WorldWideScience

Sample records for open source tools

  1. Handbook of Open Source Tools

    CERN Document Server

    Koranne, Sandeep

    2011-01-01

    Handbook of Open Source Tools introduces a comprehensive collection of advanced open source tools useful in developing software applications. The book contains information on more than 200 open-source tools which include software construction utilities for compilers, virtual-machines, database, graphics, high-performance computing, OpenGL, geometry, algebra, graph theory , GUIs and more. Special highlights for software construction utilities and application libraries are included. Each tool is covered in the context of a real like application development setting. This unique handbook presents

  2. Intrusion Detection using Open Source Tools

    Directory of Open Access Journals (Sweden)

    Jack TIMOFTE

    2008-01-01

    Full Text Available We have witnessed in the recent years that open source tools have gained popularity among all types of users, from individuals or small businesses to large organizations and enterprises. In this paper we will present three open source IDS tools: OSSEC, Prelude and SNORT.

  3. System level modelling with open source tools

    DEFF Research Database (Denmark)

    Jakobsen, Mikkel Koefoed; Madsen, Jan; Niaki, Seyed Hosein Attarzadeh;

    , called ForSyDe. ForSyDe is available under the open Source approach, which allows small and medium enterprises (SME) to get easy access to advanced modeling capabilities and tools. We give an introduction to the design methodology through the system level modeling of a simple industrial use case, and we...

  4. A survey of open source tools for business intelligence

    DEFF Research Database (Denmark)

    Thomsen, Christian; Pedersen, Torben Bach

    2005-01-01

    The industrial use of open source Business Intelligence (BI) tools is not yet common. It is therefore of interest to explore which possibilities are available for open source BI and compare the tools. In this survey paper, we consider the capabilities of a number of open source tools for BI...

  5. An Open Source Tool to Test Interoperability

    Science.gov (United States)

    Bermudez, L. E.

    2012-12-01

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

  6. 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.

  7. Building Eclectic Personal Learning Landscapes with Open Source Tools

    NARCIS (Netherlands)

    Kalz, Marco

    2008-01-01

    Kalz, M. (2005). Building Eclectic Personal Learning Landscapes with Open Source Tools. In F. de Vries, G. Attwell, R. Elferink & A. Tödt (Eds.), Open Source for Education in Europe. Research & Practice (= Proceedings of the Open Source for Education in Europe Conference) (pp. 163-168). 2005, Heerle

  8. Building Eclectic Personal Learning Landscapes with Open Source Tools

    NARCIS (Netherlands)

    Kalz, Marco

    2008-01-01

    Kalz, M. (2005). Building Eclectic Personal Learning Landscapes with Open Source Tools. In F. de Vries, G. Attwell, R. Elferink & A. Tödt (Eds.), Open Source for Education in Europe. Research & Practice (= Proceedings of the Open Source for Education in Europe Conference) (pp. 163-168). 2005,

  9. A Survey of Open Source Tools for Business Intelligence

    DEFF Research Database (Denmark)

    Thomsen, Christian; Pedersen, Torben Bach

    2009-01-01

    The industrial use of open source Business Intelligence (BI) tools is becoming more common, but is still not as widespread as for other types of software. It is therefore of interest to explore which possibilities are available for open source BI and compare the tools. In this survey paper, we...

  10. A Survey of Open Source Tools for Business Intelligence

    DEFF Research Database (Denmark)

    Thomsen, Christian; Pedersen, Torben Bach

    2009-01-01

    The industrial use of open source Business Intelligence (BI) tools is becoming more common, but is still not as widespread as for other types of software. It is therefore of interest to explore which possibilities are available for open source BI and compare the tools. In this survey paper, we...... consider the capabilities of a number of open source tools for BI. In the paper, we consider a number of Extract-Transform-Load (ETL) tools, database management systems (DBMSs), On-Line Analytical Processing (OLAP) servers, and OLAP clients. We find that, unlike the situation a few years ago, there now...

  11. The GPS Toolkit: Open Source Clock Tools

    Science.gov (United States)

    2008-12-01

    gnuplot . ALLANPLOT (allanplot) allanplot is a Python plotting script. The script opens an interface that allows the user to view the plot and a...Allan deviation. The script opens a gnuplot window with the input data plotted. The x, y, and z axis are plotted logarithmically, with x and y

  12. Open source Modeling and optimization tools for Planning

    Energy Technology Data Exchange (ETDEWEB)

    Peles, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-10

    Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward to complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.

  13. Open Source and Proprietary Project Management Tools for SMEs.

    Directory of Open Access Journals (Sweden)

    Veronika Abramova

    2017-05-01

    Full Text Available The dimensional growth and increasing difficulty in project management promoted the development of different tools that serve to facilitate project management and track project schedule, resources and overall progress. These tools offer a variety of features, from task and time management, up to integrated CRM (Customer Relationship Management and ERP (Enterprise Resource Planning modules. Currently, a large number of project management software is available, to assist project team during the entire project lifecycle. We present the main differences between open source and proprietary project management tools and how those could be important for SMEs, describing the key features and how those can assist the project manager and the development team. In this paper, we analyse four open-source project management tools: OpenProject, ProjectLibre, Redmine, LibrePlan and four proprietary tools: Bitrix24, JIRA, Microsoft Project and Asana.

  14. 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…

  15. Large Data Visualization with Open-Source Tools

    CERN Document Server

    CERN. Geneva

    2015-01-01

    Visualization and post-processing of large data have become increasingly challenging and require more and more tools to support the diversity of data to process. In this seminar, we will present a suite of open-source tools supported and developed by Kitware to perform large-scale data visualization and analysis. In particular, we will present ParaView, an open-source tool for parallel visualization of massive datasets, the Visualization Toolkit (VTK), an open-source toolkit for scientific visualization, and Tangelohub, a suite of tools for large data analytics. About the speaker Julien Jomier is directing Kitware's European subsidiary in Lyon, France, where he focuses on European business development. Julien works on a variety of projects in the areas of parallel and distributed computing, mobile computing, image processing, and visualization. He is one of the developers of the Insight Toolkit (ITK), the Visualization Toolkit (VTK), and ParaView. Julien is also leading the CDash project, an open-source co...

  16. Collecting, Analyzing and Visualizing Tweets using Open Source Tools

    OpenAIRE

    Yang, Seungwon; Kavanaugh, Andrea L.

    2011-01-01

    This tutorial will teach participants how to collect, analyze and visualize results from twitter data. We will demonstrate several different free, open-source web-based tools that participants can use to collect twitter data (e.g., Archivist, 140kit.com, TwapperKeeper), and show them a few different methods, tools or programs they can use to analyze the data in a given collection. Finally, we will show participants visualization tools and programs they can use to present the analyses, such ...

  17. Developing Free and Open Source Interactive Teaching Tools

    Science.gov (United States)

    Nelson, E.

    2016-12-01

    Online learning has become an embedded component of education, but existing resources are often provided as institution-hosted content management systems (that may or may not be closed source). Creating interactive online applets to enhance student education is an alternative to these limited-customization systems that can be accomplished on a small budget. This presentation will break down the anatomy of author-developed online teaching tools created with open source packages to provide a survey of the development tools utilized—from the underlying website framework to interfacing with the scientific data. The availability of hosting and maintaining interactive teaching tools, whether static or dynamic, on no- or low-cost platforms will also be discussed. By constructing an interactive teaching tool from the ground up, scientists and educators are afforded complete flexibility and creativity in the design.

  18. A Survey of Open Source Tools for Business Intelligence

    DEFF Research Database (Denmark)

    Thomsen, Christian; Pedersen, Torben Bach

    The industrial use of open source Business Intelligence (BI) tools is becoming more common, but is still not as widespread as for other types of software.  It is therefore of interest to explore which possibilities are available for open source BI and compare the tools. In this survey paper, we c......The industrial use of open source Business Intelligence (BI) tools is becoming more common, but is still not as widespread as for other types of software.  It is therefore of interest to explore which possibilities...

  19. 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.

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

    Science.gov (United States)

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

    2015-12-01

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

  1. Open source engineering and sustainability tools for the built environment

    NARCIS (Netherlands)

    Coenders, J.L.

    2013-01-01

    This paper presents two novel open source software developments for design and engineering in the built environment. The first development, called “sustainability-open” [1], aims on providing open source design, analysis and assessment software source code for (environmental) performance of building

  2. Open source engineering and sustainability tools for the built environment

    NARCIS (Netherlands)

    Coenders, J.L.

    2013-01-01

    This paper presents two novel open source software developments for design and engineering in the built environment. The first development, called “sustainability-open” [1], aims on providing open source design, analysis and assessment software source code for (environmental) performance of

  3. VSEARCH: a versatile open source tool for metagenomics

    Science.gov (United States)

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

    2016-01-01

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

  4. 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.

