seismic reflection in detecting cavities and to test the use of open-source software in modeling possible scenarios. It should be noted that OSI inspections are conducted under specific constraints regarding duration and logistics. These constraints are likely to significantly impact active seismic surveying, as a seismic survey typically requires considerable equipment, effort, and expertise. For the purposes of this study, which is a first-order feasibility study, these issues will not be considered. This report provides a brief description of the seismic reflection method along with some commonly used software packages. This is followed by an outline of a simple processing stream based on a synthetic model, along with results from a set of models representing underground cavities. A set of scripts used to generate the models are presented in an appendix. We do not consider detection of underground facilities in this work and the geologic setting used in these tests is an extremely simple one.

  5. OpenFluo: a free open-source software for optophysiological data analyses.

    Science.gov (United States)

    Dupuy, Fabienne; Casas, Jérôme; Bagnères, Anne-Geneviève; Lazzari, Claudio R

    2009-10-15

    Optophysiological imaging methods can be used to record the activity in vivo of groups of neurons from particular areas of the nervous system (e.g. the brain) or of cell cultures. Such methods are used, for example, in the spatio-temporal coding and processing of sensory information. However, the data generated by optophysiological methods must be processed carefully if relevant results are to be obtained. The raw fluorescence data must be digitally filtered and analyzed appropriately to obtain activity maps and fluorescence time course for single spots. We used a Matlab environment to implement the necessary procedures in a user-friendly manner. We developed OpenFluo, a program for people inexperienced in optophysiological methods and for advanced users wishing to perform simple, rapid data analyses without the need for complex, time-consuming programming procedures. This program will be made available as stand-alone software and as an open-source Matlab tool. It will therefore be possible for experienced users to integrate their own routines. We validated this software by assessing its ability to process both artificial recordings and real biological data corresponding to recordings of the honeybee brain.

  6. ChemT, an open-source software for building template-based chemical libraries.

    Science.gov (United States)

    Abreu, R M V; Froufe, H J C; Daniel, P O M; Queiroz, M J R P; Ferreira, I C F R

    2011-01-01

    In computational chemistry, vast quantities of compounds are generated, and there is a need for cheminformatic tools to efficiently build chemical compound libraries. Several software tools for drawing and editing compound structures are available, but they lack options for automatic generation of chemical libraries. We have implemented ChemT, an easy-to-use open-source software tool that automates the process of preparing custom-made template-based chemical libraries. ChemT automatically generates three-dimensional chemical libraries by inputting a chemical template and the functional groups of interest. The graphical user interface of ChemT is self-explanatory, and a complete tutorial is provided. Several file formats are accepted by ChemT, and it is possible to filter the generated compounds according to different physicochemical properties. The compounds can be subject to force field minimization, and the resulting three-dimensional structures recorded on commonly used file formats. ChemT may be a valuable tool for investigators interested in using in silico virtual screening tools, such as quantitative structure-activity relationship modelling or molecular docking, in order to prioritize compounds for further chemical synthesis. To demonstrate the usefulness of ChemT, we describe an example based on a thieno[3,2-b]pyridine template. ChemT is available free of charge from our website at http://www.esa.ipb.pt/~ruiabreu/chemt .

  7. Enablers of Open Source Software adoption: A case study of APS organisations

    Directory of Open Access Journals (Sweden)

    Kavitha Gurusamy

    2012-04-01

    Full Text Available Despite a considerable body of literature investigating factors involved in the Open Source Software (OSS adoption process, there is little research into adoption of OSS by public sector organisations. So it was important to reassess the factors enabling OSS adoption in order to enhance OSS utilization within public sector organisations. This study explored various factors that may enable OSS adoption within Australian Public Sector (APS organisations by interviewing those involved in software procurement. The findings were analysed through the lenses of technology adoption theories (i.e, Diffusion of Innovation (DOI theory and Technology Acceptance Model (TAM, and OSS adoption literature. Success of OSS in government agencies was found to be contingent on critical aspects such as availability of support and maintainability of OSS products, ability to meet organisational business needs in a cost effective manner, economic value associated with OSS such as maintenance and training costs, and attitude of staff toward OSS. The findings suggested that Rogers’ relative advantage and compatibility constructs are major enablers while organisational attributes, environmental attributes, and TAM’s attributes also had some influence on OSS adoption.

  8. Informed-Proteomics: Open Source Software Package for Top-down Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jung Kap; Piehowski, Paul D.; Wilkins, Christopher S.; Zhou, Mowei; Mendoza, Joshua A.; Fujimoto, Grant M.; Gibbons, Bryson C.; Shaw, Jared B.; Shen, Yufeng; Shukla, Anil K.; Moore, Ronald J.; Liu, Tao; Petyuk, Vladislav A.; Tolic, Nikola; Pasa Tolic, Ljiljana; Smith, Richard D.; Payne, Samuel H.; Kim, Sangtae

    2017-08-07

    Top-down proteomics involves the analysis of intact proteins. This approach is very attractive as it allows for analyzing proteins in their endogenous form without proteolysis, preserving valuable information about post-translation modifications, isoforms, proteolytic processing or their combinations collectively called proteoforms. Moreover, the quality of the top-down LC-MS/MS datasets is rapidly increasing due to advances in the liquid chromatography and mass spectrometry instrumentation and sample processing protocols. However, the top-down mass spectra are substantially more complex compare to the more conventional bottom-up data. To take full advantage of the increasing quality of the top-down LC-MS/MS datasets there is an urgent need to develop algorithms and software tools for confident proteoform identification and quantification. In this study we present a new open source software suite for top-down proteomics analysis consisting of an LC-MS feature finding algorithm, a database search algorithm, and an interactive results viewer. The presented tool along with several other popular tools were evaluated using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.

  9. CACTI: free, open-source software for the sequential coding of behavioral interactions.

    Science.gov (United States)

    Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

    2012-01-01

    The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.

  10. CACTI: free, open-source software for the sequential coding of behavioral interactions.

    Directory of Open Access Journals (Sweden)

    Lisa H Glynn

    Full Text Available The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI. Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.

  11. Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.

    Science.gov (United States)

    Rosenberg, David M; Horn, Charles C

    2016-08-01

    Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus-a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software-an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research.

  12. Development of an exploration land robot using low-cost and Open Source platforms for educational purposes

    Science.gov (United States)

    Hernández, D.; Trejo, H.; Ordoñez, E.

    2015-01-01

    In this paper we present the didactic experience of building a low-cost robot composed of sensors, actuators, general electronics and already available frameworks. The control of the robot is through the usage of commercial Open Source platforms as Arduino; and the Raspberry Pi. The experience ranges from general conceptualization, mechanical, electric and electronic design, microcontroller programming and communications.

  13. Toward a methodology for studying the application of open source innovation practices in non-software domains

    Science.gov (United States)

    Tanev, Stoyan

    2007-05-01

    This article represents an initial step in the development of a research methodology that will be applied later to study open source innovation practices in company projects where the released technology or asset is other than software code. A brief review of four possible analytical approaches is presented based on the research literature on open innovation, horizontal user innovation networks, business ecosystems and value creation and appropriation. The OpenAccess project of the Silicon Integration Initiative (Si2) is considered as a potential case study of non-software open source project.

  14. The Big Effects of Short-term Efforts: Mentorship and Code Integration in Open Source Scientific Software

    Directory of Open Access Journals (Sweden)

    Erik H Trainer

    2014-07-01

    Full Text Available Scientific progress relies crucially on software, yet in practice there are significant challenges to scientific software production and maintenance. We conducted a case study of a bioinformatics software library called Biopython to investigate the promise of Google Summer of Code (GSoC, a program that pays students to work on open-source projects for the summer, for addressing these challenges. We find three positive outcomes of GSoC in the Biopython community: the addition of new features to the Biopython codebase, training, and personal development. We also find, however, that mentors face several challenges related to GSoC project selection and ranking. We believe that because GSoC provides an occasion to extend the software with capabilities that can be used to produce new knowledge, and to train successive generations of potential contributors to the software, it can play a vital role in the sustainability of open-source scientific software.

  15. R-CMap-An open-source software for concept mapping.

    Science.gov (United States)

    Bar, Haim; Mentch, Lucas

    2017-02-01

    Planning and evaluating projects often involves input from many stakeholders. Fusing and organizing many different ideas, opinions, and interpretations into a coherent and acceptable plan or project evaluation is challenging. This is especially true when seeking contributions from a large number of participants, especially when not all can participate in group discussions, or when some prefer to contribute their perspectives anonymously. One of the major breakthroughs in the area of evaluation and program planning has been the use of graphical tools to represent the brainstorming process. This provides a quantitative framework for organizing ideas and general concepts into simple-to-interpret graphs. We developed a new, open-source concept mapping software called R-CMap, which is implemented in R. This software provides a graphical user interface to guide users through the analytical process of concept mapping. The R-CMap software allows users to generate a variety of plots, including cluster maps, point rating and cluster rating maps, as well as pattern matching and go-zone plots. Additionally, R-CMap is capable of generating detailed reports that contain useful statistical summaries of the data. The plots and reports can be embedded in Microsoft Office tools such as Word and PowerPoint, where users may manually adjust various plot and table features to achieve the best visual results in their presentations and official reports. The graphical user interface of R-CMap allows users to define cluster names, change the number of clusters, select rating variables for relevant plots, and importantly, select subsets of respondents by demographic criteria. The latter is particularly useful to project managers in order to identify different patterns of preferences by subpopulations. R-CMap is user-friendly, and does not require any programming experience. However, proficient R users can add to its functionality by directly accessing built-in functions in R and sharing new

  16. OxMaR: open source free software for online minimization and randomization for clinical trials.

    Science.gov (United States)

    O'Callaghan, Christopher A

    2014-01-01

    Minimization is a valuable method for allocating participants between the control and experimental arms of clinical studies. The use of minimization reduces differences that might arise by chance between the study arms in the distribution of patient characteristics such as gender, ethnicity and age. However, unlike randomization, minimization requires real time assessment of each new participant with respect to the preceding distribution of relevant participant characteristics within the different arms of the study. For multi-site studies, this necessitates centralized computational analysis that is shared between all study locations. Unfortunately, there is no suitable freely available open source or free software that can be used for this purpose. OxMaR was developed to enable researchers in any location to use minimization for patient allocation and to access the minimization algorithm using any device that can connect to the internet such as a desktop computer, tablet or mobile phone. The software is complete in itself and requires no special packages or libraries to be installed. It is simple to set up and run over the internet using online facilities which are very low cost or even free to the user. Importantly, it provides real time information on allocation to the study lead or administrator and generates real time distributed backups with each allocation. OxMaR can readily be modified and customised and can also be used for standard randomization. It has been extensively tested and has been used successfully in a low budget multi-centre study. Hitherto, the logistical difficulties involved in minimization have precluded its use in many small studies and this software should allow more widespread use of minimization which should lead to studies with better matched control and experimental arms. OxMaR should be particularly valuable in low resource settings.

  17. OxMaR: open source free software for online minimization and randomization for clinical trials.

    Directory of Open Access Journals (Sweden)

    Christopher A O'Callaghan

    Full Text Available Minimization is a valuable method for allocating participants between the control and experimental arms of clinical studies. The use of minimization reduces differences that might arise by chance between the study arms in the distribution of patient characteristics such as gender, ethnicity and age. However, unlike randomization, minimization requires real time assessment of each new participant with respect to the preceding distribution of relevant participant characteristics within the different arms of the study. For multi-site studies, this necessitates centralized computational analysis that is shared between all study locations. Unfortunately, there is no suitable freely available open source or free software that can be used for this purpose. OxMaR was developed to enable researchers in any location to use minimization for patient allocation and to access the minimization algorithm using any device that can connect to the internet such as a desktop computer, tablet or mobile phone. The software is complete in itself and requires no special packages or libraries to be installed. It is simple to set up and run over the internet using online facilities which are very low cost or even free to the user. Importantly, it provides real time information on allocation to the study lead or administrator and generates real time distributed backups with each allocation. OxMaR can readily be modified and customised and can also be used for standard randomization. It has been extensively tested and has been used successfully in a low budget multi-centre study. Hitherto, the logistical difficulties involved in minimization have precluded its use in many small studies and this software should allow more widespread use of minimization which should lead to studies with better matched control and experimental arms. OxMaR should be particularly valuable in low resource settings.

  18. A systematic literature review of open source software quality assessment models.

    Science.gov (United States)

    Adewumi, Adewole; Misra, Sanjay; Omoregbe, Nicholas; Crawford, Broderick; Soto, Ricardo

    2016-01-01

    Many open source software (OSS) quality assessment models are proposed and available in the literature. However, there is little or no adoption of these models in practice. In order to guide the formulation of newer models so they can be acceptable by practitioners, there is need for clear discrimination of the existing models based on their specific properties. Based on this, the aim of this study is to perform a systematic literature review to investigate the properties of the existing OSS quality assessment models by classifying them with respect to their quality characteristics, the methodology they use for assessment, and their domain of application so as to guide the formulation and development of newer models. Searches in IEEE Xplore, ACM, Science Direct, Springer and Google Search is performed so as to retrieve all relevant primary studies in this regard. Journal and conference papers between the year 2003 and 2015 were considered since the first known OSS quality model emerged in 2003. A total of 19 OSS quality assessment model papers were selected. To select these models we have developed assessment criteria to evaluate the quality of the existing studies. Quality assessment models are classified into five categories based on the quality characteristics they possess namely: single-attribute, rounded category, community-only attribute, non-community attribute as well as the non-quality in use models. Our study reflects that software selection based on hierarchical structures is found to be the most popular selection method in the existing OSS quality assessment models. Furthermore, we found that majority (47%) of the existing models do not specify any domain of application. In conclusion, our study will be a valuable contribution to the community and helps the quality assessment model developers in formulating newer models and also to the practitioners (software evaluators) in selecting suitable OSS in the midst of alternatives.