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

    Science.gov (United States)

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

    2011-03-01

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

  6. Windows Developer Power Tools Turbocharge Windows development with more than 170 free and open source tools

    CERN Document Server

    Avery, James

    2007-01-01

    Software developers need to work harder and harder to bring value to their development process in order to build high quality applications and remain competitive. Developers can accomplish this by improving their productivity, quickly solving problems, and writing better code. A wealth of open source and free software tools are available for developers who want to improve the way they create, build, deploy, and use software. Tools, components, and frameworks exist to help developers at every point in the development process. Windows Developer Power Tools offers an encyclopedic guide to m

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

    Science.gov (United States)

    Porth, Tricia

    1994-01-01

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

  8. An open source tool for heart rate variability spectral analysis.

    Science.gov (United States)

    Rodríguez-Liñares, L; Méndez, A J; Lado, M J; Olivieri, D N; Vila, X A; Gómez-Conde, I

    2011-07-01

    In this paper we describe a software package for developing heart rate variability analysis. This package, called RHRV, is a third party extension for the open source statistical environment R, and can be freely downloaded from the R-CRAN repository. We review the state of the art of software related to the analysis of heart rate variability (HRV). Based upon this review, we motivate the development of an open source software platform which can be used for developing new algorithms for studying HRV or for performing clinical experiments. In particular, we show how the RHRV package greatly simplifies and accelerates the work of the computer scientist or medical specialist in the HRV field. We illustrate the utility of our package with practical examples.

  9. Business intelligence tools for radiology: creating a prototype model using open-source tools.

    Science.gov (United States)

    Prevedello, Luciano M; Andriole, Katherine P; Hanson, Richard; Kelly, Pauline; Khorasani, Ramin

    2010-04-01

    Digital radiology departments could benefit from the ability to integrate and visualize data (e.g. information reflecting complex workflow states) from all of their imaging and information management systems in one composite presentation view. Leveraging data warehousing tools developed in the business world may be one way to achieve this capability. In total, the concept of managing the information available in this data repository is known as Business Intelligence or BI. This paper describes the concepts used in Business Intelligence, their importance to modern Radiology, and the steps used in the creation of a prototype model of a data warehouse for BI using open-source tools.

  10. Neural Monkey: An Open-source Tool for Sequence Learning

    Directory of Open Access Journals (Sweden)

    Helcl Jindřich

    2017-04-01

    Full Text Available In this paper, we announce the development of Neural Monkey – an open-source neural machine translation (NMT and general sequence-to-sequence learning system built over the TensorFlow machine learning library. The system provides a high-level API tailored for fast prototyping of complex architectures with multiple sequence encoders and decoders. Models’ overall architecture is specified in easy-to-read configuration files. The long-term goal of the Neural Monkey project is to create and maintain a growing collection of implementations of recently proposed components or methods, and therefore it is designed to be easily extensible. Trained models can be deployed either for batch data processing or as a web service. In the presented paper, we describe the design of the system and introduce the reader to running experiments using Neural Monkey.

  11. Using Open Source Tools to Create a Mobile Optimized, Crowdsourced Translation Tool

    Directory of Open Access Journals (Sweden)

    Evviva Weinraub Lajoie

    2014-04-01

    Full Text Available In late 2012, OSU Libraries and Press partnered with Maria's Libraries, an NGO in Rural Kenya, to provide users the ability to crowdsource translations of folk tales and existing children's books into a variety of African languages, sub-languages, and dialects. Together, these two organizations have been creating a mobile optimized platform using open source libraries such as Wink Toolkit (a library which provides mobile-friendly interaction from a website and Globalize3 to allow for multiple translations of database entries in a Ruby on Rails application. Research regarding successes of similar tools has been utilized in providing a consistent user interface. The OSU Libraries & Press team delivered a proof-of-concept tool that has the opportunity to promote technology exploration, improve early childhood literacy, change the way we approach foreign language learning, and to provide opportunities for cost-effective, multi-language publishing.

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Science.gov (United States)

    Ozdamli, Fezile

    2007-01-01

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

  14. Oral Development for LSP via Open Source Tools

    Directory of Open Access Journals (Sweden)

    Alejandro Curado Fuentes

    2015-11-01

    Full Text Available For the development of oral abilities in LSP, few computer-based teaching and learning resources have actually focused intensively on web-based listening and speaking. Many more do on reading, writing, vocabulary and grammatical activities. Our aim in this paper is to approach oral communication in the online environment of Moodle by striving to make it suitable for a learning project which incorporates oral skills. The paper describes a blended process in which both individual and collaborative learning strategies can be combined and exploited through the implementation of specific tools and resources which may go hand in hand with traditional face-to-face conversational classes. The challenge with this new perspective is, ultimately, to provide effective tools for oral LSP development in an apparently writing skill-focused medium.

  15. Development and validation of an open source quantification tool for DSC-MRI studies.

    Science.gov (United States)

    Gordaliza, P M; Mateos-Pérez, J M; Montesinos, P; Guzmán-de-Villoria, J A; Desco, M; Vaquero, J J

    2015-03-01

    This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license. This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared. Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots). An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    Plieger, Maarten; de Vreede, Ernst

    2015-04-01

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

  17. Applying open source data visualization tools to standard based medical data.

    Science.gov (United States)

    Kopanitsa, Georgy; Taranik, Maxim

    2014-01-01

    Presentation of medical data in personal health records (PHRs) requires flexible platform independent tools to ensure easy access to the information. Different backgrounds of the patients, especially elder people require simple graphical presentation of the data. Data in PHRs can be collected from heterogeneous sources. Application of standard based medical data allows development of generic visualization methods. Focusing on the deployment of Open Source Tools, in this paper we applied Java Script libraries to create data presentations for standard based medical data.

  18. Un tool Open Source per la ricerca dispersi in ambiente montano

    Directory of Open Access Journals (Sweden)

    Tiziano Cosso

    2013-08-01

    Full Text Available G4MoRe, Gter-for Mountain Rescue, è un tool interamente sviluppato con prodotti Open Source e pensato come supporto alle attività di ricerca dispersi in ambiente montano, prodotto e supportato da Gter srl.G4MoRe, Gter-for Mountain Rescue, is a tool developed entirely with Open Source products and designed as support to research activitiesof missing people in the mountains, manufactured and supported by Gter srl.

  19. Text mining and visualization case studies using open-source tools

    CERN Document Server

    Chisholm, Andrew

    2016-01-01

    Text Mining and Visualization: Case Studies Using Open-Source Tools provides an introduction to text mining using some of the most popular and powerful open-source tools: KNIME, RapidMiner, Weka, R, and Python. The contributors-all highly experienced with text mining and open-source software-explain how text data are gathered and processed from a wide variety of sources, including books, server access logs, websites, social media sites, and message boards. Each chapter presents a case study that you can follow as part of a step-by-step, reproducible example. You can also easily apply and extend the techniques to other problems. All the examples are available on a supplementary website. The book shows you how to exploit your text data, offering successful application examples and blueprints for you to tackle your text mining tasks and benefit from open and freely available tools. It gets you up to date on the latest and most powerful tools, the data mining process, and specific text mining activities.

  20. Half-Day Tutorial: Collecting, Analyzing, and Visualizing Tweets Using Open Source Tools

    OpenAIRE

    Yang, Seungwon; Kavanaugh, Andrea L.

    2011-01-01

    This tutorial introduces various open source tools and methods to archive tweets on a user's local machine and convert them into topic clouds for quick content analysis. For more in-depth techniques such as n-grams and term extraction are introduced along with PHP/Python scripting. Digital Government '11, June 12-15, 2011, College Park, MD

  1. 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

  2. An open source GIS-based tool to integrate the fragmentation mechanism in rockfall propagation

    Science.gov (United States)

    Matas, Gerard; Lantada, Nieves; Gili, Josep A.; Corominas, Jordi

    2015-04-01

    Rockfalls are frequent instability processes in road cuts, open pit mines and quarries, steep slopes and cliffs. Even though the stability of rock slopes can be determined using analytical approaches, the assessment of large rock cliffs require simplifying assumptions due to the difficulty of working with a large amount of joints, the scattering of both the orientations and strength parameters. The attitude and persistency of joints within the rock mass define the size of kinematically unstable rock volumes. Furthermore the rock block will eventually split in several fragments during its propagation downhill due its impact with the ground surface. Knowledge of the size, energy, trajectory… of each block resulting from fragmentation is critical in determining the vulnerability of buildings and protection structures. The objective of this contribution is to present a simple and open source tool to simulate the fragmentation mechanism in rockfall propagation models and in the calculation of impact energies. This tool includes common modes of motion for falling boulders based on the previous literature. The final tool is being implemented in a GIS (Geographic Information Systems) using open source Python programming. The tool under development will be simple, modular, compatible with any GIS environment, open source, able to model rockfalls phenomena correctly. It could be used in any area susceptible to rockfalls with a previous adjustment of the parameters. After the adjustment of the model parameters to a given area, a simulation could be performed to obtain maps of kinetic energy, frequency, stopping density and passing heights. This GIS-based tool and the analysis of the fragmentation laws using data collected from recent rockfall have being developed within the RockRisk Project (2014-2016). This project is funded by the Spanish Ministerio de Economía y Competitividad and entitled "Rockfalls in cliffs: risk quantification and its prevention"(BIA2013-42582-P).

  3. REFINED SATELLITE IMAGE ORIENTATION IN THE FREE OPEN-SOURCE PHOTOGRAMMETRIC TOOLS APERO/MICMAC

    OpenAIRE

    E. Rupnik; M. Pierrot Deseilligny; Delorme, A.; Klinger, Y

    2016-01-01

    This publication presents the RPC-based bundle adjustment implemented in the freeware open-source photogrammetric tool Apero/MicMac. The bundle adjustment model is based on some polynomial correction functions, enriched with a physical constraint that introduces the notion of a global sensor rotation into the model. The devised algorithms are evaluated against two datasets consisting of two stereo and a triplet pair of the Pleiades images. Two sets of correction functions and a number of G...

  4. ThinkHazard!: an open-source, global tool for understanding hazard information

    Science.gov (United States)

    Fraser, Stuart; Jongman, Brenden; Simpson, Alanna; Nunez, Ariel; Deparday, Vivien; Saito, Keiko; Murnane, Richard; Balog, Simone

    2016-04-01

    Rapid and simple access to added-value natural hazard and disaster risk information is a key issue for various stakeholders of the development and disaster risk management (DRM) domains. Accessing available data often requires specialist knowledge of heterogeneous data, which are often highly technical and can be difficult for non-specialists in DRM to find and exploit. Thus, availability, accessibility and processing of these information sources are crucial issues, and an important reason why many development projects suffer significant impacts from natural hazards. The World Bank's Global Facility for Disaster Reduction and Recovery (GFDRR) is currently developing a new open-source tool to address this knowledge gap: ThinkHazard! The main aim of the ThinkHazard! project is to develop an analytical tool dedicated to facilitating improvements in knowledge and understanding of natural hazards among non-specialists in DRM. It also aims at providing users with relevant guidance and information on handling the threats posed by the natural hazards present in a chosen location. Furthermore, all aspects of this tool will be open and transparent, in order to give users enough information to understand its operational principles. In this presentation, we will explain the technical approach behind the tool, which translates state-of-the-art probabilistic natural hazard data into understandable hazard classifications and practical recommendations. We will also demonstrate the functionality of the tool, and discuss limitations from a scientific as well as an operational perspective.

  5. 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.

  6. EpiTools: An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics.

    Science.gov (United States)

    Heller, Davide; Hoppe, Andreas; Restrepo, Simon; Gatti, Lorenzo; Tournier, Alexander L; Tapon, Nicolas; Basler, Konrad; Mao, Yanlan

    2016-01-11

    Epithelia grow and undergo extensive rearrangements to achieve their final size and shape. Imaging the dynamics of tissue growth and morphogenesis is now possible with advances in time-lapse microscopy, but a true understanding of their complexities is limited by automated image analysis tools to extract quantitative data. To overcome such limitations, we have designed a new open-source image analysis toolkit called EpiTools. It provides user-friendly graphical user interfaces for accurately segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is designed for a broad audience, especially biologists with no computer-science background. Quantitative data extraction is integrated into a larger bioimaging platform, Icy, to increase the visibility and usability of our tools. We demonstrate the usefulness of EpiTools by analyzing Drosophila wing imaginal disc growth, revealing previously overlooked properties of this dynamic tissue, such as the patterns of cellular rearrangements.

  7. Analyzing Kepler/K2 pixel data using open source tools

    Science.gov (United States)

    Barentsen, Geert

    2016-06-01

    I will demonstrate three new open source command-line tools which have been developed at Kepler/K2 Guest Observer Office to help the community analyze and interpret pixel data from NASA's K2 mission: (1) "k2flix" enables the visual inspection of pixel files for artifacts; (2) "k2mosaic" enables pixel files to be mosaiced into contiguous images; and (3) "k2lightcurve" extracts and detrends photometry. I will also highlight the "k2ephem" and "k2fov" tools which aid target selection, and the "kadenza" tool which enables access to the raw spacecraft data during the Campaign 9 microlensing experiment. Finally, I will explain how these tools may be adapted to aid the upcoming TESS and PLATO missions.

  8. An integrated, open-source set of tools for urban vulnerability monitoring from Earth observation data

    Science.gov (United States)

    De Vecchi, Daniele; Harb, Mostapha; Dell'Acqua, Fabio; Aurelio Galeazzo, Daniel

    2015-04-01

    Aim: The paper introduces an integrated set of open-source tools designed to process medium and high-resolution imagery with the aim to extract vulnerability indicators [1]. Problem: In the context of risk monitoring [2], a series of vulnerability proxies can be defined, such as the extension of a built-up area or buildings regularity [3]. Different open-source C and Python libraries are already available for image processing and geospatial information (e.g. OrfeoToolbox, OpenCV and GDAL). They include basic processing tools but not vulnerability-oriented workflows. Therefore, it is of significant importance to provide end-users with a set of tools capable to return information at a higher level. Solution: The proposed set of python algorithms is a combination of low-level image processing and geospatial information handling tools along with high-level workflows. In particular, two main products are released under the GPL license: source code, developers-oriented, and a QGIS plugin. These tools were produced within the SENSUM project framework (ended December 2014) where the main focus was on earthquake and landslide risk. Further development and maintenance is guaranteed by the decision to include them in the platform designed within the FP 7 RASOR project . Conclusion: With the lack of a unified software suite for vulnerability indicators extraction, the proposed solution can provide inputs for already available models like the Global Earthquake Model. The inclusion of the proposed set of algorithms within the RASOR platforms can guarantee support and enlarge the community of end-users. Keywords: Vulnerability monitoring, remote sensing, optical imagery, open-source software tools References [1] M. Harb, D. De Vecchi, F. Dell'Acqua, "Remote sensing-based vulnerability proxies in the EU FP7 project SENSUM", Symposium on earthquake and landslide risk in Central Asia and Caucasus: exploiting remote sensing and geo-spatial information management, 29-30th January 2014

  9. Open source tools for the information theoretic analysis of neural data.

    Science.gov (United States)

    Ince, Robin A A; Mazzoni, Alberto; Petersen, Rasmus S; Panzeri, Stefano

    2010-01-01

    The recent and rapid development of open source software tools for the analysis of neurophysiological datasets consisting of simultaneous multiple recordings of spikes, field potentials and other neural signals holds the promise for a significant advance in the standardization, transparency, quality, reproducibility and variety of techniques used to analyze neurophysiological data and for the integration of information obtained at different spatial and temporal scales. In this review we focus on recent advances in open source toolboxes for the information theoretic analysis of neural responses. We also present examples of their use to investigate the role of spike timing precision, correlations across neurons, and field potential fluctuations in the encoding of sensory information. These information toolboxes, available both in MATLAB and Python programming environments, hold the potential to enlarge the domain of application of information theory to neuroscience and to lead to new discoveries about how neurons encode and transmit information.

  10. Interactive, open source, travel time scenario modelling: tools to facilitate participation in health service access analysis.

    Science.gov (United States)

    Fisher, Rohan; Lassa, Jonatan

    2017-04-18

    Modelling travel time to services has become a common public health tool for planning service provision but the usefulness of these analyses is constrained by the availability of accurate input data and limitations inherent in the assumptions and parameterisation. This is particularly an issue in the developing world where access to basic data is limited and travel is often complex and multi-modal. Improving the accuracy and relevance in this context requires greater accessibility to, and flexibility in, travel time modelling tools to facilitate the incorporation of local knowledge and the rapid exploration of multiple travel scenarios. The aim of this work was to develop simple open source, adaptable, interactive travel time modelling tools to allow greater access to and participation in service access analysis. Described are three interconnected applications designed to reduce some of the barriers to the more wide-spread use of GIS analysis of service access and allow for complex spatial and temporal variations in service availability. These applications are an open source GIS tool-kit and two geo-simulation models. The development of these tools was guided by health service issues from a developing world context but they present a general approach to enabling greater access to and flexibility in health access modelling. The tools demonstrate a method that substantially simplifies the process for conducting travel time assessments and demonstrate a dynamic, interactive approach in an open source GIS format. In addition this paper provides examples from empirical experience where these tools have informed better policy and planning. Travel and health service access is complex and cannot be reduced to a few static modeled outputs. The approaches described in this paper use a unique set of tools to explore this complexity, promote discussion and build understanding with the goal of producing better planning outcomes. The accessible, flexible, interactive and

  11. Toward Transparent and Reproducible Science: Using Open Source "Big Data" Tools for Water Resources Assessment

    Science.gov (United States)

    Buytaert, W.; Zulkafli, Z. D.; Vitolo, C.

    2014-12-01

    Transparency and reproducibility are fundamental properties of good science. In the current era of large and diverse datasets and long and complex workflows for data analysis and inference, ensuring such transparency and reproducibility is challenging. Hydrological science is a good case in point, because the discipline typically uses a large variety of datasets ranging from local observations to large-scale remotely sensed products. These data are often obtained from various different sources, and integrated using complex yet uncertain modelling tools. In this paper, we present and discuss methods of ensuring transparency and reproducibility in scientific workflows for hydrological data analysis for the purpose of water resources assessment, using relevant examples of emerging open source "big data" tools. First, we discuss standards for data storage, access, and processing that allow improving the modularity of a hydrological analysis workflow. In particular standards emerging from the Open Geospatial Consortium, such as the Sensor Observation Service, the Web Coverage Service, hold promise. However, some bottlenecks such as the availability of data models and the ability to work with spatio-temperal subsets of large datasets, need further development. Next, we focus on available methods to build transparent data processing workflows. Again, standards such as OGC's Web Processing Service are being developed to facilitate web-based analytics. Yet, in practice, the experimental nature of these standards and web services in general often requires a more pragmatic approach. The availability of web technologies in popular open source data analysis environments such as R and Python often makes them an attractive solution for workflow creation and sharing. Lastly, we elaborate on the potential of open source solutions hold in the context of participatory approaches to data collection and knowledge generation. Using examples from the tropical Andes and the Himalayas, we

  12. Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

    Science.gov (United States)

    Barre, Arnaud; Armand, Stéphane

    2014-04-01

    C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X).