  19. Accuracy of open-source software segmentation and paper-based printed three-dimensional models.

    Science.gov (United States)

    Szymor, Piotr; Kozakiewicz, Marcin; Olszewski, Raphael

    2016-02-01

    In this study, we aimed to verify the accuracy of models created with the help of open-source Slicer 3.6.3 software (Surgical Planning Lab, Harvard Medical School, Harvard University, Boston, MA, USA) and the Mcor Matrix 300 paper-based 3D printer. Our study focused on the accuracy of recreating the walls of the right orbit of a cadaveric skull. Cone beam computed tomography (CBCT) of the skull was performed (0.25-mm pixel size, 0.5-mm slice thickness). Acquired DICOM data were imported into Slicer 3.6.3 software, where segmentation was performed. A virtual model was created and saved as an .STL file and imported into Netfabb Studio professional 4.9.5 software. Three different virtual models were created by cutting the original file along three different planes (coronal, sagittal, and axial). All models were printed with a Selective Deposition Lamination Technology Matrix 300 3D printer using 80 gsm A4 paper. The models were printed so that their cutting plane was parallel to the paper sheets creating the model. Each model (coronal, sagittal, and axial) consisted of three separate parts (∼200 sheets of paper each) that were glued together to form a final model. The skull and created models were scanned with a three-dimensional (3D) optical scanner (Breuckmann smart SCAN) and were saved as .STL files. Comparisons of the orbital walls of the skull, the virtual model, and each of the three paper models were carried out with GOM Inspect 7.5SR1 software. Deviations measured between the models analysed were presented in the form of a colour-labelled map and covered with an evenly distributed network of points automatically generated by the software. An average of 804.43 ± 19.39 points for each measurement was created. Differences measured in each point were exported as a .csv file. The results were statistically analysed using Statistica 10, with statistical significance set at p 3D printer is comparable to those of other commonly used 3-dimensional printers and

  20. PyGaze : An open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments

    NARCIS (Netherlands)

    Dalmaijer, Edwin S.; Mathot, Sebastiaan; Van der Stigchel, Stefan

    2014-01-01

    The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexi

  1. PyGaze : An open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments

    NARCIS (Netherlands)

    Dalmaijer, Edwin S.; Mathot, Sebastiaan; Van der Stigchel, Stefan

    2014-01-01

    The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexi

  2. gprMax: Open source software to simulate electromagnetic wave propagation for Ground Penetrating Radar

    Science.gov (United States)

    Warren, Craig; Giannopoulos, Antonios; Giannakis, Iraklis

    2016-12-01

    gprMax is open source software that simulates electromagnetic wave propagation, using the Finite-Difference Time-Domain (FDTD) method, for the numerical modelling of Ground Penetrating Radar (GPR). gprMax was originally developed in 1996 when numerical modelling using the FDTD method and, in general, the numerical modelling of GPR were in their infancy. Current computing resources offer the opportunity to build detailed and complex FDTD models of GPR to an extent that was not previously possible. To enable these types of simulations to be more easily realised, and also to facilitate the addition of more advanced features, gprMax has been redeveloped and significantly modernised. The original C-based code has been completely rewritten using a combination of Python and Cython programming languages. Standard and robust file formats have been chosen for geometry and field output files. New advanced modelling features have been added including: an unsplit implementation of higher order Perfectly Matched Layers (PMLs) using a recursive integration approach; diagonally anisotropic materials; dispersive media using multi-pole Debye, Drude or Lorenz expressions; soil modelling using a semi-empirical formulation for dielectric properties and fractals for geometric characteristics; rough surface generation; and the ability to embed complex transducers and targets.

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

    Science.gov (United States)

    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/.

  4. Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data

    Directory of Open Access Journals (Sweden)

    Etienne Combrisson

    2017-09-01

    Full Text Available We introduce Sleep, a new Python open-source graphical user interface (GUI dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1 Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2 Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM, (3 Implementation of practical signal processing tools such as re-referencing or filtering, and (4 Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module.

  5. AxonSeg: Open Source Software for Axon and Myelin Segmentation and Morphometric Analysis.

    Science.gov (United States)

    Zaimi, Aldo; Duval, Tanguy; Gasecka, Alicja; Côté, Daniel; Stikov, Nikola; Cohen-Adad, Julien

    2016-01-01

    Segmenting axon and myelin from microscopic images is relevant for studying the peripheral and central nervous system and for validating new MRI techniques that aim at quantifying tissue microstructure. While several software packages have been proposed, their interface is sometimes limited and/or they are designed to work with a specific modality (e.g., scanning electron microscopy (SEM) only). Here we introduce AxonSeg, which allows to perform automatic axon and myelin segmentation on histology images, and to extract relevant morphometric information, such as axon diameter distribution, axon density and the myelin g-ratio. AxonSeg includes a simple and intuitive MATLAB-based graphical user interface (GUI) and can easily be adapted to a variety of imaging modalities. The main steps of AxonSeg consist of: (i) image pre-processing; (ii) pre-segmentation of axons over a cropped image and discriminant analysis (DA) to select the best parameters based on axon shape and intensity information; (iii) automatic axon and myelin segmentation over the full image; and (iv) atlas-based statistics to extract morphometric information. Segmentation results from standard optical microscopy (OM), SEM and coherent anti-Stokes Raman scattering (CARS) microscopy are presented, along with validation against manual segmentations. Being fully-automatic after a quick manual intervention on a cropped image, we believe AxonSeg will be useful to researchers interested in large throughput histology. AxonSeg is open source and freely available at: https://github.com/neuropoly/axonseg.

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

    Science.gov (United States)

    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.

  7. Free/Libre Open Source Software in Health Care: A Review

    Science.gov (United States)

    Schmuhl, Holger; Demski, Hans

    2014-01-01

    Objectives To assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC). Methods The review is based on a narrative review of the scientific literature as well as sources in the context of FLOSS-HC available through the Internet. All relevant available sources have been integrated into the MedFLOSS database and are freely available to the community. Results The literature review reveals that publications about FLOSS-HC are scarce. The largest part of information about FLOSS-HC is available on dedicated websites and not in the academic literature. There are currently FLOSS alternatives available for nearly every specialty in health care. Maturity and quality varies considerably and there is little information available on the percentage of systems that are actually used in health care delivery. Conclusions The global impact of FLOSS-HC is still very limited and no figures on the penetration and usage of FLOSS-HC are available. However, there has been a considerable growth in the last 5 to 10 years. While there where only few systems available a decade ago, in the meantime many systems got available (e.g., more than 300 in the MedFLOSS database). While FLOSS concepts play an important role in most IT related sectors (e.g., telecommunications, embedded devices) the healthcare industry is lagging behind this trend. PMID:24627814

  8. AxonSeg: open source software for axon and myelin segmentation and morphometric analysis

    Directory of Open Access Journals (Sweden)

    Aldo Zaimi

    2016-08-01

    Full Text Available Segmenting axon and myelin from microscopic images is relevant for studying the peripheral and central nervous system and for validating new MRI techniques that aim at quantifying tissue microstructure. While several software packages have been proposed, their interface is sometimes limited and/or they are designed to work with a specific modality (e.g., scanning electron microscopy only. Here we introduce AxonSeg, which allows to perform automatic axon and myelin segmentation on histology images, and to extract relevant morphometric information, such as axon diameter distribution, axon density and the myelin g-ratio. AxonSeg includes a simple and intuitive MATLAB-based graphical user interface and can easily be adapted to a variety of imaging modalities. The main steps of AxonSeg consist of: (i image pre-processing, (ii pre-segmentation of axons over a cropped image and discriminant analysis to select the best parameters based on axon shape and intensity information, (iii automatic axon and myelin segmentation over the full image and (iv atlas-based statistics to extract morphometric information. Segmentation results from standard optical microscopy (OM, scanning electron microscopy (SEM and coherent anti-Stokes Raman scattering (CARS microscopy are presented, along with validation against manual segmentations. Being fully-automatic after a quick manual intervention on a cropped image, we believe AxonSeg will be useful to researchers interested in large throughput histology. AxonSeg is open source and freely available at: https://github.com/neuropoly/axonseg.

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

    Science.gov (United States)

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

    2015-04-01

    Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of

  10. Woefzela - An open-source platform for ASR data collection in the developing world

    CSIR Research Space (South Africa)

    De Vries, NJ

    2011-08-01

    Full Text Available Building transcribed speech corpora for under-resourced languages plays a pivotal role in developing speech technologies for such languages. The authors have developed an open-source tool for devices running the Android operating system...

  11. Towards the Application of Open Source Software in Developing National Electronic Health Record-Narrative Review Article.

    Directory of Open Access Journals (Sweden)

    Farzaneh Aminpour

    2013-12-01

    Full Text Available Electronic Health Record (EHR is a repository of patient health information shared among multiple authorized users. As a modern method of storing and processing health information, it is a solution for improving quality, safety and efficiency of patient care and health system. However, establishment of EHR requires a significant investment of time and money. While many of healthcare providers have very limited capital, application of open source software would be considered as a solution in developing national electronic health record especially in countries with low income. The evidence showed that financial limitation is one of the obstacles to implement electronic health records in developing countries. Therefore, establishment of an open source EHR system capable of modifications according to the national requirements seems to be inevitable in Iran. The present study identifies the impact of application of open source software in developing national electronic health record in Iran.

  12. Towards the Application of Open Source Software in Developing National Electronic Health Record-Narrative Review Article.

    Science.gov (United States)

    Aminpour, Farzaneh; Sadoughi, Farahnaz; Ahmadi, Maryam

    2013-12-01

    Electronic Health Record (EHR) is a repository of patient health information shared among multiple authorized users. As a modern method of storing and processing health information, it is a solution for improving quality, safety and efficiency of patient care and health system. However, establishment of EHR requires a significant investment of time and money. While many of healthcare providers have very limited capital, application of open source software would be considered as a solution in developing national electronic health record especially in countries with low income. The evidence showed that financial limitation is one of the obstacles to implement electronic health records in developing countries. Therefore, establishment of an open source EHR system capable of modifications according to the national requirements seems to be inevitable in Iran. The present study identifies the impact of application of open source software in developing national electronic health record in Iran.

  13. Paleomagnetism.org: An online multi-platform open source environment for paleomagnetic data analysis

    Science.gov (United States)

    Koymans, Mathijs R.; Langereis, Cor G.; Pastor-Galán, Daniel; van Hinsbergen, Douwe J. J.

    2016-08-01

    This contribution provides an overview of Paleomagnetism.org, an open-source, multi-platform online environment for paleomagnetic data analysis. Paleomagnetism.org provides an interactive environment where paleomagnetic data can be interpreted, evaluated, visualized, and exported. The Paleomagnetism.org application is split in to an interpretation portal, a statistics portal, and a portal for miscellaneous paleomagnetic tools. In the interpretation portal, principle component analysis can be performed on visualized demagnetization diagrams. Interpreted directions and great circles can be combined to find great circle solutions. These directions can be used in the statistics portal, or exported as data and figures. The tools in the statistics portal cover standard Fisher statistics for directions and VGPs, including other statistical parameters used as reliability criteria. Other available tools include an eigenvector approach foldtest, two reversal test including a Monte Carlo simulation on mean directions, and a coordinate bootstrap on the original data. An implementation is included for the detection and correction of inclination shallowing in sediments following TK03.GAD. Finally we provide a module to visualize VGPs and expected paleolatitudes, declinations, and inclinations relative to widely used global apparent polar wander path models in coordinates of major continent-bearing plates. The tools in the miscellaneous portal include a net tectonic rotation (NTR) analysis to restore a body to its paleo-vertical and a bootstrapped oroclinal test using linear regressive techniques, including a modified foldtest around a vertical axis. Paleomagnetism.org provides an integrated approach for researchers to work with visualized (e.g. hemisphere projections, Zijderveld diagrams) paleomagnetic data. The application constructs a custom exportable file that can be shared freely and included in public databases. This exported file contains all data and can later be

  14. Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping.

    Science.gov (United States)

    Klukas, Christian; Chen, Dijun; Pape, Jean-Michel

    2014-06-01

    High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites to quantify plant growth and performance based on phenotypic traits. Issues include data management, image analysis, and result visualization of large-scale phenotypic data sets. Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping. IAP provides user-friendly interfaces, and its core functions are highly adaptable. Our system supports image data transfer from different acquisition environments and large-scale image analysis for different plant species based on real-time imaging data obtained from different spectra. Due to the huge amount of data to manage, we utilized a common data structure for efficient storage and organization of data for both input data and result data. We implemented a block-based method for automated image processing to extract a representative list of plant phenotypic traits. We also provide tools for build-in data plotting and result export. For validation of IAP, we performed an example experiment that contains 33 maize (Zea mays 'Fernandez') plants, which were grown for 9 weeks in an automated greenhouse with nondestructive imaging. Subsequently, the image data were subjected to automated analysis with the maize pipeline implemented in our system. We found that the computed digital volume and number of leaves correlate with our manually measured data in high accuracy up to 0.98 and 0.95, respectively. In summary, IAP provides a multiple set of functionalities for import/export, management, and automated analysis of high-throughput plant phenotyping data, and its analysis results are highly reliable.

  15. An open-source analytical platform for analysis of C. elegans swimming-induced paralysis.

    Science.gov (United States)

    Hardaway, J Andrew; Wang, Jing; Fleming, Paul A; Fleming, Katherine A; Whitaker, Sarah M; Nackenoff, Alex; Snarrenberg, Chelsea L; Hardie, Shannon L; Zhang, Bing; Blakely, Randy D

    2014-07-30

    The nematode Caenhorhabditis elegans offers great power for the identification and characterization of genes that regulate behavior. In support of this effort, analytical methods are required that provide dimensional analyses of subcomponents of behavior. Previously, we demonstrated that loss of the presynaptic dopamine (DA) transporter, dat-1, evokes DA-dependent Swimming-Induced Paralysis (Swip) (Mcdonald et al., 2007), a behavior compatible with forward genetic screens (Hardaway et al., 2012). Here, we detail the development and implementation of SwimR, a set of tools that provide for an automated, kinetic analysis of C. elegans Swip. SwimR relies on open source programs that can be freely implemented and modified. We show that SwimR can display time-dependent alterations of swimming behavior induced by drug-treatment, illustrating this capacity with the dat-1 blocker and tricyclic antidepressant imipramine (IMI). We demonstrate the capacity of SwimR to extract multiple kinetic parameters that are impractical to obtain in manual assays. Standard measurements of C. elegans swimming utilizes manual assessments of the number of animals exhibiting swimming versus paralysis. Our approach deconstructs the time course and rates of movement in an automated fashion, offering a significant increase in the information that can be obtained from swimming behavior. The SwimR platform is a powerful tool for the deconstruction of worm thrashing behavior in the context of both genetic and pharmacological manipulations that can be used to segregate pathways that underlie nematode swimming mechanics. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Modeling of fire smoke movement in multizone garments building using two open source platforms

    Science.gov (United States)

    Khandoker, Md. Arifur Rahman; Galib, Musanna; Islam, Adnan; Rahman, Md. Ashiqur

    2017-06-01

    Casualty of garment factory workers from factory fire in Bangladesh is a recurring tragedy. Smoke, which is more fatal than fire itself, often propagates through different pathways from lower to upper floors during building fire. Among the toxic gases produced from a building fire, carbon monoxide (CO) can be deadly, even in small amounts. This paper models the propagation and transportation of fire induced smoke (CO) that resulted from the burning of synthetic polyester fibers using two open source platforms, CONTAM and Fire Dynamics Simulator (FDS). Smoke migration in a generic multistoried garment factory building in Bangladesh is modeled using CONTAM where each floor is compartmentalized by different zones. The elevator and stairway shafts are modeled by phantom zones to simulate contaminant (CO) transport from one floor to upper floors. FDS analysis involves burning of two different stacks of polyester jacket of six feet height and with a maximum heat release rate per unit area of 1500kw/m2 over a storage area 50m2 and 150m2, respectively. The resulting CO generation and removal rates from FDS are used in CONTAM to predict fire-borne CO propagation in different zones of the garment building. Findings of the study exhibit that the contaminant flow rate is a strong function of the position of building geometry, location of initiation of fire, amount of burnt material, presence of AHU and contaminant generation and removal rate of CO from the source location etc. The transport of fire-smoke in the building Hallways, stairways and lifts are also investigated in detail to examine the safe egress of the occupants in case of fire.