  13. Refined Satellite Image Orientation in the Free Open-Source Photogrammetric Tools Apero/micmac

    Science.gov (United States)

    Rupnik, E.; Pierrot Deseilligny, M.; Delorme, A.; Klinger, Y.

    2016-06-01

    This publication presents the RPC-based bundle adjustment implemented in the freeware open-source photogrammetric tool Apero/MicMac. The bundle adjustment model is based on some polynomial correction functions, enriched with a physical constraint that introduces the notion of a global sensor rotation into the model. The devised algorithms are evaluated against two datasets consisting of two stereo and a triplet pair of the Pleiades images. Two sets of correction functions and a number of GCPs configurations are examined. The obtained geo-referencing accuracy falls below the size of 1GSD.

  14. OSS4EVA: Using Open-Source Tools to Fulfill Digital Preservation Requirements

    Directory of Open Access Journals (Sweden)

    Heidi Dowding

    2016-10-01

    Full Text Available This paper builds on the findings of a workshop held at the 2015 International Conference on Digital Preservation (iPRES, entitled, “Using Open-Source Tools to Fulfill Digital Preservation Requirements” (OSS4PRES hereafter. This day-long workshop brought together participants from across the library and archives community, including practitioners, proprietary vendors, and representatives from open-source projects. The resulting conversations were surprisingly revealing: while OSS’ significance within the preservation landscape was made clear, participants noted that there are a number of roadblocks that discourage or altogether prevent its use in many organizations. Overcoming these challenges will be necessary to further widespread, sustainable OSS adoption within the digital preservation community. This article will mine the rich discussions that took place at OSS4PRES to (1 summarize the workshop’s key themes and major points of debate, (2 provide a comprehensive analysis of the opportunities, gaps, and challenges that using OSS entails at a philosophical, institutional, and individual level, and (3 offer a tangible set of recommendations for future work designed to broaden community engagement and enhance the sustainability of open source initiatives, drawing on both participants’ experience as well as additional research.

  15. jSPyDB, an open source database-independent tool for data management

    Science.gov (United States)

    Pierro, Giuseppe Antonio; Cavallari, Francesca; Di Guida, Salvatore; Innocente, Vincenzo

    2011-12-01

    Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web-based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. Moreover, thanks to jQuery libraries, this tool supports export of data in different formats, such as XML and JSON. Finally, by using a set of pre-defined functions, users are allowed to create their customized views for a better data visualization. In this way, we optimize the performance of database servers by avoiding short connections and concurrent sessions. In addition, security is enforced since we do not provide users the possibility to directly execute any SQL statement.

  16. jSPyDB, an open source database-independent tool for data management

    CERN Document Server

    Pierro, Giuseppe Antonio

    2010-01-01

    Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different Database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. ...

  17. The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires.

    Science.gov (United States)

    D'Angelo, Sara; Glanville, Jacob; Ferrara, Fortunato; Naranjo, Leslie; Gleasner, Cheryl D; Shen, Xiaohong; Bradbury, Andrew R M; Kiss, Csaba

    2014-01-01

    In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1-2 million reads can be accomplished in 10-15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.

  18. An open source GIS tool to quantify the visual impact of wind turbines and photovoltaic panels

    Energy Technology Data Exchange (ETDEWEB)

    Minelli, Annalisa, E-mail: Annalisa.Minelli@univ-brest.fr [Insitute Universitaire Européen de la Mer, Université de la Bretagne Occidentale, Rue Dumont D' Urville, 29280 Plouzané (France); Marchesini, Ivan, E-mail: Ivan.Marchesini@irpi.cnr.it [National Research Council (CNR), Research Insitute for Geo-hydrological Protection (IRPI), Strada della Madonna Alta 126, 06125 Perugia (Italy); Taylor, Faith E., E-mail: Faith.Taylor@kcl.ac.uk [Earth and Environmental Dynamics Research Group, Department of Geography, King' s College London, Strand, London WC2R 2LS (United Kingdom); De Rosa, Pierluigi, E-mail: Pierluigi.Derosa@unipg.it [Physics and Geology Department, University of Perugia, Via Zefferino Faina 4, 06123 Perugia (Italy); Casagrande, Luca, E-mail: Luca.Casagrande@gfosservices.it [Gfosservices S.A., Open Source GIS-WebGIS Solutions, Spatial Data Infrastructures, Planning and Counseling, Via F.lli Cairoli 24, 06127 Perugia (Italy); Cenci, Michele, E-mail: mcenci@regione.umbria.it [Servizio Energia qualità dell' ambiente, rifiuti, attività estrattive, Regione Umbia, Corso Vannucci 96, 06121 Perugia (Italy)

    2014-11-15

    Although there are clear economic and environmental incentives for producing energy from solar and wind power, there can be local opposition to their installation due to their impact upon the landscape. To date, no international guidelines exist to guide quantitative visual impact assessment of these facilities, making the planning process somewhat subjective. In this paper we demonstrate the development of a method and an Open Source GIS tool to quantitatively assess the visual impact of these facilities using line-of-site techniques. The methods here build upon previous studies by (i) more accurately representing the shape of energy producing facilities, (ii) taking into account the distortion of the perceived shape and size of facilities caused by the location of the observer, (iii) calculating the possible obscuring of facilities caused by terrain morphology and (iv) allowing the combination of various facilities to more accurately represent the landscape. The tool has been applied to real and synthetic case studies and compared to recently published results from other models, and demonstrates an improvement in accuracy of the calculated visual impact of facilities. The tool is named r.wind.sun and is freely available from GRASS GIS AddOns. - Highlights: • We develop a tool to quantify wind turbine and photovoltaic panel visual impact. • The tool is freely available to download and edit as a module of GRASS GIS. • The tool takes into account visual distortion of the shape and size of objects. • The accuracy of calculation of visual impact is improved over previous methods.

  19. REDBACK: an Open-Source Highly Scalable Simulation Tool for Rock Mechanics with Dissipative Feedbacks

    Science.gov (United States)

    Poulet, T.; Veveakis, M.; Paesold, M.; Regenauer-Lieb, K.

    2014-12-01

    Multiphysics modelling has become an indispensable tool for geoscientists to simulate the complex behaviours observed in their various fields of study where multiple processes are involved, including thermal, hydraulic, mechanical and chemical (THMC) laws. This modelling activity involves simulations that are computationally expensive and its soaring uptake is tightly linked to the increasing availability of supercomputing power and easy access to powerful nonlinear solvers such as PETSc (http://www.mcs.anl.gov/petsc/). The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework (http://mooseframework.org) that can harness such computational power and allow scientists to develop easily some tightly-coupled fully implicit multiphysics simulations that run automatically in parallel on large clusters. This open-source framework provides a powerful tool to collaborate on numerical modelling activities and we are contributing to its development with REDBACK (https://github.com/pou036/redback), a module for Rock mEchanics with Dissipative feedBACKs. REDBACK builds on the tensor mechanics finite strain implementation available in MOOSE to provide a THMC simulator where the energetic formulation highlights the importance of all dissipative terms in the coupled system of equations. We show first applications of fully coupled dehydration reactions triggering episodic fluid transfer through shear zones (Alevizos et al, 2014). The dimensionless approach used allows focusing on the critical underlying variables which are driving the resulting behaviours observed and this tool is specifically designed to study material instabilities underpinning geological features like faulting, folding, boudinage, shearing, fracturing, etc. REDBACK provides a collaborative and educational tool which captures the physical and mathematical understanding of such material instabilities and provides an easy way to apply this knowledge to realistic

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

    Energy Technology Data Exchange (ETDEWEB)

    Nayar, R. Daniel

    2005-08-01

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

  1. OPEN SOURCE IMAGE-PROCESSING TOOLS FOR LOW-COST UAV-BASED LANDSLIDE INVESTIGATIONS

    Directory of Open Access Journals (Sweden)

    U. Niethammer

    2012-09-01

    Full Text Available In recent years, the application of unmanned aerial vehicles (UAVs has become more common and the availability of lightweight digital cameras has enabled UAV-systems to represent affordable and practical remote sensing platforms, allowing flexible and high- resolution remote sensing investigations. In the course of numerous UAV-based remote sensing campaigns significant numbers of airborne photographs of two different landslides have been acquired. These images were used for ortho-mosaic and digital terrain model (DTM generation, thus allowing for high-resolution landslide monitoring. Several new open source image- and DTM- processing tools are now providing a complete remote sensing working cycle with the use of no commercial hard- or software.

  2. FREEWAT: an HORIZON 2020 project to build open source tools for water management.

    Science.gov (United States)

    Rossetto, Rudy; Borsi, Iacopo; Foglia, Laura

    2015-04-01

    tools for better producing feasibility and management plans; (ii) a set of activities devoted to fix bugs and to provide a well-integrated interface for the different tools implemented. Further capabilities to be integrated are: - a dedicated module for water management and planning that will help to manage and aggregate all the distributed data coming from the simulation scenarios; - a whole module for calibration, uncertainty and sensitivity analysis; - a module for solute transport in the unsaturated zone; - a module for crop growth and water requirements in agriculture; - tools for dealing with groundwater quality issues; - tools for the analysis, interpretation and visualization of hydrogeological data. Through creating a common environment among water research/professionals, policy makers and implementers, FREEWAT main impact will be on enhancing science- and participatory approach and evidence-based decision making in water resource management, hence producing relevant and appropriate outcomes for policy implementation. The Consortium is constituted by partners from various water sectors from 10 EU countries, plus Turkey and Ukraine. Synergies with the UNESCO HOPE initiative on free and open source software in water management greatly boost the value of the project. Large stakeholders involvement is thought to guarantee results dissemination and exploitation. Acknowledgements This paper is presented within the framework of the project FREEWAT, which has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement n. 642224. References MARSOL (2014). Demonstrating Managed Aquifer Recharge as a Solution to Water Scarcity and Drought www.marsol.eu [accessed 4 January 2015] Rossetto, R., Borsi, I., Schifani, C., Bonari, E., Mogorovich P. & Primicerio M. (2013) - SID&GRID: integrating hydrological modeling in GIS environment hydroinformatics system for the management of the water resource. Rendiconti Online Societa

  3. Land use mapping from CBERS-2 images with open source tools by applying different classification algorithms

    Science.gov (United States)

    Sanhouse-García, Antonio J.; Rangel-Peraza, Jesús Gabriel; Bustos-Terrones, Yaneth; García-Ferrer, Alfonso; Mesas-Carrascosa, Francisco J.

    2016-02-01

    Land cover classification is often based on different characteristics between their classes, but with great homogeneity within each one of them. This cover is obtained through field work or by mean of processing satellite images. Field work involves high costs; therefore, digital image processing techniques have become an important alternative to perform this task. However, in some developing countries and particularly in Casacoima municipality in Venezuela, there is a lack of geographic information systems due to the lack of updated information and high costs in software license acquisition. This research proposes a low cost methodology to develop thematic mapping of local land use and types of coverage in areas with scarce resources. Thematic mapping was developed from CBERS-2 images and spatial information available on the network using open source tools. The supervised classification method per pixel and per region was applied using different classification algorithms and comparing them among themselves. Classification method per pixel was based on Maxver algorithms (maximum likelihood) and Euclidean distance (minimum distance), while per region classification was based on the Bhattacharya algorithm. Satisfactory results were obtained from per region classification, where overall reliability of 83.93% and kappa index of 0.81% were observed. Maxver algorithm showed a reliability value of 73.36% and kappa index 0.69%, while Euclidean distance obtained values of 67.17% and 0.61% for reliability and kappa index, respectively. It was demonstrated that the proposed methodology was very useful in cartographic processing and updating, which in turn serve as a support to develop management plans and land management. Hence, open source tools showed to be an economically viable alternative not only for forestry organizations, but for the general public, allowing them to develop projects in economically depressed and/or environmentally threatened areas.

  4. 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

  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. FREEWAT: an HORIZON 2020 project to build open source tools for water management.

    Science.gov (United States)

    Foglia, L.; Rossetto, R.; Borsi, I.; Mehl, S.; Velasco Mansilla, V.

    2015-12-01

    FREEWAT is an HORIZON 2020 EU project. FREEWAT main result will be an open source and public domain GIS integrated modelling environment for the simulation of water quantity and quality in surface water and groundwater with an integrated water management and planning module. FREEWAT aims at promoting water resource management by simplifying the application of the Water Framework Directive and related Directives. Specific objectives of the project are: to coordinate previous EU and national funded research to integrate existing software modules for water management in a single environment into the GIS based FREEWAT and to support the FREEWAT application in an innovative participatory approach gathering technical staff and relevant stakeholders (policy and decision makers) in designing scenarios for application of water policies. The open source characteristics of the platform allow to consider this an initiative "ad includendum", as further institutions or developers may contribute to the development. Core of the platform is the SID&GRID framework (GIS integrated physically-based distributed numerical hydrological model based on a modified version of MODFLOW 2005; Rossetto et al. 2013) in its version ported to QGIS desktop. Activities are carried out on two lines: (i) integration of modules to fulfill the end-users requirements, including tools for producing feasibility and management plans; (ii) a set of activities to fix bugs and to provide a well-integrated interface for the different tools implemented. Further capabilities to be integrated are: - module for water management and planning; - calibration, uncertainty and sensitivity analysis; - module for solute transport in unsaturated zone; - module for crop growth and water requirements in agriculture; - tools for groundwater quality issues and for the analysis, interpretation and visualization of hydrogeological data. Through creating a common environment among water research/professionals, policy makers and

  7. 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

  8. Exploring TechQuests Through Open Source and Tools That Inspire Digital Natives

    Science.gov (United States)

    Hayden, K.; Ouyang, Y.; Kilb, D.; Taylor, N.; Krey, B.

    2008-12-01

    "There is little doubt that K-12 students need to understand and appreciate the Earth on which they live. They can achieve this understanding only if their teachers are well prepared". Dan Barstow, Director of Center for Earth and Space Science Education at TERC. The approach of San Diego County's Cyberinfrastructure Training, Education, Advancement, and Mentoring (SD Cyber-TEAM) project is to build understandings of Earth systems for middle school teachers and students through a collaborative that has engaged the scientific community in the use of cyber-based tools and environments for learning. The SD Cyber-TEAM has used Moodle, an open source management system with social networking tools, that engage digital native students and their teachers in collaboration and sharing of ideas and research related to Earth science. Teachers participate in on-line professional dialog through chat, wikis, blogs, forums, journals and other tools and choose the tools that will best fit their classroom. The use of Moodle during the Summer Cyber Academy developed a cyber-collaboratory environment where teaching strategies were discussed, supported and actualized by participants. These experiences supported digital immigrants (teachers) in adapting teaching strategies using technologies that are most attractive and familiar to students (digital natives). A new study by the National School Boards Association and Grunwald Associates LLC indicated that "the online behaviors of U.S. teens and 'tweens shows that 96 percent of students with online access use social networking technologies, such as chatting, text messaging, blogging, and visiting online communities such as Facebook, MySpace, and Webkinz". While SD Cyber-TEAM teachers are implementing TechQuests in classrooms they use these social networking elements to capture student interest and address the needs of digital natives. Through the Moodle environment, teachers have explored a variety of learning objects called Tech

  9. 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.

  10. An open source automatic quality assurance (OSAQA) tool for the ACR MRI phantom.

    Science.gov (United States)

    Sun, Jidi; Barnes, Michael; Dowling, Jason; Menk, Fred; Stanwell, Peter; Greer, Peter B

    2015-03-01

    Routine quality assurance (QA) is necessary and essential to ensure MR scanner performance. This includes geometric distortion, slice positioning and thickness accuracy, high contrast spatial resolution, intensity uniformity, ghosting artefact and low contrast object detectability. However, this manual process can be very time consuming. This paper describes the development and validation of an open source tool to automate the MR QA process, which aims to increase physicist efficiency, and improve the consistency of QA results by reducing human error. The OSAQA software was developed in Matlab and the source code is available for download from http://jidisun.wix.com/osaqa-project/. During program execution QA results are logged for immediate review and are also exported to a spreadsheet for long-term machine performance reporting. For the automatic contrast QA test, a user specific contrast evaluation was designed to improve accuracy for individuals on different display monitors. American College of Radiology QA images were acquired over a period of 2 months to compare manual QA and the results from the proposed OSAQA software. OSAQA was found to significantly reduce the QA time from approximately 45 to 2 min. Both the manual and OSAQA results were found to agree with regard to the recommended criteria and the differences were insignificant compared to the criteria. The intensity homogeneity filter is necessary to obtain an image with acceptable quality and at the same time keeps the high contrast spatial resolution within the recommended criterion. The OSAQA tool has been validated on scanners with different field strengths and manufacturers. A number of suggestions have been made to improve both the phantom design and QA protocol in the future.

  11. OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

    Science.gov (United States)

    Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio

    2017-10-01

    The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open-source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Pre-Eminance of Open Source Eda Tools and Its Types in The Arena of Commercial Electronics

    Directory of Open Access Journals (Sweden)

    Geeta Yadav

    2013-01-01

    Full Text Available Digital synthesis with a goal of chip designing in the commercial electronics arena is packed into large EDA Software providers like, Synopsys, Cadence, or MentorGraphics. These commercial tools being expensive and having closed file structures. It is also a financial constraint for the startup companies sometimes who have their budget limitations. Any bug-fixes or add features cannot be made with ease; in such scenario the company is forced to opt for an alternative cost effective EDA software. This paper deals with the advantages of using open source EDA tools like Icarus Verilog, Verilator, GTKwave viewer, GHDL VHDL simulator, gEDA, etc. that are available as a free source and focuses on the Icarus Verilog simulator tool. It can be seen as a big encouragement for startups in Semiconductor domain. Thereby, these open source EDA tools make the design process more cost-effective, less time consuming and affordable as well.