  17. Open-Source Colorimeter

    Science.gov (United States)

    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

  18. PALEOMAGNETISM.ORG - AN Online Multi-Platform and Open Source Environment for Paleomagnetic Analysis

    Science.gov (United States)

    Koymans, M. R.; Langereis, C. G.; Pastor-Galán, D.; Van Hinsbergen, D. J. J.

    2015-12-01

    This contribution provides an overview of the features of Paleomagnetism.org, a new open-source online environment for paleomagnetic analysis that is supported by all modern browsers on multiple platforms. The core functionality of Paleomagnetism.org is written in JavaScript and maintains an interactive website in which paleomagnetic data can be interpreted, evaluated, visualized, and exported. Although being an online platform, the data processing is performed client-sided within the browser to respect the integrity of the data and users. In the interpretation portal, principle component analysis (Kirschvink et al., 1981) can be applied on visualized demagnetization data (Zijderveld, 1967). The interpreted directions and great circles can be combined using the iterative procedure of (McFadden and McElhinny, 1988). The resulting magnetic directions can be used in the statistics portal or exported as raw tabulated data and figures. The available tools in the statistics portal cover standard Fisher statistics for directional data and virtual geomagnetic poles (Fisher, 1953; Butler, 1992; Deenen et al., 2011). Other tools include the eigenvector approach foldtest (Tauxe and Watson, 1994), a bootstrapped reversal test (Tauxe et al., 2009), and the classical reversal test of (McFadden and McElhinny, 1990). An implementation exists for the detection and correction of inclination shallowing in sediments (Tauxe and Kent, 2004; Tauxe et al., 2008) and a module to visualize custom or default APWP reference frames (Torsvik et al., 2012; Kent and Irving, 2010; Besse and Courtillot, 2002) for continent-bearing plates. Paleomagnetism.org provides an integrated approach for researchers to export tabulated and visualized (e.g. equal area projections) paleomagnetic data. The portals construct a custom exportable file that can be shared with other researchers and included in public databases. With a publication, this custom file can be appended and would contain all data used in the

  19. Celeris: A GPU-accelerated open source software with a Boussinesq-type wave solver for real-time, interactive simulation and visualization

    CERN Document Server

    Tavakkol, Sasan

    2016-01-01

    In this paper, we introduce an interactive coastal wave simulation and visualization software, called Celeris. Celeris is an open source software which needs minimum preparation to run on a Windows machine. The software solves the extended Boussinesq equations using a hybrid finite volume - finite difference method and supports moving shoreline boundaries. The simulation and visualization are performed on the GPU using Direct3D libraries, which enables the software to run faster than real-time. Celeris provides a first-of-its-kind interactive modeling platform for coastal wave applications and it supports simultaneous visualization with both photorealistic and colormapped rendering capabilities. We validate our software through comparison with three standard benchmarks for non-breaking and breaking waves.

  20. UNESCO's HOPE Initiative—Providing Free and Open-Source Hydrologic Software for Effective and Sustainable Management of Africa's Water Resources Temporary Title

    Science.gov (United States)

    Barlow, P. M.; Filali-Meknassi, Y.; Sanford, W. E.; Winston, R. B.; Kuniansky, E.; Dawson, C.

    2015-12-01

    UNESCO's HOPE Initiative—the Hydro Free and (or) Open-source Platform of Experts—was launched in June 2013 as part of UNESCO's International Hydrological Programme. The Initiative arose in response to a recognized need to make free and (or) open-source water-resources software more widely accessible to Africa's water sector. A kit of software is being developed to provide African water authorities, teachers, university lecturers, and researchers with a set of programs that can be enhanced and (or) applied to the development of efficient and sustainable management strategies for Africa's water resources. The Initiative brings together experts from the many fields of water resources to identify software that might be included in the kit, to oversee an objective process for selecting software for the kit, and to engage in training and other modes of capacity building to enhance dissemination of the software. To date, teams of experts from the fields of wastewater treatment, groundwater hydrology, surface-water hydrology, and data management have been formed to identify relevant software from their respective fields. An initial version of the HOPE Software Kit was released in late August 2014 and consists of the STOAT model for wastewater treatment developed by the Water Research Center (United Kingdom) and the MODFLOW-2005 model for groundwater-flow simulation developed by the U.S. Geological Survey. The Kit is available on the UNESCO HOPE website (http://www.hope-initiative.net/).Training in the theory and use of MODFLOW-2005 is planned in southern Africa in conjunction with UNESCO's study of the Kalahari-Karoo/Stampriet Transboundary Aquifer, which extends over an area that includes parts of Botswana, Namibia, and South Africa, and in support of the European Commission's Horizon 2020 FREEWAT project (FREE and open source software tools for WATer resource management; see the UNESCO HOPE website).

  1. ANALISIS FAKTOR-FAKTOR YANG MEMPENGARUHI PERILAKU PENGGUNA UNTUK MENDORONG PENGGUNAAN OPEN SOURCE SOFTWARE DAN IMPLIKASI MANAJERIALNYA

    Directory of Open Access Journals (Sweden)

    Erry Ricardo Nurzal

    2011-08-01

    Full Text Available Normal 0 false false false This study has two objectives namely (1 To measure the acceptance of Open Source Software, (2 To determine whether OSS quality, OSS availability, personal innovativeness, gender, income, social influence, cultural affinity and type of university influence users using or not using Open Source Software.Data used in this research were primary data. The data collected were data from informatic engineering or computer science students using OSS in Bogor Agricultural University, Bandung Institute of Technology, University of Indonesia, University of Gunadarma, University of Bina Nusantara and University of Budi Luhur. Questionnaire was used to collect the data. Sampling technique was done randomly.The study results show that students accepting OSS were 77,6 % and students not accepting OSS were 22,4 % at the state university groups. Meanwhile, students accepting OSS were 49,9 % and students not accepting OSS were 50,1 % in the private university groups.. External factors directly influencing users for using Open Source Software were personal innovativeness, income and status of university. Moreover,   external factors indirectly influencing users for using or not using Open Source Software were OSS quality, OSS availability, personal innovativeness, gender, cultural affinity and  status of university.

  2. Pro Linux system administration learn to build systems for your business using free and open source software

    CERN Document Server

    Matotek, Dennis; Lieverdink, Peter

    2017-01-01

    This book aims to ease the entry of businesses to the world of zero-cost software running on Linux. It takes a layered, component-based approach to open source business systems, while training system administrators as the builders of business infrastructure.

  3. Socio-Technical Deliberation about Free and Open Source Software: Accounting for the Status of Artifacts in Public Life

    Science.gov (United States)

    Benoit-Barne, Chantal

    2007-01-01

    This essay investigates the rhetorical practices of socio-technical deliberation about free and open source (F/OS) software, providing support for the idea that a public sphere is a socio-technical ensemble that is discursive and fluid, yet tangible and organized because it is enacted by both humans and non-humans. In keeping with the empirical…

  4. VMStools: Open-source software for the processing, analysis and visualisation of fisheries logbook and VMS data

    NARCIS (Netherlands)

    Hintzen, N.T.; Bastardie, F.; Beare, D.J.; Piet, G.J.; Ulrich, C.; Deporte, N.; Egekvist, J.; Degel, H.

    2012-01-01

    VMStools is a package of open-source software, build using the freeware environment R, specifically developed for the processing, analysis and visualisation of landings (logbooks) and vessel location data (VMS) from commercial fisheries. Analyses start with standardized data formats for logbook (EFL

  5. VMStools: Open-source software for the processing, analysis and visualization of fisheries logbook and VMS data

    DEFF Research Database (Denmark)

    Hintzen, Niels T.; Bastardie, Francois; Beare, Doug

    2012-01-01

    VMStools is a package of open-source software, build using the freeware environment R, specifically developed for the processing, analysis and visualisation of landings (logbooks) and vessel location data (VMS) from commercial fisheries. Analyses start with standardized data formats for logbook (...

  6. VMStools: Open-source software for the processing, analysis and visualisation of fisheries logbook and VMS data

    NARCIS (Netherlands)

    Hintzen, N.T.; Bastardie, F.; Beare, D.J.; Piet, G.J.; Ulrich, C.; Deporte, N.; Egekvist, J.; Degel, H.

    2012-01-01

    VMStools is a package of open-source software, build using the freeware environment R, specifically developed for the processing, analysis and visualisation of landings (logbooks) and vessel location data (VMS) from commercial fisheries. Analyses start with standardized data formats for logbook (EFL

  7. Lots of Librarians Can Keep Stuff Safe: Libraries Are Able to Safeguard Content with LOCKSS, Open Source Digital Preservation Software

    Science.gov (United States)

    Schneider, Karen G.

    2007-01-01

    Over the next several decades, libraries will face the potential loss of all the e-journals, ebooks, electronic theses, local digital collections, and other "e-stuff" curated for the public good. A solution to this problem is LOCKSS ("Lots of Copies Keep Stuff Safe"), a free, open-source digital-preservation software from Stanford University that…

  8. VMStools: Open-source software for the processing, analysis and visualisation of fisheries logbook and VMS data

    NARCIS (Netherlands)

    Hintzen, N.T.; Bastardie, F.; Beare, D.J.; Piet, G.J.; Ulrich, C.; Deporte, N.; Egekvist, J.; Degel, H.

    2012-01-01

    VMStools is a package of open-source software, build using the freeware environment R, specifically developed for the processing, analysis and visualisation of landings (logbooks) and vessel location data (VMS) from commercial fisheries. Analyses start with standardized data formats for logbook

  9. Review: Niels C. Taubert (2006. Produktive Anarchie? Netzwerke freier Softwareentwicklung [Productive Anarchy? Networks of Open Source Software Development

    Directory of Open Access Journals (Sweden)

    Matthias Groß

    2007-01-01

    Full Text Available Open source software is software designed to allow anyone to use and make changes in the software. This practice often renders the product superior to more centralized models such as those used in commercial software companies. How is such a phenomenon possible in a time where nothing seems to be acquirable save by purchase? Niels C. TAUBERT's book Productive Anarchy? Networks of Open Source Software Development aims at a sociological understanding of the prerequisites and conditions for the success of open source software. One of the conclusions of TAUBERT's book is that the process of open software development needs to be understood as adaptive and experimental. A continuous feedback between the context of production and the context of application is the basis for robust and successful software production. One of the surprising results of the book is that the most important requirement for this feedback process is a set of norms—neutrality, communism, disinterestedness, and universalism—norms that Robert MERTON associated with academic science in the 1940s. If TAUBERT is right that these norms are to be found outside the world of institutional science in open source software development projects today, then his case study can be seen as an indicator for a new form of knowledge production in the 21st century, where the social relevance and responsibility of a research process are keys to successful innovation. With this book, which deserves a wide readership, TAUBERT makes an important contribution to our understanding of the successful organization of technology development. URN: urn:nbn:de:0114-fqs0701109

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

    Science.gov (United States)

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

    2017-04-18

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

  11. A Flexible Method for Producing F.E.M. Analysis of Bone Using Open-Source Software

    Science.gov (United States)

    Boppana, Abhishektha; Sefcik, Ryan; Meyers, Jerry G.; Lewandowski, Beth E.

    2016-01-01

    This project, performed in support of the NASA GRC Space Academy summer program, sought to develop an open-source workflow methodology that segmented medical image data, created a 3D model from the segmented data, and prepared the model for finite-element analysis. In an initial step, a technological survey evaluated the performance of various existing open-source software that claim to perform these tasks. However, the survey concluded that no single software exhibited the wide array of functionality required for the potential NASA application in the area of bone, muscle and bio fluidic studies. As a result, development of a series of Python scripts provided the bridging mechanism to address the shortcomings of the available open source tools. The implementation of the VTK library provided the most quick and effective means of segmenting regions of interest from the medical images; it allowed for the export of a 3D model by using the marching cubes algorithm to build a surface mesh. To facilitate the development of the model domain from this extracted information required a surface mesh to be processed in the open-source software packages Blender and Gmsh. The Preview program of the FEBio suite proved to be sufficient for volume filling the model with an unstructured mesh and preparing boundaries specifications for finite element analysis. To fully allow FEM modeling, an in house developed Python script allowed assignment of material properties on an element by element basis by performing a weighted interpolation of voxel intensity of the parent medical image correlated to published information of image intensity to material properties, such as ash density. A graphical user interface combined the Python scripts and other software into a user friendly interface. The work using Python scripts provides a potential alternative to expensive commercial software and inadequate, limited open-source freeware programs for the creation of 3D computational models. More work

  12. DataViewer3D: An open-source, cross-platform multi-modal neuroimaging data visualization tool

    Directory of Open Access Journals (Sweden)

    Andre D Gouws

    2009-03-01

    Full Text Available Integration and display of results from multiple neuroimaging modalities (e.g. MRI, MEG, EEG relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK for 2D and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE™ and DICOM formats for MRI data display (including statistical data overlay. Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additonal format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.