  13. Open Source

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    一场秋雨一场凉,开源社区的气温却丝毫没有降。刚在北京闭幕的“2006中国开源世界高峰论坛”足以让世界侧目。国际大师云集是最大的亮点,很多熟悉的名字:Andrew Morton(Linux内核开发大师及2.6版本监护人)、Brian Behlendorf(Apache创始人)、David Axmark(MySQL创始人)、Marc Fleury(JBoss创始人)、Larry Augustin(Source Forge创始人)等;其次是中国政府、学术界的支持,包括国家信产部陈英司长和中国工程院倪光南院士、沈昌祥院士等;当然.少不了诸多跨国公司和国内知名企业的参与。

  14. HisTOOLogy: an open-source tool for quantitative analysis of histological sections.

    Science.gov (United States)

    Magliaro, C; Tirella, A; Mattei, G; Pirone, A; Ahluwalia, A

    2015-12-01

    HisTOOLogy is an open-source software for the quantification of digital colour images of histological sections. The simple graphical user interface enables both expert and non-expert users to rapidly extract useful information from stained tissue sections. The software's main feature is a generalizable colour separation algorithm based on k-means clustering which accurately and reproducibly returns the amount of colour per unit area for any stain, thus allowing the quantification of tissue components. Here we describe HisTOOLogy's algorithms and graphical user interface structure, showing how it can be used to separate different dye colours in several classical stains. In addition, to demonstrate how the tool can be employed to obtain quantitative information on biological tissues, the effect of different hepatic tissue decellularization protocols on cell removal and matrix preservation was assessed through image analysis using HisTOOLogy and compared with conventional DNA and total protein content assays. HisTOOLogy's performance was also compared with ImageJ's colour deconvolution plug-in, demonstrating its advantages in terms of ease of use and speed of colour separation.

  15. IPeak: An open source tool to combine results from multiple MS/MS search engines.

    Science.gov (United States)

    Wen, Bo; Du, Chaoqin; Li, Guilin; Ghali, Fawaz; Jones, Andrew R; Käll, Lukas; Xu, Shaohang; Zhou, Ruo; Ren, Zhe; Feng, Qiang; Xu, Xun; Wang, Jun

    2015-09-01

    Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/.

  16. The FEMM Package: A Simple, Fast, and Accurate Open Source Electromagnetic Tool in Science and Engineering

    Directory of Open Access Journals (Sweden)

    K. B. Baltzis

    2008-01-01

    Full Text Available The finite element method (FEM is one of the most successful computational techniques for obtaining approximate solutions to the partial differential equations that arise in many scientific and engineering applications. Finite Element Method Magnetics (FEMM is a software package for solving electromagnetic problems using FEM. The program addresses 2D planar and 3D axisymmetric linear and nonlinear harmonic low frequency magnetic and magnetostatic problems and linear electrostatic problems. It is a simple, accurate, and low computational cost open source product, popular in science, engineering, and education. In this paper the main characteristics and functions of the package are presented. In order to demonstrate its use and exhibit the aid it offers in the study of electromagnetics a series of illustrative examples are given. The aim of the paper is to demonstrate the capability of FEMM to meet as a complementary tool the needs of science and technology especially when factors like the economic cost or the software complexity do not allow the use of commercial products.

  17. "I CAMMINI DELLA REGINA" - Open Source based tools for preserving and culturally exploring historical traffic routes.

    Science.gov (United States)

    Cannata, Massimiliano; Colombo, Massimo; Antonovic, Milan; Cardoso, Mirko; Delucchi, Andrea; Gianocca, Giancarlo; Brovelli, Maria Antonia

    2015-04-01

    "I CAMMINI DELLA REGINA" (The Via Regina Paths) is an Interreg project funded within the transnational cooperation program between Italy and Switzerland 2007-2013. The aim of this project is the preservation and valorization of the cultural heritage linked to the walking historically paths crossing, connecting and serving the local territories. With the approach of leveraging the already existing tools, which generally consist of technical descriptions of the paths, the project uses the open source geospatial technologies to deploy innovative solutions which can fill some of the gaps in historical-cultural tourism offers. The Swiss part, and particularly the IST-SUPSI team, has been focusing its activities in the realization of two innovative solutions: a mobile application for the survey of historical paths and a storytelling system for immersive cultural exploration of the historical paths. The former, based on Android, allows to apply in a revised manner a consolidated and already successfully used methodology of survey focused on the conservation of the historical paths (Inventory of historical traffic routes in Switzerland). Up to now operators could rely only on hand work based on a combination of notes, pictures and GPS devices synthesized in manually drawn maps; this procedure is error prone and shows many problems both in data updating and extracting for elaborations. Thus it has been created an easy to use interface which allows to map, according to a newly developed spatially enabled data model, paths, morphological elements, and multimedia notes. When connected to the internet the application can send the data to a web service which, after applying linear referencing and further elaborating the data, makes them available using open standards. The storytelling system has been designed to provide users with cultural insights embedded in a multimedial and immersive geospatial portal. Whether the tourist is exploring physically or virtually the desired

  18. Free and Open Source Tools (FOSTs): An Empirical Investigation of Pre-Service Teachers' Competencies, Attitudes, and Pedagogical Intentions

    Science.gov (United States)

    Asing-Cashman, Joyce G.; Gurung, Binod; Limbu, Yam B.; Rutledge, David

    2014-01-01

    This study examines the digital native pre-service teachers' (DNPSTs) perceptions of their competency, attitude, and pedagogical intention to use free and open source tools (FOSTs) in their future teaching. Participants were 294 PSTs who responded to pre-course surveys at the beginning of an educational technology course. Using the structural…

  19. Open Source Physics

    CERN Document Server

    Wee, Loo Kang

    2013-01-01

    Open Source Physics (Brown, 2012; Christian, 2010; Esquembre, 2012; Hwang, 2010) empowers teachers and students to create and use these free tools with the associated intellectual property rights given to customise (Wee & Mak, 2009) the computer models/tools to suit their teaching and learning needs. Open Source Physics (OSP) focuses on design of computer models, such as Easy Java Simulations (EJS) and the use of video modeling and analysis (Tracker). They allow students to investigate, explore and analyse data which is either real or simulated. The OSP approach helps users overcome barriers in creating, using and scaling up meaningful ICT use in education. In Singapore, teachers and students have created or customised existing computer models to design and re-purpose EJS models to suit their context and learning needs. Tracker tools allow students to analyse different aspects of a physics phenomena to deepen their understanding of abstract physics concepts. Using Tracker, students record the motion of ob...

  20. Establishing a Web-Based DICOM Teaching File Authoring Tool Using Open-Source Public Software

    OpenAIRE

    Lee, Wen-Jeng; Yang, Chung-Yi; Liu, Kao-Lang; Liu, Hon-Man; Ching, Yu-Tai; Chen, Shyh-Jye

    2005-01-01

    Online teaching files are an important source of educational and referential materials in the radiology community. The commonly used Digital Imaging and Communications in Medicine (DICOM) file format of the radiology community is not natively supported by common Web browsers. The ability of the Web server to convert and parse DICOM is important when the DICOM-converting tools are not available. In this paper, we describe our approach to develop a Web-based teaching file authoring tool. Our se...

  1. Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information

    Directory of Open Access Journals (Sweden)

    Khushi Matloob

    2013-02-01

    Full Text Available Abstract Background Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is hampered by their large file sizes. Results We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large digital slide into a desired quality JPEG image. The image is linked to the patient’s clinical and treatment information in a customised open source cancer data management software (Caisis in use at the Australian Breast Cancer Tissue Bank (ABCTB and then published on the ABCTB website (http://www.abctb.org.au using Deep Zoom open source technology. Using the ABCTB online search engine, digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Conclusions Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of digital microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis. Virtual Slides The virtual slide(s for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5330903258483934

  2. Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information.

    Science.gov (United States)

    Khushi, Matloob; Edwards, Georgina; de Marcos, Diego Alonso; Carpenter, Jane E; Graham, J Dinny; Clarke, Christine L

    2013-02-12

    Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is hampered by their large file sizes. We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large digital slide into a desired quality JPEG image. The image is linked to the patient's clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website (http://www.abctb.org.au) using Deep Zoom open source technology. Using the ABCTB online search engine, digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of digital microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5330903258483934.

  3. 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

  4. Open Source Tools for Numerical Simulation of Urban Greenhouse Gas Emissions

    Science.gov (United States)

    Nottrott, A.; Tan, S. M.; He, Y.

    2016-12-01

    There is a global movement toward urbanization. Approximately 7% of the global population lives in just 28 megacities, occupying less than 0.1% of the total land area used by human activity worldwide. These cities contribute a significant fraction of the global budget of anthropogenic primary pollutants and greenhouse gasses. The 27 largest cities consume 9.9%, 9.3%, 6.7% and 3.0% of global gasoline, electricity, energy and water use, respectively. This impact motivates novel approaches to quantify and mitigate the growing contribution of megacity emissions to global climate change. Cities are characterized by complex topography, inhomogeneous turbulence, and variable pollutant source distributions. These features create a scale separation between local sources and urban scale emissions estimates known as the Grey-Zone. Modern computational fluid dynamics (CFD) techniques provide a quasi-deterministic, physically based toolset to bridge the scale separation gap between source level dynamics, local measurements, and urban scale emissions inventories. CFD has the capability to represent complex building topography and capture detailed 3D turbulence fields in the urban boundary layer. This presentation discusses the application of OpenFOAM to urban CFD simulations of natural gas leaks in cities. OpenFOAM is an open source software for advanced numerical simulation of engineering and environmental fluid flows. When combined with free or low cost computer aided drawing and GIS, OpenFOAM generates a detailed, 3D representation of urban wind fields. OpenFOAM was applied to model methane (CH4) emissions from various components of the natural gas distribution system, to investigate the impact of urban meteorology on mobile CH4 measurements. The numerical experiments demonstrate that CH4 concentration profiles are highly sensitive to the relative location of emission sources and buildings. Sources separated by distances of 5-10 meters showed significant differences in

  5. 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.

  6. Development of Environmental Decision Support System: Unifying Cross-Discipline Data Access Through Open Source Tools

    Science.gov (United States)

    Freeman, S.; Darmenova, K.; Higgins, G. J.; Apling, D.

    2012-12-01

    A common theme when it comes to accessing climate and environmental datasets is that it can be difficult to answer the five basic questions: Who, What, When, Where, and Why. Sometimes even the act of locating a data set or determining how it was generated can prove difficult. It is even more challenging for non-scientific individuals such as planners and policy makers who need to access and include such information in their work. Our Environmental Decision Support System (EDSS) attempts to address this issue by integrating several open source packages to create a simple yet robust web application for conglomerating, searching, viewing, and downloading environmental information for both scientists and decision makers alike. The system is comprised of several open source components, each playing an important role in the EDSS. The Geoportal web application provides an intuitive interface for searching and managing metadata ingested from data sets/data sources. The GeoServer and ncWMS web applications provide overlays and information for visual presentations of the data through web mapping services (WMS) by ingesting ESRI shapefiles, NetCDF, and HDF files. Users of the EDSS can browse the catalog of available products, enter a simple search string, or even constrain searches by temporal and spatial extents. Combined with a custom visualization web application, the EDSS provides a simple yet efficient means for users to not only access and manipulate climate and environmental data, but also trace the data source and the analytical methods used in the final decision aids products.

  7. Free and open source simulation tools for the design of power processing units for photovoltaic systems

    Directory of Open Access Journals (Sweden)

    Sergio Morales-Hernández

    2015-06-01

    Full Text Available Renewable energy sources, including solar photovoltaic, require electronic circuits that serve as interface between the transducer device and the device or system that uses energy. Moreover, the energy efficiency and the cost of the system can be compromised if such electronic circuit is not designed properly. Given that the electrical characteristics of the photovoltaic devices are nonlinear and that the most efficient electronic circuits for power processing are naturally discontinuous, a detailed dynamic analysis to optimize the design is required. This analysis should be supported by computer simulation tools. In this paper a comparison between two software tools for dynamic system simulation is performed to determinate its usefulness in the design process of photovoltaic systems, mainly in what corresponds to the power processing units. Using as a case of study a photovoltaic system for battery charging it was determined that Scicoslab tool was the most suitable.

  8. Open Source and Open Standards

    NARCIS (Netherlands)

    Koper, Rob

    2006-01-01

    Publication reference: Koper, R. (2008). Open Source and Open Standards. In J. M. Spector, M. Merrill, J. van Merriënboer & M. P. Driscol (Eds.), Handbook of Research on Educational Communications and Technology (3rd ed., pp. 355-368). New York: Routledge.

  9. SpectraFox: A free open-source data management and analysis tool for scanning probe microscopy and spectroscopy

    Science.gov (United States)

    Ruby, Michael

    In the last decades scanning probe microscopy and spectroscopy have become well-established tools in nanotechnology and surface science. This opened the market for many commercial manufacturers, each with different hardware and software standards. Besides the advantage of a wide variety of available hardware, the diversity may software-wise complicate the data exchange between scientists, and the data analysis for groups working with hardware developed by different manufacturers. Not only the file format differs between manufacturers, but also the data often requires further numerical treatment before publication. SpectraFox is an open-source and independent tool which manages, processes, and evaluates scanning probe spectroscopy and microscopy data. It aims at simplifying the documentation in parallel to measurement, and it provides solid evaluation tools for a large number of data.

  10. SpectraFox: A free open-source data management and analysis tool for scanning probe microscopy and spectroscopy

    Directory of Open Access Journals (Sweden)

    Michael Ruby

    2016-01-01

    Full Text Available In the last decades scanning probe microscopy and spectroscopy have become well-established tools in nanotechnology and surface science. This opened the market for many commercial manufacturers, each with different hardware and software standards. Besides the advantage of a wide variety of available hardware, the diversity may software-wise complicate the data exchange between scientists, and the data analysis for groups working with hardware developed by different manufacturers. Not only the file format differs between manufacturers, but also the data often requires further numerical treatment before publication. SpectraFox is an open-source and independent tool which manages, processes, and evaluates scanning probe spectroscopy and microscopy data. It aims at simplifying the documentation in parallel to measurement, and it provides solid evaluation tools for a large number of data.

  11. 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

  12. TACIT: An open-source text analysis, crawling, and interpretation tool.

    Science.gov (United States)

    Dehghani, Morteza; Johnson, Kate M; Garten, Justin; Boghrati, Reihane; Hoover, Joe; Balasubramanian, Vijayan; Singh, Anurag; Shankar, Yuvarani; Pulickal, Linda; Rajkumar, Aswin; Parmar, Niki Jitendra

    2016-03-04

    As human activity and interaction increasingly take place online, the digital residues of these activities provide a valuable window into a range of psychological and social processes. A great deal of progress has been made toward utilizing these opportunities; however, the complexity of managing and analyzing the quantities of data currently available has limited both the types of analysis used and the number of researchers able to make use of these data. Although fields such as computer science have developed a range of techniques and methods for handling these difficulties, making use of those tools has often required specialized knowledge and programming experience. The Text Analysis, Crawling, and Interpretation Tool (TACIT) is designed to bridge this gap by providing an intuitive tool and interface for making use of state-of-the-art methods in text analysis and large-scale data management. Furthermore, TACIT is implemented as an open, extensible, plugin-driven architecture, which will allow other researchers to extend and expand these capabilities as new methods become available.

  13. Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information

    Directory of Open Access Journals (Sweden)

    Pedamallu Chandra Sekhar

    2010-08-01

    Full Text Available Abstract Background Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Information about interactions can hint at molecular causes of diseases, and can provide clues for new therapeutic approaches. Several (usually expensive and time consuming experimental methods can probe protein - protein interactions. Data sets, derived from such experiments make the development of prediction methods feasible, and make the creation of protein-protein interaction network predicting tools possible. Methods Here we report the development of a simple open source program module (OpenPPI_predictor that can generate a putative protein-protein interaction network for target genomes. This tool uses the orthologous interactome network data from a related, experimentally studied organism. Results Results from our predictions can be visualized using the Cytoscape visualization software, and can be piped to downstream processing algorithms. We have employed our program to predict protein-protein interaction network for the human parasite roundworm Brugia malayi, using interactome data from the free living nematode Caenorhabditis elegans. Availability The OpenPPI_predictor source code is available from http://tools.neb.com/~posfai/.

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

    Science.gov (United States)

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

    2015-08-01

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

  15. Superplot3d: an open source GUI tool for 3d trajectory visualisation and elementary processing.

    Science.gov (United States)

    Whitehorn, Luke J; Hawkes, Frances M; Dublon, Ian An

    2013-09-30

    When acquiring simple three-dimensional (3d) trajectory data it is common to accumulate large coordinate data sets. In order to examine integrity and consistency of object tracking, it is often necessary to rapidly visualise these data. Ordinarily, to achieve this the user must either execute 3d plotting functions in a numerical computing environment or manually inspect data in two dimensions, plotting each individual axis.Superplot3d is an open source MATLAB script which takes tab delineated Cartesian data points in the form x, y, z and time and generates an instant visualization of the object's trajectory in free-rotational three dimensions. Whole trajectories may be instantly presented, allowing for rapid inspection. Executable from the MATLAB command line (or deployable as a compiled standalone application) superplot3d also provides simple GUI controls to obtain rudimentary trajectory information, allow specific visualization of trajectory sections and perform elementary processing.Superplot3d thus provides a framework for non-programmers and programmers alike, to recreate recently acquired 3d object trajectories in rotatable 3d space. It is intended, via the use of a preference driven menu to be flexible and work with output from multiple tracking software systems. Source code and accompanying GUIDE .fig files are provided for deployment and further development.

  16. 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.

  17. System Solver: an open source tool for mathematically modelling dynamical systems

    Directory of Open Access Journals (Sweden)

    Efraín Domínguez

    2010-10-01

    Full Text Available The following paper presents a freeware modelling tool simulating dynamic systems that can be represented by either an ordinary differential equation (ODE or a set of differential equations of different orders. The main idea leading to this software development is related to the fact that many physiccal, biological, ecological, economical, chemical, social and engineering problems can be expressed in this way. Furthermore, the solution to these problems requires some expertise in numerical methods and programming. Such knowledge is uncommon in some of the experts in such scientific domains. A tool to fill in this knowledge gap, increase productivity within modelling-related research and support the teaching of mathematical modelling topics is thus needed. This paper introduces System Solver, a computer application that facilitates the formulation of initial value problems for ODE systems, numerically solves these problems and provides a user with not only the solution but also debugged Visual Basic source code for the application. The obtained code can be easily shared among researchers, which facilitates the replication of numerical experiments even across different operating systems. This software’s introduction is accompanied by examples from different domains, including one example from stochastic modelling.