  13. The Evolving Role of Open Source Software in Medicine and Health Services

    Directory of Open Access Journals (Sweden)

    Sevket Seref Arikan

    2013-01-01

    Full Text Available The past five decades have witnessed immense coevolution of methods and tools of information technology, and their practical and experimental application within the medical and healthcare domain. Healthcare itself continues to evolve in response to change in healthcare needs, progress in the scientific foundations of treatments, and in professional and managerial organization of affordable and effective services, in which patients and their families and carers increasingly participate. Taken together, these trends impose highly complex underlying challenges for the design, development, and sustainability of the quality of supporting information services and software infrastructure that are needed. The challenges are multidisciplinary and multiprofessional in scope, and they require deeper study and learning to inform policy and promote public awareness of the problems health services have faced in this area for many years. The repeating pattern of failure to live up to expectations of policy-driven national health IT initiatives has proved very costly and remains frustrating and unproductive for all involved. In this article, we highlight the barriers to progress and discuss the dangers of pursuing a standardization framework devoid of empirical testing and iterative development. We give the example of the openEHR Foundation, which was established at University College London (UCL in London, England, with members in 80 countries. The Foundation is a not-for-profit company providing open specifications and working for generic standards for electronic records, informed directly by a wide range of implementation experience. We also introduce the Opereffa open source framework, which was developed at UCL based on these specifications and which has been downloaded in some 70 countries. We argue that such an approach is now essential to support good discipline, innovation, and governance at the heart of medicine and health services, in line with the

  14. Open Source Subtitle Editor Software Study for Section 508 Close Caption Applications

    Science.gov (United States)

    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.

  15. Low-cost photometers and open source software for Light Pollution research

    Science.gov (United States)

    Zamorano, Jaime; Nievas, Miguel; Sánchez de Miguel, Alejandro; Tapia, Carlos; García, Cristóbal; Pascual, Sergio; Ocaña, Francisco; Gallego, Jesús

    2015-08-01

    Astronomical observatories have been measuring the brightness of the sky (NSB) using the methods of astronomical photometry with telescopes, photoelectric photometers and CCD cameras. The observations are disperse and sporadic. This is why some dedicated devices (including all-sky cameras) have been designed to automatically monitor the sky brightness at the observatories.These sophisticated and expensive instruments are restricted to research groups since they are out of reach for the interested citizens who wish to make a contribution to light pollution research. Most of them are using sky photometers (sky quality meter, SQM) a commercial photometer, designed to measure NSB in a photometric band that mimics the human eye response, that provide reliable data at an affordable budget.We are designing and building low cost devices to measure night sky brightness that could be widely distributed. The final designs will be calibrated and distributed to the community as open hardware. The researchers and also the interested people could acquire the parts and replicate the photometers from the instructions provided. Among the new features for these photometers we plan to add the capability to automatically send data to a repository located in a server, the autonomous operation with solar panels and batteries in remote places and the ability to measure in different spectral bands.We also present open source software for NSB research. PySQM, designed for SQM photometers, records the NSB data in the IDA-IAU standard data format and also builds the plots along the night. PyASB analyses all-sky images to determine photometric parameters and to build all-sky NSB maps

  16. Open-Source GIS

    Energy Technology Data Exchange (ETDEWEB)

    Vatsavai, Raju [ORNL; Burk, Thomas E [University of Minnesota; Lime, Steve [Minnesota Department of Natural Resources

    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.

  17. JGrass-NewAge hydrological system: an open-source platform for the replicability of science.

    Science.gov (United States)

    Bancheri, Marialaura; Serafin, Francesco; Formetta, Giuseppe; Rigon, Riccardo; David, Olaf

    2017-04-01

    JGrass-NewAge is an open source semi-distributed hydrological modelling system. It is based on the object modelling framework (OMS version 3), on the JGrasstools and on the Geotools. OMS3 allows to create independent packages of software which can be connected at run-time in a working modelling solution. These components are available as library/dependency or as repository to fork in order to add further features. Different tools are adopted to make easier the integration, the interoperability and the use of each package. Most of the components are Gradle integrated, since it represents the state-of-art of the building systems, especially for Java projects. The continuous integration is a further layer between local source code (client-side) and remote repository (server-side) and ensures the building and the testing of the source code at each commit. Finally, the use of Zenodo makes the code hosted in GitHub unique, citable and traceable, with a defined DOI. Following the previous standards, each part of the hydrological cycle is implemented in JGrass-NewAge as a component that can be selected, adopted, and connected to obtain a user "customized" hydrological model. A variety of modelling solutions are possible, allowing a complete hydrological analysis. Moreover, thanks to the JGrasstools and the Geotools, the visualization of the data and of the results using a selected GIS is possible. After the geomorphological analysis of the watershed, the spatial interpolation of the meteorological inputs can be performed using both deterministic (IDW) and geostatistic (Kriging) algorithms. For the radiation balance, the shortwave and longwave radiation can be estimated, which are, in turn, inputs for the simulation of the evapotranspiration, according to Priestly-Taylor and Penman-Monteith formulas. Three degree-day models are implemented for the snow melting and SWE. The runoff production can be simulated using two different components, "Adige" and "Embedded Reservoirs

  18. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools

    OpenAIRE

    Ham, Timothy S.; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna (Kuei-Yen); Nathan J Hillson; Jay D Keasling

    2012-01-01

    The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE install...

  19. Building a world-wide open source community around a software framework: progress, dos, and don'ts

    Science.gov (United States)

    Ibsen, Jorge; Antognini, Jonathan; Avarias, Jorge; Caproni, Alessandro; Fuessling, Matthias; Gimenez, Guillermo; Verma, Khushbu; Mora, Matias; Schwarz, Joseph; Staig, Tomás.

    2016-08-01

    As we all know too well, building up a collaborative community around a software infrastructure is not easy. Besides recruiting enthusiasts to work as part of it, mostly for free, to succeed you also need to overcome a number of technical, sociological, and, to our surprise, some political hurdles. The ALMA Common Software (ACS) was developed at ESO and partner institutions over the course of more than 10 years. While it was mainly intended for the ALMA Observatory, it was early on thought as a generic distributed control framework. ACS has been periodically released to the public through an LGPL license, which encouraged around a dozen non-ALMA institutions to make use of ACS for both industrial and educational applications. In recent years, the Cherenkov Telescope Array and the LLAMA Observatory have also decided to adopt the framework for their own control systems. The aim of the "ACS Community" is to support independent initiatives in making use of the ACS framework and to further contribute to its development. The Community provides access to a growing network of volunteers eager to develop ACS in areas that are not necessarily in ALMA's interests, and/or were not within the original system scope. Current examples are: support for additional OS platforms, extension of supported hardware interfaces, a public code repository and a build farm. The ACS Community makes use of existing collaborations with Chilean and Brazilian universities, reaching out to promising engineers in the making. At the same time, projects actively using ACS have committed valuable resources to assist the Community's work. Well established training programs like the ACS Workshops are also being continued through the Community's work. This paper aims to give a detailed account of the ongoing (second) journey towards establishing a world-wide open source collaboration around ACS. The ACS Community is growing into a horizontal partnership across a decentralized and diversified group of

  20. VideoHacking: Automated Tracking and Quantification of Locomotor Behavior with Open Source Software and Off-the-Shelf Video Equipment.

    Science.gov (United States)

    Conklin, Emily E; Lee, Kathyann L; Schlabach, Sadie A; Woods, Ian G

    2015-01-01

    Differences in nervous system function can result in differences in behavioral output. Measurements of animal locomotion enable the quantification of these differences. Automated tracking of animal movement is less labor-intensive and bias-prone than direct observation, and allows for simultaneous analysis of multiple animals, high spatial and temporal resolution, and data collection over extended periods of time. Here, we present a new video-tracking system built on Python-based software that is free, open source, and cross-platform, and that can analyze video input from widely available video capture devices such as smartphone cameras and webcams. We validated this software through four tests on a variety of animal species, including larval and adult zebrafish (Danio rerio), Siberian dwarf hamsters (Phodopus sungorus), and wild birds. These tests highlight the capacity of our software for long-term data acquisition, parallel analysis of multiple animals, and application to animal species of different sizes and movement patterns. We applied the software to an analysis of the effects of ethanol on thigmotaxis (wall-hugging) behavior on adult zebrafish, and found that acute ethanol treatment decreased thigmotaxis behaviors without affecting overall amounts of motion. The open source nature of our software enables flexibility, customization, and scalability in behavioral analyses. Moreover, our system presents a free alternative to commercial video-tracking systems and is thus broadly applicable to a wide variety of educational settings and research programs.

  1. VideoHacking: Automated Tracking and Quantification of Locomotor Behavior with Open Source Software and Off-the-Shelf Video Equipment

    Science.gov (United States)

    Conklin, Emily E.; Lee, Kathyann L.; Schlabach, Sadie A.; Woods, Ian G.

    2015-01-01

    Differences in nervous system function can result in differences in behavioral output. Measurements of animal locomotion enable the quantification of these differences. Automated tracking of animal movement is less labor-intensive and bias-prone than direct observation, and allows for simultaneous analysis of multiple animals, high spatial and temporal resolution, and data collection over extended periods of time. Here, we present a new video-tracking system built on Python-based software that is free, open source, and cross-platform, and that can analyze video input from widely available video capture devices such as smartphone cameras and webcams. We validated this software through four tests on a variety of animal species, including larval and adult zebrafish (Danio rerio), Siberian dwarf hamsters (Phodopus sungorus), and wild birds. These tests highlight the capacity of our software for long-term data acquisition, parallel analysis of multiple animals, and application to animal species of different sizes and movement patterns. We applied the software to an analysis of the effects of ethanol on thigmotaxis (wall-hugging) behavior on adult zebrafish, and found that acute ethanol treatment decreased thigmotaxis behaviors without affecting overall amounts of motion. The open source nature of our software enables flexibility, customization, and scalability in behavioral analyses. Moreover, our system presents a free alternative to commercial video-tracking systems and is thus broadly applicable to a wide variety of educational settings and research programs. PMID:26240518

  2. The Seismic Tool-Kit (STK): an open source software for seismology and signal processing.

    Science.gov (United States)

    Reymond, Dominique

    2016-04-01

    We present an open source software project (GNU public license), named STK: Seismic ToolKit, that is dedicated mainly for seismology and signal processing. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 19 500 downloads at the date of writing. The STK project is composed of two main branches: First, a graphical interface dedicated to signal processing (in the SAC format (SAC_ASCII and SAC_BIN): where the signal can be plotted, zoomed, filtered, integrated, derivated, ... etc. (a large variety of IFR and FIR filter is proposed). The estimation of spectral density of the signal are performed via the Fourier transform, with visualization of the Power Spectral Density (PSD) in linear or log scale, and also the evolutive time-frequency representation (or sonagram). The 3-components signals can be also processed for estimating their polarization properties, either for a given window, or either for evolutive windows along the time. This polarization analysis is useful for extracting the polarized noises, differentiating P waves, Rayleigh waves, Love waves, ... etc. Secondly, a panel of Utilities-Program are proposed for working in a terminal mode, with basic programs for computing azimuth and distance in spherical geometry, inter/auto-correlation, spectral density, time-frequency for an entire directory of signals, focal planes, and main components axis, radiation pattern of P waves, Polarization analysis of different waves (including noize), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. A MINimum library of Linear AlGebra (MIN-LINAG) is also provided for computing the main matrix process like: QR/QL decomposition, Cholesky solve of linear system, finding eigen value/eigen vectors, QR-solve/Eigen-solve of linear equations systems ... etc. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. Usefull links: http

  3. OpenBEM - An open source Boundary Element Method software in Acoustics

    DEFF Research Database (Denmark)

    Cutanda Henriquez, Vicente; Juhl, Peter Møller

    2010-01-01

    OpenBEM is a collection of open source programs for solving the Helmholtz Equation using the Boundary Element Method. The collection is written in Matlab by the authors and contains codes for dealing with exterior and interior problems in two or three dimensions as well as implementation of axi...

  4. eSlide suite: an open source software system for whole slide imaging.

    Science.gov (United States)

    Della Mea, V; Bortolotti, N; Beltrami, C A

    2009-08-01

    This short report briefly describes the principles underlying the telepathology technique known as whole slide imaging, and the design and implementation of a system for acquisition and visualisation of digital slides. The developed system, including an acquisition module and a visualisation module, is available as an open source on the Internet, together with sample acquired slides.

  5. Energy Tracking Software Platform

    Energy Technology Data Exchange (ETDEWEB)

    Ryan Davis; Nathan Bird; Rebecca Birx; Hal Knowles

    2011-04-04

    Acceleration has created an interactive energy tracking and visualization platform that supports decreasing electric, water, and gas usage. Homeowners have access to tools that allow them to gauge their use and track progress toward a smaller energy footprint. Real estate agents have access to consumption data, allowing for sharing a comparison with potential home buyers. Home builders have the opportunity to compare their neighborhood's energy efficiency with competitors. Home energy raters have a tool for gauging the progress of their clients after efficiency changes. And, social groups are able to help encourage members to reduce their energy bills and help their environment. EnergyIT.com is the business umbrella for all energy tracking solutions and is designed to provide information about our energy tracking software and promote sales. CompareAndConserve.com (Gainesville-Green.com) helps homeowners conserve energy through education and competition. ToolsForTenants.com helps renters factor energy usage into their housing decisions.

  6. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data

    Energy Technology Data Exchange (ETDEWEB)

    Kyle, Jennifer E.; Crowell, Kevin L.; Casey, Cameron P.; Fujimoto, Grant M.; Kim, Sangtae; Dautel, Sydney E.; Smith, Richard D.; Payne, Samuel H.; Metz, Thomas O.

    2017-01-31

    We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species.

  7. Free Open Source Software: FOSS Based e-learning, Mobile Learning Systems Together with Blended Learning System

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2013-11-01

    Full Text Available Free Open Source Software: FOSS based e-learning system is proposed together with blended learning and mobile learning. Mashup search engine for e-learning contents search and content adaptation from e-learning to mobile learning content are also implemented. Through implementation of the proposed system, it is found that the system does work well for improvement of learning efficiency.

  8. Towards the Application of Open Source Software in Developing National Electronic Health Record-Narrative Review Article

    OpenAIRE

    2013-01-01

    Abstract Electronic Health Record (EHR) is a repository of patient health information shared among multiple authorized users. As a modern method of storing and processing health information, it is a solution for improving quality, safety and efficiency of patient care and health system. However, establishment of EHR requires a significant investment of time and money. While many of healthcare providers have very limited capital, application of open source software would be considered as a sol...

  9. The MyHealthService approach for chronic disease management based on free open source software and low cost components.

    Science.gov (United States)

    Vognild, Lars K; Burkow, Tatjana M; Luque, Luis Fernandez

    2009-01-01

    In this paper we present an approach to building personal health services, supporting following-up, physical exercising, health education, and psychosocial support for the chronically ill, based on free open source software and low-cost computers, mobile devices, and consumer health and fitness devices. We argue that this will lower the cost of the systems, which is important given the increasing number of people with chronicle diseases and limited healthcare budgets.

  10. Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain.

    Directory of Open Access Journals (Sweden)

    Lev E Givon

    Full Text Available We have developed an open software platform called Neurokernel for collaborative development of comprehensive models of the brain of the fruit fly Drosophila melanogaster and their execution and testing on multiple Graphics Processing Units (GPUs. Neurokernel provides a programming model that capitalizes upon the structural organization of the fly brain into a fixed number of functional modules to distinguish between these modules' local information processing capabilities and the connectivity patterns that link them. By defining mandatory communication interfaces that specify how data is transmitted between models of each of these modules regardless of their internal design, Neurokernel explicitly enables multiple researchers to collaboratively model the fruit fly's entire brain by integration of their independently developed models of its constituent processing units. We demonstrate the power of Neurokernel's model integration by combining independently developed models of the retina and lamina neuropils in the fly's visual system and by demonstrating their neuroinformation processing capability. We also illustrate Neurokernel's ability to take advantage of direct GPU-to-GPU data transfers with benchmarks that demonstrate scaling of Neurokernel's communication performance both over the number of interface ports exposed by an emulation's constituent modules and the total number of modules comprised by an emulation.

  11. Open source molecular modeling.

    Science.gov (United States)

    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.

  12. Knowledge creation in virtual communities – Exploring practices in open source software hacker communities

    OpenAIRE

    Matheus, Thomas; Sarma, Meera

    2015-01-01

    This paper offers an exploratory conceptual and theoretical examination of knowledge creation within virtual communities of hackers. By distinguishing between different types of virtual communities, we argue that hacker communities involved in free and open source activities possess special structural and processual characteristics that are conducive to innovative product development. Drawing on diverse literatures, this paper thus builds an initial understanding of how a hacker community is ...

  13. Open source non-invasive prenatal testing platform and its performance in a public health laboratory

    DEFF Research Database (Denmark)

    Johansen, Peter; Richter, Stine R; Balslev-Harder, Marie

    2016-01-01

    : The pipeline correctly detected 27/27 trisomy 21, 4/4 trisomy 18, and 3/3 trisomy 13 fetuses. Neither false negatives nor false positives (chromosomes 13, 18, and 21) were observed in our validation dataset. Fetal sex was identified correctly in all but one triploid fetus (172/173). SeqFF showed a strong......OBJECTIVE: The objective of this study was to introduce non-invasive prenatal testing (NIPT) for fetal autosomal trisomies and gender in a Danish public health setting, using semi-conductor sequencing and published open source scripts for analysis. METHODS: Plasma-derived DNA from a total of 375...

  14. A Survey on Open-Source Flight Control Platforms of Unmanned Aerial Vehicle

    DEFF Research Database (Denmark)

    Ebeid, Emad Samuel Malki; Skriver, Martin; Jin, Jie

    2017-01-01

    Recently, Unmanned Aerial Vehicle (UAV), so-called drones, have gotten a lot of attention in academic research and commercial applications due to their simple structure, ease of operations and low-cost hardware components. Flight controller, embedded electronics component, represents the core part...... of the drone. It aims at performing the main operations of the drone (e.g., autonomous control and navigation). There are various types of flight controllers and each of them has its own characteristics and features. This paper presents an extensive survey on the publicly available open-source flight...

  15. Improving flood risk mapping in Italy: the FloodRisk open-source software

    Science.gov (United States)

    Albano, Raffaele; Mancusi, Leonardo; Craciun, Iulia; Sole, Aurelia; Ozunu, Alexandru

    2017-04-01

    Time and again, floods around the world illustrate the devastating impact they can have on societies. Furthermore, the expectation that the flood damages can increase over time with climate, land-use change and social growth in flood prone-areas has raised the public and other stakeholders' (governments, international organization, re-insurance companies and emergency responders) awareness for the need to manage risks in order to mitigate their causes and consequences. In this light, the choice of appropriate measures, the assessment of the costs and effects of such measures, and their prioritization are crucial for decision makers. As a result, a priori flood risk assessment has become a key part of flood management practices with the aim of minimizing the total costs related to the risk management cycle. In this context, The EU Flood Directive 2007/60 requires the delineation of flood risk maps on the bases of most appropriate and advanced tools, with particular attention on limiting required economic efforts. The main aim of these risk maps is to provide the required knowledge for the development of flood risk management plans (FRMPs) by considering both costs and benefits of alternatives and results from consultation with all interested parties. In this context, this research project developed a free and open-source (FOSS) GIS software, called FloodRisk, to operatively support stakeholders in their compliance with the FRMPs. FloodRisk aims to facilitate the development of risk maps and the evaluation and management of current and future flood risk for multi-purpose applications. This new approach overcomes the limits of the expert-drive qualitative (EDQ) approach currently adopted in several European countries, such as Italy, which does not permit a suitable evaluation of the effectiveness of risk mitigation strategies, because the vulnerability component cannot be properly assessed. Moreover, FloodRisk is also able to involve the citizens in the flood

  16. PhysioNet: physiologic signals, time series and related open source software for basic, clinical, and applied research.

    Science.gov (United States)

    Moody, George B; Mark, Roger G; Goldberger, Ary L

    2011-01-01

    PhysioNet provides free web access to over 50 collections of recorded physiologic signals and time series, and related open-source software, in support of basic, clinical, and applied research in medicine, physiology, public health, biomedical engineering and computing, and medical instrument design and evaluation. Its three components (PhysioBank, the archive of signals; PhysioToolkit, the software library; and PhysioNetWorks, the virtual laboratory for collaborative development of future PhysioBank data collections and PhysioToolkit software components) connect researchers and students who need physiologic signals and relevant software with researchers who have data and software to share. PhysioNet's annual open engineering challenges stimulate rapid progress on unsolved or poorly solved questions of basic or clinical interest, by focusing attention on achievable solutions that can be evaluated and compared objectively using freely available reference data.

  17. AquaResp® — free open-source software for measuring oxygen consumption of resting aquatic animals

    DEFF Research Database (Denmark)

    Svendsen, Morten Bo S.; Skov, Peter Vilhelm; Bushnell, Peter G.

    AquaResp® is a free open-source software program developed to measure the oxygen consumption of aquatic animals using intermittent flow techniques. This free program is based on Microsoft Excel, and uses the MCC Universal Library and a data acquisition board to acquire analogue readings from up...... manufacturers. AquaResp was developed with the intention of automating data acquisition and control by programming in commonly-available software (Microsoft Excel) and allowing customization by the user without restrictions. The program has been tested in different laboratories for an extended period...

  18. Biogem: an effective tool based approach for scaling up open source software development in bioinformatics

    NARCIS (Netherlands)

    Bonnal, R.J.P.; Smant, G.; Prins, J.C.P.

    2012-01-01

    Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software ge

  19. Open source software implementation of an integrated testing strategy for skin sensitization potency based on a Bayesian network.

    Science.gov (United States)

    Pirone, Jason R; Smith, Marjolein; Kleinstreuer, Nicole C; Burns, Thomas A; Strickland, Judy; Dancik, Yuri; Morris, Richard; Rinckel, Lori A; Casey, Warren; Jaworska, Joanna S

    2014-01-01

    An open-source implementation of a previously published integrated testing strategy (ITS) for skin sensitization using a Bayesian network has been developed using R, a free and open-source statistical computing language. The ITS model provides probabilistic predictions of skin sensitization potency based on in silico and in vitro information as well as skin penetration characteristics from a published bioavailability model (Kasting et al., 2008). The structure of the Bayesian network was designed to be consistent with the adverse outcome pathway published by the OECD (Jaworska et al., 2011, 2013). In this paper, the previously published data set (Jaworska et al., 2013) is improved by two data corrections and a modified application of the Kasting model. The new data set implemented in the original commercial software package and the new R version produced consistent results. The data and a fully documented version of the code are publicly available (http://ntp.niehs.nih.gov/go/its).

  20. JETSPIN: a specific-purpose open-source software for simulations of nanofiber electrospinning

    CERN Document Server

    Lauricella, Marco; Coluzza, Ivan; Pisignano, Dario; Succi, Sauro

    2015-01-01

    We present the open-source computer program JETSPIN, specifically designed to simulate the electrospinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to parallel processor workstations. This paper provides an overview of JETSPIN, focusing primarily on its structure, parallel implementations, functionality, performance, and availability.

  1. Open-Source Development Experiences in Scientific Software: The HANDE Quantum Monte Carlo Project

    Directory of Open Access Journals (Sweden)

    J. S. Spencer

    2015-11-01

    Full Text Available The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed team with a variety of backgrounds in computational science. In the course of preparing a public, open-source release, we have taken this opportunity to step back and look at what we have done and what we hope to do in the future. We pay particular attention to development processes, the approach taken to train students joining the project, and how a flat hierarchical structure aids communication.

  2. AtomicJ: An open source software for analysis of force curves

    Science.gov (United States)

    Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

    2014-06-01

    We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

  3. AtomicJ: An open source software for analysis of force curves

    Energy Technology Data Exchange (ETDEWEB)

    Hermanowicz, Paweł, E-mail: pawel.hermanowicz@uj.edu.pl; Gabryś, Halina [Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Kraków (Poland); Sarna, Michał; Burda, Kvetoslava [Department of Medical Physics and Biophysics, Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, al. Mickiewicza 30, 30-059 Kraków (Poland)

    2014-06-15

    We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

  4. A Quantitative Analysis of Open Source Software's Acceptability as Production-Quality Code

    Science.gov (United States)

    Fischer, Michael

    2011-01-01

    The difficulty in writing defect-free software has been long acknowledged both by academia and industry. A constant battle occurs as developers seek to craft software that works within aggressive business schedules and deadlines. Many tools and techniques are used in attempt to manage these software projects. Software metrics are a tool that has…

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

    Science.gov (United States)

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

    2009-12-01

    This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the

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

    Science.gov (United States)

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

    2015-01-01

    Many biological laboratories that deal with genomic samples are facing the problem of sample tracking, both for pure laboratory management and for efficiency. Our laboratory exploits PCR techniques and Next Generation Sequencing (NGS) methods to perform high-throughput integration site monitoring in different clinical trials and scientific projects. Because of the huge amount of samples that we process every year, which result in hundreds of millions of sequencing reads, we need to standardize data management and tracking systems, building up a scalable and flexible structure with web-based interfaces, which are usually called Laboratory Information Management System (LIMS). We started collecting end-users' requirements, composed of desired functionalities of the system and Graphical User Interfaces (GUI), and then we evaluated available tools that could address our requirements, spanning from pure LIMS to Content Management Systems (CMS) up to enterprise information systems. Our analysis identified ADempiere ERP, an open source Enterprise Resource Planning written in Java J2EE, as the best software that also natively implements some highly desirable technological advances, such as the high usability and modularity that grants high use-case flexibility and software scalability for custom solutions. We extended and customized ADempiere ERP to fulfil LIMS requirements and we developed adLIMS. It has been validated by our end-users verifying functionalities and GUIs through test cases for PCRs samples and pre-sequencing data and it is currently in use in our laboratories. adLIMS implements authorization and authentication policies, allowing multiple users management and roles definition that enables specific permissions, operations and data views to each user. For example, adLIMS allows creating sample sheets from stored data using available exporting operations. This simplicity and process standardization may avoid manual errors and information backtracking, features

  7. AERIAL SURVEYING UAV BASED ON OPEN-SOURCE HARDWARE AND SOFTWARE

    Directory of Open Access Journals (Sweden)

    J. Mészáros

    2012-09-01

    Full Text Available In the last years the functionality and type of UAV-systems increased fast, but unfortunately these systems are hardly available for researchers in some cases. A simple and low-cost solution was developed to build an autonomous aerial surveying airplane, which can fulfil the necessities (aerial photographs with very-high resolution of other departments at the university and very useful and practical for teaching photogrammetry.. The base was a commercial, remote controlled model airplane and an open-source GPS/IMU system (MatrixPilot was adapted to achieve the semi-automatic or automatic stabilization and navigation of the model airplane along predefined trajectory. The firmware is completely open-source and easily available on the website of the project. The first used camera system was a low-budget, low-quality video camera, which could provide only 1.2 megapixel photographs or low resolution video depending on the light conditions and the desired spatial resolution. A field measurement test was carried out with the described system: the aerial surveying of an undiscovered archaeological site, signed by a crop-mark in mountain Pilis (Hungary.

  8. Aerial Surveying Uav Based on Open-Source Hardware and Software

    Science.gov (United States)

    Mészáros, J.

    2011-09-01

    In the last years the functionality and type of UAV-systems increased fast, but unfortunately these systems are hardly available for researchers in some cases. A simple and low-cost solution was developed to build an autonomous aerial surveying airplane, which can fulfil the necessities (aerial photographs with very-high resolution) of other departments at the university and very useful and practical for teaching photogrammetry.. The base was a commercial, remote controlled model airplane and an open-source GPS/IMU system (MatrixPilot) was adapted to achieve the semi-automatic or automatic stabilization and navigation of the model airplane along predefined trajectory. The firmware is completely open-source and easily available on the website of the project. The first used camera system was a low-budget, low-quality video camera, which could provide only 1.2 megapixel photographs or low resolution video depending on the light conditions and the desired spatial resolution. A field measurement test was carried out with the described system: the aerial surveying of an undiscovered archaeological site, signed by a crop-mark in mountain Pilis (Hungary).

  9. QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

    Energy Technology Data Exchange (ETDEWEB)

    Giannozzi, Paolo; Baroni, Stefano; Dal Corso, Andrea; De Gironcoli, Stefano; Fabris, Stefano; Gebauer, Ralph; Kokalj, Anton; Martin-Samos, Layla [CNR-INFM Democritos National Simulation Center, 34100 Trieste (Italy); Bonini, Nicola; Ceresoli, Davide [Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Calandra, Matteo; Gougoussis, Christos; Lazzeri, Michele [Institut de Mineralogie et de Physique des Milieux Condenses, Universite Pierre et Marie Curie, CNRS, IPGP, 140 rue de Lourmel, 75015 Paris (France); Car, Roberto [Department of Chemistry, Princeton University, Princeton, NJ 08544 (United States); Cavazzoni, Carlo [CINECA National Supercomputing Center, Casalecchio di Reno, 40033 Bologna (Italy); Chiarotti, Guido L [SPIN s.r.l., via del Follatoio 12, 34148 Trieste (Italy); Cococcioni, Matteo [Department of Chemical Engineering and Materials Science, University of Minnesota, 151 Amundson Hall, 421 Washington Avenue SE, Minneapolis, MN 55455 (United States); Dabo, Ismaila [Universite Paris-Est, CERMICS, Projet Micmac ENPC-INRIA, 6-8 avenue Blaise Pascal, 77455 Marne-la-Vallee Cedex 2 (France); Fratesi, Guido [Dipartimento di Scienza dei Materiali, Universita degli Studi di Milano-Bicocca, via Cozzi 53, 20125 Milano (Italy); Gerstmann, Uwe [Theoretische Physik, Universitaet Paderborn, D-33098 Paderborn (Germany)

    2009-09-30

    QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

  10. Open source community organization

    CSIR Research Space (South Africa)

    Molefe, Onkgopotse M

    2009-05-01

    Full Text Available Open Source communities (OSCs), sometimes referred to as virtual or online communities play a significant role in terms of the contribution they continue to make in producing user-friendly Open Source Software (OSS) solutions. Many projects have...

  11. The Application Of Open-Source And Free Photogrammetric Software For The Purposes Of Cultural Heritage Documentation

    Directory of Open Access Journals (Sweden)

    Bartoš Karol

    2014-07-01

    Full Text Available The documentation of cultural heritage is an essential part of appropriate care of historical monuments, representing a part of our history. At present, it represents the current issue, for which considerable funds are being spent, as well as for the documentation of immovable historical monuments in a form of castle ruins, among the others. Non-contact surveying technologies - terrestrial laser scanning and digital photogrammetry belong to the most commonly used technologies, by which suitable documentation can be obtained, however their use may be very costly. In recent years, various types of software products and web services based on the SfM (or MVS method and developed as open-source software, or as a freely available and free service, relying on the basic principles of photogrammetry and computer vision, have started to get into the spotlight. By using the services and software, acquired digital images of a given object can be processed into a point cloud, serving directly as a final output or as a basis for further processing. The aim of this paper, based on images of various objects of the Slanec castle ruins obtained by the DSLR Pentax K5, is to assess the suitability of different types of open-source and free software and free web services and their reliability in terms of surface reconstruction and photo-texture quality for the purposes of castle ruins documentation.

  12. Operation and test of hybridized silicon p-i-n arrays using open-source array control hardware and software

    Science.gov (United States)

    Moore, Andrew C.; Ninkov, Zoran; Burley, Gregory S.; Forrest, William J.; McMurtry, Craig W.; Avery, Lars E.

    2003-05-01

    A system for controlling and testing high-resolution non-destructive astronomical imagers was constructed using open-source components, both hardware and software. The open-source electronics design, originated by Carnegie Observatories (OCIW) for CCD cameras, was modified, assembled, and augmented with new circuitry which facilitates monitoring of voltages and currents. The electronics was run from Python user interface software based on a design from the University of Rochester. This new software utilized the Numarray and pyFITS modules developed at the Space Telescope Science Institute (STScI). Interfacing to the "dv" FITS image analysis package from the NASA IRTF was also implemented. Python (the STScI language of choice) was used as the primary language for systems integration, scripts for data acquisition, and scripts for data analysis. The DSP clocking software was a mixture of C and Motorola 56303 assembly. An interrupt-driven kernel-mode PCI device driver for Red Hat Linux was written in C, and used the PC processor and memory for image processing and acquisition. Two 1Κ × 1Κ Raytheon SB226-based hybridized silicon p-i-n arrays were operated and tested with the new system at temperatures as low as 10K. Signal path gain, node capacitance, well depth, dark current, and MTF measurements were made and are presented here.

  13. PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments.

    Science.gov (United States)

    Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

    2014-12-01

    The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

  14. Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.

    Science.gov (United States)

    Moutsatsos, Ioannis K; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J; Jenkins, Jeremy L; Holway, Nicholas; Tallarico, John; Parker, Christian N

    2017-03-01

    High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

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

    Science.gov (United States)

    Behrends, Knut; Conze, Ronald

    2013-04-01

    Geology/geophysics is a highly interdisciplinary science, overlapping with, for instance, physics, biology and chemistry. In today's software-intensive work environments, geoscientists often encounter new open-source software from scientific fields that are only remotely related to the own field of expertise. We show how web-mining techniques can help to carry out systematic discovery and evaluation of such software. In a first step, we downloaded ~500 abstracts (each consisting of ~1 kb UTF-8 text) from agu-fm12.abstractcentral.com. This web site hosts the abstracts of all publications presented at AGU Fall Meeting 2012, the world's largest annual geology/geophysics conference. All abstracts belonged to the category "Earth and Space Science Informatics", an interdisciplinary label cross-cutting many disciplines such as "deep biosphere", "atmospheric research", and "mineral physics". Each publication was represented by a highly structured record with ~20 short data attributes, the largest authorship-record being the unstructured "abstract" field. We processed texts of the abstracts with the statistics software "R" to calculate a corpus and a term-document matrix. Using R package "tm", we applied text-mining techniques to filter data and develop hypotheses about software-development activities happening in various geology/geophysics fields. Analyzing the term-document matrix with basic techniques (e.g., word frequencies, co-occurences, weighting) as well as more complex methods (clustering, classification) several key pieces of information were extracted. For example, text-mining can be used to identify scientists who are also developers of open-source scientific software, and the names of their programming projects and codes can also be identified. In a second step, based on the intermediate results found by processing the conference-abstracts, any new hypotheses can be tested in another webmining subproject: by merging the dataset with open data from github

  16. Development of an IHE MRRT-compliant open-source web-based reporting platform

    Energy Technology Data Exchange (ETDEWEB)

    Pinto dos Santos, Daniel; Klos, G.; Kloeckner, R.; Oberle, R.; Dueber, C.; Mildenberger, P. [University Medical Center of the Johannes Gutenberg-University Mainz, Department of Diagnostic and Interventional Radiology, Mainz (Germany)

    2017-01-15

    To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. (orig.)

  17. UMMPerfusion: an open source software tool towards quantitative MRI perfusion analysis in clinical routine.

    Science.gov (United States)

    Zöllner, Frank G; Weisser, Gerald; Reich, Marcel; Kaiser, Sven; Schoenberg, Stefan O; Sourbron, Steven P; Schad, Lothar R

    2013-04-01

    To develop a generic Open Source MRI perfusion analysis tool for quantitative parameter mapping to be used in a clinical workflow and methods for quality management of perfusion data. We implemented a classic, pixel-by-pixel deconvolution approach to quantify T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in. It features parallel computing capabilities and an automated reporting scheme for quality management. Furthermore, by our implementation design, it could be easily extendable to other perfusion algorithms. Obtained results are saved as DICOM objects and directly added to the patient study. The plug-in was evaluated on ten MR perfusion data sets of the prostate and a calibration data set by comparing obtained parametric maps (plasma flow, volume of distribution, and mean transit time) to a widely used reference implementation in IDL. For all data, parametric maps could be calculated and the plug-in worked correctly and stable. On average, a deviation of 0.032 ± 0.02 ml/100 ml/min for the plasma flow, 0.004 ± 0.0007 ml/100 ml for the volume of distribution, and 0.037 ± 0.03 s for the mean transit time between our implementation and a reference implementation was observed. By using computer hardware with eight CPU cores, calculation time could be reduced by a factor of 2.5. We developed successfully an Open Source OsiriX plug-in for T1-DCE-MRI perfusion analysis in a routine quality managed clinical environment. Using model-free deconvolution, it allows for perfusion analysis in various clinical applications. By our plug-in, information about measured physiological processes can be obtained and transferred into clinical practice.

  18. Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

    Directory of Open Access Journals (Sweden)

    Yu-Hua Dean Fang

    2014-01-01

    Full Text Available Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA toolbox, and provide it to the research community as a free, open-source project. Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC cancer patients treated with definitive radiotherapies. Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC. Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.. Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at http://code.google.com/p/cgita.

  19. Development and evaluation of an open-source software package "CGITA" for quantifying tumor heterogeneity with molecular images.

    Science.gov (United States)

    Fang, Yu-Hua Dean; Lin, Chien-Yu; Shih, Meng-Jung; Wang, Hung-Ming; Ho, Tsung-Ying; Liao, Chun-Ta; Yen, Tzu-Chen

    2014-01-01

    The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA) toolbox, and provide it to the research community as a free, open-source project. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC) cancer patients treated with definitive radiotherapies. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC). Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.). CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at http://code.google.com/p/cgita.

  20. AquaResp® - free open-source software for measuring oxygen consumption of resting aquatic animals

    DEFF Research Database (Denmark)

    Steffensen, John Fleng

    2012-01-01

    Soc for experimental Biol Annual Meeting - Salzburg 2012 Morten Bo S. Svendsen (University of Copenhagen, Denmark), Peter V. Skov (Technical University of Denmark, Denmark), Peter G .Bushnell (Indiana University South Bend, Indiana) and John F. Steffensen (University of Copenhagen, Denmark) Aqua......Resp" is a free open-source software program developed to measure the oxygen consumption of aquatic animals using intermittent flow techniques. This free program is based on Microsoft Excel, and uses the MCC Universal Library and a data acquisition board to acquire analogue readings from up to four input ports...

  1. Free and Open-Source Software is not an Emerging Property but Rather the Result of Studied Design

    CERN Document Server

    Magrassi, Paolo

    2010-01-01

    Free and open source software (FOSS) is considered by many, along with Wikipedia, the proof of an ongoing paradigm shift from hierarchically-managed and market-driven production of knowledge to heterarchical, collaborative and commons-based production styles. In such perspective, it has become common place to refer to FOSS as a manifestation of collective intelligence where deliverables and artefacts emerge by virtue of mere cooperation, with no need for supervising leadership. The paper argues that this assumption is based on limited understanding of the software development process, and may lead to wrong conclusions as to the potential of peer production. The development of a less than trivial piece of software, irrespective of whether it be FOSS or proprietary, is a complex cooperative effort requiring the participation of many (often thousands of) individuals. A subset of the participants always play the role of leading system and subsystem designers, determining architecture and functionality; the rest o...

  2. Analyzing the State of Static Analysis: A Large-Scale Evaluation in Open Source Software

    NARCIS (Netherlands)

    Beller, M.; Bholanath, R.; McIntosh, S.; Zaidman, A.E.

    2016-01-01

    The use of automatic static analysis has been a software engineering best practice for decades. However, we still do not know a lot about its use in real-world software projects: How prevalent is the use of Automated Static Analysis Tools (ASATs) such as FindBugs and JSHint? How do developers use th

  3. osni.info-Using free/libre/open source software to build a virtual international community for open source nursing informatics.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2010-08-02

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

  5. Open Source Approach to Project Management Tools

    Directory of Open Access Journals (Sweden)

    Romeo MARGEA

    2011-01-01

    Full Text Available Managing large projects involving different groups of people and complex tasks can be challenging. The solution is to use Project management software, which allows a more efficient management of projects. However, famous project management systems can be costly and may require expensive custom servers. Even if free software is not as complex as Microsoft Project, is noteworthy to think that not all projects need all the features, amenities and power of such systems. There are free and open source software alternatives that meet the needs of most projects, and that allow Web access based on different platforms and locations. A starting stage in adopting an OSS in-house is finding and identifying existing open source solution. In this paper we present an overview of Open Source Project Management Software (OSPMS based on articles, reviews, books and developers’ web sites, about those that seem to be the most popular software in this category.

  6. Open source software for semi-automated histomorphometry of bone resorption and formation parameters.

    Science.gov (United States)

    van 't Hof, Rob J; Rose, Lorraine; Bassonga, Euphemie; Daroszewska, Anna

    2017-06-01

    Micro-CT analysis has become the standard method for assessing bone volume and architecture in small animals. However, micro-CT does not allow the assessment of bone turnover parameters such as bone formation rate and osteoclast (OC) number and surface. For these crucial variables histomorphometric analysis is still an essential technique. Histomorphometry however, is time consuming and, especially in mouse bones, OCs can be difficult to detect. The main purpose of this study was to develop and validate a relatively easy and rapid method to measure static and dynamic bone histomorphometry parameters. Here we present the adaptation of established staining protocols and three novel open source image analysis packages: TrapHisto, OsteoidHisto and CalceinHisto that allow rapid, semi-automated analysis of histomorphometric bone resorption, osteoid, and calcein double labelling parameters respectively. These three programs are based on ImageJ, but use a relatively simple user interface that hides the underlying complexity of the image analysis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Web-based education in Spanish Universities. A Comparison of Open Source E-Learning Platforms.

    OpenAIRE

    José María Fuentes; Álvaro Ramírez-Gómez; Ana Isabel García; Francisco Ayuga

    2012-01-01

    Web-based education or 'e-learning‟ has become a critical component in higher education for the last decade, replacing other distance learning methods, such as traditional computer training or correspondence learning. The number of university students who take on-line courses is continuously increasing all over the world. In Spain, nearly a 90% of the universities have an institutional e-learning platform and over 60% of the traditional on-site courses use this technology as a suppl...

  8. Image reconstruction of mMR PET data using the open source software STIR

    Energy Technology Data Exchange (ETDEWEB)

    Markiewicz, Pawel [Centre for Medical Image Computing, University College London, London (United Kingdom); Thielemans, Kris [Institute of Nuclear Medicine, University College London, London (United Kingdom); Burgos, Ninon [Centre for Medical Image Computing, University College London, London (United Kingdom); Manber, Richard [Institute of Nuclear Medicine, University College London, London (United Kingdom); Jiao, Jieqing [Centre for Medical Image Computing, University College London, London (United Kingdom); Barnes, Anna [Institute of Nuclear Medicine, University College London, London (United Kingdom); Atkinson, David [Centre for Medical Imaging, University College London, London (United Kingdom); Arridge, Simon R [Centre for Medical Image Computing, University College London, London (United Kingdom); Hutton, Brian F [Institute of Nuclear Medicine, University College London, London (United Kingdom); Ourselin, Sébastien [Centre for Medical Image Computing, University College London, London (United Kingdom); Dementia Research Centre, University College London, London (United Kingdom)

    2014-07-29

    Simultaneous PET and MR acquisitions have now become possible with the new hybrid Biograph Molecular MR (mMR) scanner from Siemens. The purpose of this work is to create a platform for mMR 3D and 4D PET image reconstruction which would be freely accessible to the community as well as fully adjustable in order to obtain optimal images for a given research task in PET imaging. The proposed platform is envisaged to prove useful in developing novel and robust image bio-markers which could then be adapted for use on the mMR scanner.

  9. ML-Ask: Open Source Affect Analysis Software for Textual Input in Japanese

    Directory of Open Access Journals (Sweden)

    Michal Ptaszynski

    2017-06-01

    Full Text Available We present ML-Ask – the first Open Source Affect Analysis system for textual input in Japanese. ML-Ask analyses the contents of an input (e.g., a sentence and annotates it with information regarding the contained general emotive expressions, specific emotional words, valence-activation dimensions of overall expressed affect, and particular emotion types expressed with their respective expressions. ML-Ask also incorporates the Contextual Valence Shifters model for handling negation in sentences to deal with grammatically expressible shifts in the conveyed valence. The system, designed to work mainly under Linux and MacOS, can be used for research on, or applying the techniques of Affect Analysis within the framework Japanese language. It can also be used as an experimental baseline for specific research in Affect Analysis, and as a practical tool for written contents annotation.   Funding statement: This research has been supported by: a Research Grant from the Nissan Science Foundation (years 2009–2010, The GCOE Program founded by Japan’s Ministry of Education, Culture, Sports, Science and Technology (years 2009–2010, (JSPS KAKENHI Grant-in-Aid for JSPS Fellows (Project Number: 22-00358 (years 2010–2012, (JSPS KAKENHI Grant-in-Aid for Scientific Research (Project Number: 24600001 (years 2012–2015, (JSPS KAKENHI Grant-in-Aid for Research Activity Start-up (Project Number: 25880003 (years 2013–2015, and (JSPS KAKENHI Grant-in-Aid for Encouragement of Young Scientists (B (Project Number: 15K16044 (years 2015-present, project estimated to end in March 2018.

  10. LabKey Server: An open source platform for scientific data integration, analysis and collaboration

    OpenAIRE

    Lum Karl; Nathe Cory; Ramsay Sarah; Hussey Peter; Bellew Matthew; Rauch Adam; Eckels Josh; Piehler Britt; Nelson Elizabeth K; Krouse Kevin; Stearns David; Connolly Brian; Skillman Tom; Igra Mark

    2011-01-01

    Abstract Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize ...

  11. AROSICS: An Automated and Robust Open-Source Image Co-Registration Software for Multi-Sensor Satellite Data

    Directory of Open Access Journals (Sweden)

    Daniel Scheffler

    2017-07-01

    Full Text Available Geospatial co-registration is a mandatory prerequisite when dealing with remote sensing data. Inter- or intra-sensoral misregistration will negatively affect any subsequent image analysis, specifically when processing multi-sensoral or multi-temporal data. In recent decades, many algorithms have been developed to enable manual, semi- or fully automatic displacement correction. Especially in the context of big data processing and the development of automated processing chains that aim to be applicable to different remote sensing systems, there is a strong need for efficient, accurate and generally usable co-registration. Here, we present AROSICS (Automated and Robust Open-Source Image Co-Registration Software, a Python-based open-source software including an easy-to-use user interface for automatic detection and correction of sub-pixel misalignments between various remote sensing datasets. It is independent of spatial or spectral characteristics and robust against high degrees of cloud coverage and spectral and temporal land cover dynamics. The co-registration is based on phase correlation for sub-pixel shift estimation in the frequency domain utilizing the Fourier shift theorem in a moving-window manner. A dense grid of spatial shift vectors can be created and automatically filtered by combining various validation and quality estimation metrics. Additionally, the software supports the masking of, e.g., clouds and cloud shadows to exclude such areas from spatial shift detection. The software has been tested on more than 9000 satellite images acquired by different sensors. The results are evaluated exemplarily for two inter-sensoral and two intra-sensoral use cases and show registration results in the sub-pixel range with root mean square error fits around 0.3 pixels and better.

  12. SmartR: an open-source platform for interactive visual analytics for translational research data.

    Science.gov (United States)

    Herzinger, Sascha; Gu, Wei; Satagopam, Venkata; Eifes, Serge; Rege, Kavita; Barbosa-Silva, Adriano; Schneider, Reinhard

    2017-07-15

    In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR . reinhard.schneider@uni.lu. Supplementary data are available at Bioinformatics online.

  13. SWISTRACK - AN OPEN SOURCE, SOFTWARE PACKAGE APPLICABLE TO TRACKING OF FISH LOCOMOTION AND BEHAVIOUR

    DEFF Research Database (Denmark)

    Steffensen, John Fleng

    2010-01-01

    , Swistrack can be easily adopted for the tracking offish. Benefits associated with the free software include: • Contrast or marker based tracking enabling tracking of either the whole animal, or tagged marks placed upon the animal • The ability to track multiple tags placed upon an individual animal • Highly...... including swimming speed, acceleration and directionality of movements as well as the examination of locomotory panems during swimming. SWiSlrdL:k, a [n: t; and downloadable software package (available from www.sourceforge.com) is widely used for tracking robots, humans and other animals. Accordingly...... effective background subtraction algorithms and filters ensuring smooth tracking of fish • Application of tags of different colour enables the software to track multiple fish without the problem of track exchange between individuals • Low processing requirements enable tracking in real-time • Further...

  14. Analyzing the State of Static Analysis: A Large-Scale Evaluation in Open Source Software

    OpenAIRE

    2016-01-01

    The use of automatic static analysis has been a software engineering best practice for decades. However, we still do not know a lot about its use in real-world software projects: How prevalent is the use of Automated Static Analysis Tools (ASATs) such as FindBugs and JSHint? How do developers use these tools, and how does their use evolve over time? We research these questions in two studies on nine different ASATs for Java, JavaScript, Ruby, and Python with a population of 122 and 168,214 op...

  15. Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software.

    Science.gov (United States)

    Mejías, Andrés; Herrera, Reyes S; Márquez, Marco A; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

    2017-01-05

    There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user's computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.

  16. Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software

    Science.gov (United States)

    Mejías, Andrés; Herrera, Reyes S.; Márquez, Marco A.; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

    2017-01-01

    There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)—this one designed using the intuitive graphical system of EJS—located on the user’s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented. PMID:28067801

  17. Using open source software for the supervision and management of the water resources system of Athens

    Science.gov (United States)

    Kozanis, S.; Christofides, A.; Efstratiadis, A.; Koukouvinos, A.; Karavokiros, G.; Mamassis, N.; Koutsoyiannis, D.; Nikolopoulos, D.

    2012-04-01

    The water supply of Athens, Greece, is implemented through a complex water resource system, extending over an area of around 4 000 km2 and including surface water and groundwater resources. It incorporates four reservoirs, 350 km of main aqueducts, 15 pumping stations, more than 100 boreholes and 5 small hydropower plants. The system is run by the Athens Water Supply and Sewerage Company (EYDAP) Over more than 10 years we have developed, information technology tools such as GIS, database and decision support systems, to assist the management of the system. Among the software components, "Enhydris", a web application for the visualization and management of geographical and hydrometeorological data, and "Hydrognomon", a data analysis and processing tool, are now free software. Enhydris is entirely based on free software technologies such as Python, Django, PostgreSQL, and JQuery. We also created http://openmeteo.org/, a web site hosting our free software products as well as a free database system devoted to the dissemination of free data. In particular, "Enhydris" is used for the management of the hydrometeorological stations and the major hydraulic structures (aqueducts, reservoirs, boreholes, etc.), as well as for the retrieval of time series, online graphs etc. For the specific needs of EYDAP, additional GIS functionality was introduced for the display and monitoring of the water supply network. This functionality is also implemented as free software and can be reused in similar projects. Except for "Hydrognomon" and "Enhydris", we have developed a number of advanced modeling applications, which are also generic-purpose tools that have been used for a long time to provide decision support for the water resource system of Athens. These are "Hydronomeas", which optimizes the operation of complex water resource systems, based on a stochastic simulation framework, "Castalia", which implements the generation of synthetic time series, and "Hydrogeios", which employs

  18. Madagascar: open-source software project for multidimensional data analysis and reproducible computational experiments

    Directory of Open Access Journals (Sweden)

    Sergey Fomel

    2013-11-01

    Full Text Available The Madagascar software package is designed for analysis of large-scale multidimensional data, such as those occurring in exploration geophysics. Madagascar provides a framework for reproducible research. By “reproducible research” we refer to the discipline of attaching software codes and data to computational results reported in publications. The package contains a collection of (a computational modules, (b data-processing scripts, and (c research papers. Madagascar is distributed on SourceForge under a GPL v2 license https://sourceforge.net/projects/rsf/. By October 2013, more than 70 people from different organizations around the world have contributed to the project, with increasing year-to-year activity. The Madagascar website is http://www.ahay.org/.

  19. CERN Web Application Detection. Refactoring and release as open source software

    CERN Document Server

    Lizonczyk, Piotr

    2015-01-01

    This paper covers my work during my assignment as participant of CERN Summer Students 2015 programme. The project was aimed at refactoring and publication of the Web Application Detection tool, which was developed at CERN and priorly used internally by the Computer Security team. The range of tasks performed include initial refactoring of code, which was developed like a script rather than a Python package, through extracting components that were not specific to CERN usage, the subsequent final release of the source code on GitHub and the integration with third-party software i.e. the w3af tool. Ultimately, Web Application Detection software received positive responses, being downloaded ca. 1500 times at the time of writing this report.

  20. Developing open source, self-contained disease surveillance software applications for use in resource-limited settings

    Directory of Open Access Journals (Sweden)

    Campbell Timothy C

    2012-09-01

    Full Text Available Abstract Background Emerging public health threats often originate in resource-limited countries. In recognition of this fact, the World Health Organization issued revised International Health Regulations in 2005, which call for significantly increased reporting and response capabilities for all signatory nations. Electronic biosurveillance systems can improve the timeliness of public health data collection, aid in the early detection of and response to disease outbreaks, and enhance situational awareness. Methods As components of its Suite for Automated Global bioSurveillance (SAGES program, The Johns Hopkins University Applied Physics Laboratory developed two open-source, electronic biosurveillance systems for use in resource-limited settings. OpenESSENCE provides web-based data entry, analysis, and reporting. ESSENCE Desktop Edition provides similar capabilities for settings without internet access. Both systems may be configured to collect data using locally available cell phone technologies. Results ESSENCE Desktop Edition has been deployed for two years in the Republic of the Philippines. Local health clinics have rapidly adopted the new technology to provide daily reporting, thus eliminating the two-to-three week data lag of the previous paper-based system. Conclusions OpenESSENCE and ESSENCE Desktop Edition are two open-source software products with the capability of significantly improving disease surveillance in a wide range of resource-limited settings. These products, and other emerging surveillance technologies, can assist resource-limited countries compliance with the revised International Health Regulations.

  1. Earth-Base: A Free And Open Source, RESTful Earth Sciences Platform

    Science.gov (United States)

    Kishor, P.; Heim, N. A.; Peters, S. E.; McClennen, M.

    2012-12-01

    This presentation describes the motivation, concept, and architecture behind Earth-Base, a web-based, RESTful data-management, analysis and visualization platform for earth sciences data. Traditionally web applications have been built directly accessing data from a database using a scripting language. While such applications are great at bring results to a wide audience, they are limited in scope to the imagination and capabilities of the application developer. Earth-Base decouples the data store from the web application by introducing an intermediate "data application" tier. The data application's job is to query the data store using self-documented, RESTful URIs, and send the results back formatted as JavaScript Object Notation (JSON). Decoupling the data store from the application allows virtually limitless flexibility in developing applications, both web-based for human consumption or programmatic for machine consumption. It also allows outside developers to use the data in their own applications, potentially creating applications that the original data creator and app developer may not have even thought of. Standardized specifications for URI-based querying and JSON-formatted results make querying and developing applications easy. URI-based querying also allows utilizing distributed datasets easily. Companion mechanisms for querying data snapshots aka time-travel, usage tracking and license management, and verification of semantic equivalence of data are also described. The latter promotes the "What You Expect Is What You Get" (WYEIWYG) principle that can aid in data citation and verification.

  2. DEVELOPMENT OF OBSTACLE AVOIDANCE TECHNIQUE IN WEB-BASED GEOGRAPHIC INFORMATION SYSTEM FOR TRAFFIC MANAGEMENT USING OPEN SOURCE SOFTWARE

    Directory of Open Access Journals (Sweden)

    Nik Mohd Ramli Nik Yusoff

    2014-01-01

    Full Text Available The shortest path routing is one of the well-known network analysis techniques implemented in road management systems. Pg Routing as an extension of Postgre SQL/Post GIS database is an open source library that implements the Dijkstra shortest path algorithm. However, the functionality to avoid obstacles in that analysis is still limited. Therefore, this study was conducted to enable obstacle avoidance function in the existing pgRouting algorithm using OpenStreetMap road network. By implementing this function, it enhances the Dijkstra algorithm ability in network analysis. In this study a dynamic restriction feature is added at the program level to represent the obstacles on the road. With this modification the algorithm is now able to generate an alternative route by avoiding the existence of obstacles on the roads. By using OpenLayers and PHP a web-based GIS platform was developed to ease the system’s usability.

  3. Finding Code Clones for Refactoring with Clone Metrics : A Case Study of Open Source Software

    OpenAIRE

    Choi, Eunjong; Yoshida, Norihiro; IshioTakashi; Inoue, Katsuro; Sano, Tateki

    2011-01-01

    A code clone is a code fragment that has identical or similar code fragments to it in the source code. Code clone has been regarded as one of the factors that makes software maintenance more difficult. Therefore, to refactor code clones into one method is promising way to reduce maintenance cost in the future. In our previous study, we proposed a method to extract code clones for refactoring using clone metrics. We had conducted an empirical study on Java application developed by NEC Corporat...

  4. The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation.

    Science.gov (United States)

    Muth, Thilo; Behne, Alexander; Heyer, Robert; Kohrs, Fabian; Benndorf, Dirk; Hoffmann, Marcus; Lehtevä, Miro; Reichl, Udo; Martens, Lennart; Rapp, Erdmann

    2015-03-06

    The enormous challenges of mass spectrometry-based metaproteomics are primarily related to the analysis and interpretation of the acquired data. This includes reliable identification of mass spectra and the meaningful integration of taxonomic and functional meta-information from samples containing hundreds of unknown species. To ease these difficulties, we developed a dedicated software suite, the MetaProteomeAnalyzer, an intuitive open-source tool for metaproteomics data analysis and interpretation, which includes multiple search engines and the feature to decrease data redundancy by grouping protein hits to so-called meta-proteins. We also designed a graph database back-end for the MetaProteomeAnalyzer to allow seamless analysis of results. The functionality of the MetaProteomeAnalyzer is demonstrated using a sample of a microbial community taken from a biogas plant.

  5. TH-A-19A-01: An Open Source Software for Proton Treatment Planning in Heterogeneous Medium

    Energy Technology Data Exchange (ETDEWEB)

    Desplanques, M; Baroni, G [Politecnico di Milano, Milano (Italy); Wang, K [Princess Margaret Hospital, Toronto (Canada); Phillips, J; Gueorguiev, G; Sharp, G [Massachusetts General Hospital, Boston, MN (United States)

    2014-06-15

    Purpose: Due to its success in Radiation Oncology during the last decade, interest in proton therapy is on the rise. Unfortunately, despite the global enthusiasm in the field, there is presently no free, multiplatform and customizable Treatment Planning System (TPS) providing proton dose distributions in heterogenous medium. This restricts substantially the progress of clinical research for groups without access to a commercial Proton TPS. The latest implementation of our pencil beam dose calculation algorithm for proton beams within the 3D Slicer open-source environment fulfills all the conditions described above. Methods: The core dose calculation algorithm is based on the Hong algorithm (1), which was upgraded with the Kanematsu theory describing the evolution of the lateral scattering of proton beamlets in heterogeneous medium. This algorithm deals with both mono-energetic beams and Spread Out Bragg Peak (SOBP). In order to be user-friendly, we provide a graphical user interface implemented with the Qt libraries, and visualization with the 3D Slicer medical image analysis software. Two different pencil beam algorithms were developed, and the clinical proton beam line at our facility was modeled. Results: The dose distributions provided by our algorithms were compared to dose distributions coming from both commercialized XiO TPS and literature (dose measurements, GEANT4 and MCNPx) and turned out to be in a good agreement, with maximum dose discrepancies of 5% in homogeneous phantoms and 10% in heterogeneous phantoms. The algorithm of SOBP creation from an optimized weigthing of mono-energetic beams results in flat SOBP. Conclusion: We hope that our efforts in implementing this new, open-source proton TPS will help the research groups to have a free access to a useful, reliable proton dose calculation software.(1) L. Hong et al., A pencil beam algorithm for proton dose calculations, Phys. Med. Biol. 41 (1996) 1305–1330. This project is paid for by NCI

  6. Open source hard- and software: Using Arduino boards to keep old hardware running

    Energy Technology Data Exchange (ETDEWEB)

    Faugel, Helmut, E-mail: helmut.faugel@ipp.mpg.de [Max-Planck-Institut für Plasmaphysik, EURATOM Association, Garching (Germany); Bobkov, Volodymyr [Max-Planck-Institut für Plasmaphysik, EURATOM Association, Garching (Germany)

    2013-10-15

    The ASDEX Upgrade tokamak went into operation in 1991 with a proposed lifetime of 10 years. Due to major modifications ASDEX Upgrade is still in operation. Infrastructure like data acquisition, workstations, etc. is being modernized, interfaces like RS-232 are vanishing and new interfaces are being introduced. This leads to the necessity to adapt old hardware. Most of the microcontrollers used in the old hardware do not offer any support of the new interfaces and have to be replaced. A simple and efficient way is to replace them with open hardware microcontroller boards like the Arduino. These boards are based on 8-bit RISC microcontrollers and offer a software development environment with a large number of libraries. In this paper the use of Arduino boards for replacing the position unit, the stub tuner interface and its use controlling a direct digital synthesizer (DDS) with phase control capability are shown.

  7. NEuronMOrphological analysis tool: open-source software for quantitative morphometrics

    Directory of Open Access Journals (Sweden)

    Lucia eBilleci

    2013-02-01

    Full Text Available Morphometric analysis of neurons and brain tissue is relevant to the study of neuron circuitry development during the first phases of brain growth or for probing the link between microstructural morphology and degenerative diseases. As neural imaging techniques become ever more sophisticated, so does the amount and complexity of data generated. The NEuronMOrphological analysis tool NEMO was purposely developed to handle and process large numbers of optical microscopy image files of neurons in culture or slices in order to automatically run batch routines, store data and apply multivariate classification and feature extraction using3-way principal component analysis. Here we describe the software's main features, underlining the differences between NEMO and other commercial and non-commercial image processing tools, and show an example of how NEMO can be used to classify neurons from wild-type mice and from animal models of autism.

  8. Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms.

    Science.gov (United States)

    Rechner, Steffen; Berger, Annabell

    2016-01-01

    We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time.

  9. BIM Open Source Software (OSS for the documentation of cultural heritage

    Directory of Open Access Journals (Sweden)

    Sotiris Logothetis

    2016-11-01

    This paper presents a review of some recent research on the topic. We review the recent developments focusing on the OSS that can be used at various stages of BIM process in the digital documentation of cultural heritage. The results show that there is more preference in the commercial software due to the fact that the OSS is not yet complete and covers all stages of the BIM process. However, lately we have the Edificius in architectural BIM design and “BIM Vision” as Industry Foundation Classes (IFC model viewer that try to attract as many users as possible. These tools are free and they could well be used for the digital reconstruction of cultural heritage.

  10. tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.

    Science.gov (United States)

    Athey, Brian D; Braxenthaler, Michael; Haas, Magali; Guo, Yike

    2013-01-01

    tranSMART is an emerging global open source public private partnership community developing a comprehensive informatics-based analysis and data-sharing cloud platform for clinical and translational research. The tranSMART consortium includes pharmaceutical and other companies, not-for-profits, academic entities, patient advocacy groups, and government stakeholders. The tranSMART value proposition relies on the concept that the global community of users, developers, and stakeholders are the best source of innovation for applications and for useful data. Continued development and use of the tranSMART platform will create a means to enable "pre-competitive" data sharing broadly, saving money and, potentially accelerating research translation to cures. Significant transformative effects of tranSMART includes 1) allowing for all its user community to benefit from experts globally, 2) capturing the best of innovation in analytic tools, 3) a growing 'big data' resource, 4) convergent standards, and 5) new informatics-enabled translational science in the pharma, academic, and not-for-profit sectors.

  11. Software Application for Remote Monitoring of Fleets Based on Geographic Information Systems Using Open Source Technologies.

    Directory of Open Access Journals (Sweden)

    Jesse Daniel Cano

    2012-11-01

    Full Text Available Controlling a fleet usually implies to establish means of control of vehicles, to collect the data associated with the routes taken by these vehicles, to interpret and evaluate the meaning of the collected data and to make the appropriate decisions to improve the efficiency in the use of vehicles in an organization. The implementation of this process of fleet management is mainly performed manually and the solutions available on the market are costly because of the payments for licenses, it is also necessary that the people monitoring the fleets are geographically close to them. This paper aims to answer the following questions: How to reduce errors in the management of information resulting from the fleet management process? How to reduce the cost of remote fleet monitoring? To obtain the solution, we propose the use of GPS devices in each vehicle, the GPS device’s information is captured and consistently stored in a data base, then the information is consulted, analyzed and represented on a map. The result is a software application that allows users have fast and reliable information that will enable them to take the necessary decisions in the vehicle fleet they are trying to control at a low cost.

  12. Evaluating Open Source Portals

    Science.gov (United States)

    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…

  13. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

    Science.gov (United States)

    2013-01-01

    Background Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists’ capacity to use these immunoassays to evaluate human clinical trials. Results The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose–response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Conclusions Unlike other tools tailored for

  14. SpotMetrics: An Open-Source Image-Analysis Software Plugin for Automatic Chromatophore Detection and Measurement

    Science.gov (United States)

    Hadjisolomou, Stavros P.; El-Haddad, George

    2017-01-01

    Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented chromatophore organs and reflecting cells. Therefore, a lot can be learned about the cephalopod coloration system by video recording and analyzing the activation of individual chromatophores in time. The fact that adult cephalopods have small chromatophores, up to several hundred thousand in number, makes measurement and analysis over several seconds a difficult task. However, current advancements in videography enable high-resolution and high framerate recording, which can be used to record chromatophore activity in more detail and accuracy in both space and time domains. In turn, the additional pixel information and extra frames per video from such recordings result in large video files of several gigabytes, even when the recording spans only few minutes. We created a software plugin, “SpotMetrics,” that can automatically analyze high resolution, high framerate video of chromatophore organ activation in time. This image analysis software can track hundreds of individual chromatophores over several hundred frames to provide measurements of size and color. This software may also be used to measure differences in chromatophore activation during different behaviors which will contribute to our understanding of the cephalopod sensorimotor integration system. In addition, this software can potentially be utilized to detect numbers of round objects and size changes in time, such as eye pupil size or number of bacteria in a sample. Thus, we are making this software plugin freely available as open-source because we believe it will be of benefit to other colleagues both in the cephalopod biology field and also within other disciplines. PMID:28298896

  15. SpotMetrics: An Open-Source Image-Analysis Software Plugin for Automatic Chromatophore Detection and Measurement.

    Science.gov (United States)

    Hadjisolomou, Stavros P; El-Haddad, George

    2017-01-01

    Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented chromatophore organs and reflecting cells. Therefore, a lot can be learned about the cephalopod coloration system by video recording and analyzing the activation of individual chromatophores in time. The fact that adult cephalopods have small chromatophores, up to several hundred thousand in number, makes measurement and analysis over several seconds a difficult task. However, current advancements in videography enable high-resolution and high framerate recording, which can be used to record chromatophore activity in more detail and accuracy in both space and time domains. In turn, the additional pixel information and extra frames per video from such recordings result in large video files of several gigabytes, even when the recording spans only few minutes. We created a software plugin, "SpotMetrics," that can automatically analyze high resolution, high framerate video of chromatophore organ activation in time. This image analysis software can track hundreds of individual chromatophores over several hundred frames to provide measurements of size and color. This software may also be used to measure differences in chromatophore activation during different behaviors which will contribute to our understanding of the cephalopod sensorimotor integration system. In addition, this software can potentially be utilized to detect numbers of round objects and size changes in time, such as eye pupil size or number of bacteria in a sample. Thus, we are making this software plugin freely available as open-source because we believe it will be of benefit to other colleagues both in the cephalopod biology field and also within other disciplines.

  16. 基于开源架构的虚拟网络安全实验平台%Virtual network security experimental platform based on open source architecture

    Institute of Scientific and Technical Information of China (English)

    鲁先志; 胡海波

    2015-01-01

    A construction approach on virtual platform network for security experiment based upon open source architecture is proposed.The proposed scheme is implemented with KVM (Kernel-based Virtual Machine), SDN (Software-Define Networking),and based on ISCSI protocol of network storage technology as well.Two common experimental templates are presented to facilitate the usage of the proposed platform.By using the templates,users can perform variable experiments on the proposed platform,such as network exploitation test and virtual enterprise network data storage environment.Compared with VMware-based virtualization technology,the proposed mechanism manifest is beneficial to laboratory of network security with flexible network access control,less hardware costs,and without software license fees as well.%提出了基于开源架构的虚拟网络安全实验平台的解决方案,利用 KVM技术、软件定义网络技术以及基于 ISCSI协议的网络存储技术等实现了该方案,并给出了2个常用的实验模板。实验表明:使用者利用该网络安全实验平台可构建各种网络渗透实验测试环境及虚拟企业网络数据存储环境。与基于 VMware虚拟化技术解决方案相比,该网络安全实验平台具有网络访问控制灵活、无需购买商业授权以及硬件资源占用少等优点。

  17. MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

    Science.gov (United States)

    Robichaud, Guillaume; Garrard, Kenneth P; Barry, Jeremy A; Muddiman, David C

    2013-05-01

    During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

  18. Enhancing interdisciplinary collaboration and decisionmaking with J-Earth: an open source data sharing, visualization and GIS analysis platform

    Science.gov (United States)

    Prashad, L. C.; Christensen, P. R.; Fink, J. H.; Anwar, S.; Dickenshied, S.; Engle, E.; Noss, D.

    2010-12-01

    Our society currently is facing a number of major environmental challenges, most notably the threat of climate change. A multifaceted, interdisciplinary approach involving physical and social scientists, engineers and decisionmakers is critical to adequately address these complex issues. To best facilitate this interdisciplinary approach, data and models at various scales - from local to global - must be quickly and easily shared between disciplines to effectively understand environmental phenomena and human-environmental interactions. When data are acquired and studied on different scales and within different disciplines, researchers and practitioners may not be able to easily learn from each others results. For example, climate change models are often developed at a global scale, while strategies that address human vulnerability to climate change and mitigation/adaptation strategies are often assessed on a local level. Linkages between urban heat island phenomena and global climate change may be better understood with increased data flow amongst researchers and those making policy decisions. In these cases it would be useful have a single platform to share, visualize, and analyze numerical model and satellite/airborne remote sensing data with social, environmental, and economic data between researchers and practitioners. The Arizona State University 100 Cities Project and Mars Space Flight Facility are developing the open source application J-Earth, with the goal of providing this single platform, that facilitates data sharing, visualization, and analysis between researchers and applied practitioners around environmental and other sustainability challenges. This application is being designed for user communities including physical and social scientists, NASA researchers, non-governmental organizations, and decisionmakers to share and analyze data at multiple scales. We are initially focusing on urban heat island and urban ecology studies, with data and users from

  19. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

    Directory of Open Access Journals (Sweden)

    Anderson Gordon A

    2009-03-01

    Full Text Available Abstract Background Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls. Results With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to

  20. Open-source software for demand forecasting of clinical laboratory test volumes using time-series analysis

    Directory of Open Access Journals (Sweden)

    Emad A Mohammed

    2017-01-01

    Full Text Available Background: Demand forecasting is the area of predictive analytics devoted to predicting future volumes of services or consumables. Fair understanding and estimation of how demand will vary facilitates the optimal utilization of resources. In a medical laboratory, accurate forecasting of future demand, that is, test volumes, can increase efficiency and facilitate long-term laboratory planning. Importantly, in an era of utilization management initiatives, accurately predicted volumes compared to the realized test volumes can form a precise way to evaluate utilization management initiatives. Laboratory test volumes are often highly amenable to forecasting by time-series models; however, the statistical software needed to do this is generally either expensive or highly technical. Method: In this paper, we describe an open-source web-based software tool for time-series forecasting and explain how to use it as a demand forecasting tool in clinical laboratories to estimate test volumes. Results: This tool has three different models, that is, Holt-Winters multiplicative, Holt-Winters additive, and simple linear regression. Moreover, these models are ranked and the best one is highlighted. Conclusion: This tool will allow anyone with historic test volume data to model future demand.