  18. A Free and Open Source Web-based Data Catalog Evaluation Tool

    Science.gov (United States)

    O'Brien, K.; Schweitzer, R.; Burger, E. F.

    2015-12-01

    For many years, the Unified Access Framework (UAF) project has worked to provide improved access to scientific data by leveraging widely used data standards and conventions. These standards include the Climate and Forecast (CF) metadata conventions, the Data Access Protocol (DAP) and various Open Geospatial Consortium (OGC) standards such as WMS and WCS. The UAF has also worked to create a unified access point for scientific data access through THREDDS and ERDDAP catalogs. A significant effort was made by the UAF project to build a catalog-crawling tool that was designed to crawl remote catalogs, analyze their content and then build a clean catalog that 1) represented only CF compliant data; 2) provided a uniform set of access services and 3) where possible, aggregated data in time. That catalog is available at http://ferret.pmel.noaa.gov/geoide/geoIDECleanCatalog.html.Although this tool has proved immensely valuable in allowing the UAF project to create a high quality data catalog, the need for a catalog evaluation service or tool to operate on a more local level also exists. Many programs that generate data of interest to the public are recognizing the utility and power of using the THREDDS data server (TDS) to serve that data. However, for some groups that lack the resources to maintain dedicated IT personnel, it can be difficult to set up a properly configured TDS. The TDS catalog evaluating service that is under development and will be discussed in this presentation is an effort, through the UAF project, to bridge that gap. Based upon the power of the original UAF catalog cleaner, the web evaluator will have the ability to scan and crawl a local TDS catalog, evaluate the contents for compliance with CF standards, analyze the services offered, and identify datasets where possible temporal aggregation would benefit data access. The results of the catalog evaluator will guide the configuration of the dataset in TDS to ensure that it meets the standards as

  19. 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

  20. Baseliner: An open-source, interactive tool for processing sap flux data from thermal dissipation probes

    Science.gov (United States)

    Oishi, A. Christopher; Hawthorne, David A.; Oren, Ram

    Estimating transpiration from woody plants using thermal dissipation sap flux sensors requires careful data processing. Currently, researchers accomplish this using spreadsheets, or by personally writing scripts for statistical software programs (e.g., R, SAS). We developed the Baseliner software to help establish a standardized protocol for processing sap flux data. Baseliner enables users to QA/QC data and process data using a combination of automated steps, visualization, and manual editing. Data processing requires establishing a zero-flow reference value, or "baseline", which varies among sensors and with time. Since no set of algorithms currently exists to reliably QA/QC and estimate the zero-flow baseline, Baseliner provides a graphical user interface to allow visual inspection and manipulation of data. Data are first automatically processed using a set of user defined parameters. The user can then view the data for additional, manual QA/QC and baseline identification using mouse and keyboard commands. The open-source software allows for user customization of data processing algorithms as improved methods are developed.

  1. Open-source tools for dynamical analysis of Liley's mean-field cortex model

    CERN Document Server

    Green, Kevin R

    2012-01-01

    Mean-field models of the mammalian cortex treat this part of the brain as a two-dimensional excitable medium. The electrical potentials, generated by the excitatory and inhibitory neuron populations, are described by nonlinear, coupled, partial differential equations, that are known to generate complicated spatio-temporal behaviour. We focus on the model by Liley {\\sl et al.} (Network: Comput. Neural Syst. (2002) 13, 67-113). Several reductions of this model have been studied in detail, but a direct analysis of its spatio-temporal dynamics has, to the best of our knowledge, never been attempted before. Here, we describe the implementation of implicit time-stepping of the model and the tangent linear model, and solving for equilibria and time-periodic solutions, using the open-source library PETSc. By using domain decomposition for parallelization, and iterative solving of linear problems, the code is capable of parsing some dynamics of a macroscopic slice of cortical tissue with a sub-millimetre resolution.

  2. Helioviewer.org: An Open-source Tool for Visualizing Solar Data

    Science.gov (United States)

    Hughitt, V. Keith; Ireland, J.; Schmiedel, P.; Dimitoglou, G.; Mueller, D.; Fleck, B.

    2009-05-01

    As the amount of solar data available to scientists continues to increase at faster and faster rates, it is important that there exist simple tools for navigating this data quickly with a minimal amount of effort. By combining heterogeneous solar physics datatypes such as full-disk images and coronagraphs, along with feature and event information, Helioviewer offers a simple and intuitive way to browse multiple datasets simultaneously. Images are stored in a repository using the JPEG 2000 format and tiled dynamically upon a client's request. By tiling images and serving only the portions of the image requested, it is possible for the client to work with very large images without having to fetch all of the data at once. Currently, Helioviewer enables users to browse the entire SOHO data archive, updated hourly, as well as data feature/event catalog data from eight different catalogs including active region, flare, coronal mass ejection, type II radio burst data. In addition to a focus on intercommunication with other virtual observatories and browsers (VSO, HEK, etc), Helioviewer will offer a number of externally-available application programming interfaces (APIs) to enable easy third party use, adoption and extension. Future functionality will include: support for additional data-sources including TRACE, SDO and STEREO, dynamic movie generation, a navigable timeline of recorded solar events, social annotation, and basic client-side image processing.

  3. Pentaho and Jaspersoft: A Comparative Study of Business Intelligence Open Source Tools Processing Big Data to Evaluate Performances

    Directory of Open Access Journals (Sweden)

    Victor M. Parra

    2016-10-01

    Full Text Available Regardless of the recent growth in the use of “Big Data” and “Business Intelligence” (BI tools, little research has been undertaken about the implications involved. Analytical tools affect the development and sustainability of a company, as evaluating clientele needs to advance in the competitive market is critical. With the advancement of the population, processing large amounts of data has become too cumbersome for companies. At some stage in a company’s lifecycle, all companies need to create new and better data processing systems that improve their decision-making processes. Companies use BI Results to collect data that is drawn from interpretations grouped from cues in the data set BI information system that helps organisations with activities that give them the advantage in a competitive market. However, many organizations establish such systems, without conducting a preliminary analysis of the needs and wants of a company, or without determining the benefits and targets that they aim to achieve with the implementation. They rarely measure the large costs associated with the implementation blowout of such applications, which results in these impulsive solutions that are unfinished or too complex and unfeasible, in other words unsustainable even if implemented. BI open source tools are specific tools that solve this issue for organizations in need, with data storage and management. This paper compares two of the best positioned BI open source tools in the market: Pentaho and Jaspersoft, processing big data through six different sized databases, especially focussing on their Extract Transform and Load (ETL and Reporting processes by measuring their performances using Computer Algebra Systems (CAS. The ETL experimental analysis results clearly show that Jaspersoft BI has an increment of CPU time in the process of data over Pentaho BI, which is represented by an average of 42.28% in performance metrics over the six databases

  4. Making Water Chemistry Data From Volcano-Hydrothermal Systems Accessible Using Open Source Tools

    Science.gov (United States)

    Venezky, D. Y.; Mariner, R. H.; Hurwitz, S.; Evans, W. C.

    2004-12-01

    Chemical and isotopic data collected over several decades by the U.S. Geological Survey from volcano-hydrothermal systems were recently organized into a web-accessible database for public use. The data were collected by members of the Barnes and/or Mariner projects and were supplemented with data from samples submitted for analysis by other researchers with similar interests. The data are primarily chemical and isotopic analyses of waters (thermal, mineral, or fresh) and associated gas (free and/or dissolved) collected from hot springs, mineral springs, cold springs, geothermal wells, fumaroles, and gas seeps. Additional data for a few streams, lakes, and oil wells are included. The web site follows a multi-stage design, first allowing for basic access to the MySQL database, then a user-friendly GIS (Geographic Information System) interface, and finally access to additional documentation and searching features. The initial web pages allow the user to choose the type of data (site, physical parameters, major and minor dissolved constituents, dissolved and free gas composition, water isotopes, and other isotopes) and the sample location. The data are then shown in a table that can be downloaded in several formats. The second stage of the project added an open-source GIS package called WorldKit, which gives easy-to-code and easy-to-use clickable icons on a base map using XML (Extensible Markup Language). WorldKit is also adding a zoom interface (zoomify) that uses new technology to reduce the display time. The final stage of the project involves more complex queries, alternative data presentation, and integrated background information. The more complex queries allow users to select multiple types of data from multiple sites. The data can be found at http://hotspringchem.wr.usgs.gov/.

  5. Deriving phenological metrics from NDVI through an open source tool developed in QGIS

    Science.gov (United States)

    Duarte, Lia; Teodoro, A. C.; Gonçalves, Hernãni

    2014-10-01

    Vegetation indices have been commonly used over the past 30 years for studying vegetation characteristics using images collected by remote sensing satellites. One of the most commonly used is the Normalized Difference Vegetation Index (NDVI). The various stages that green vegetation undergoes during a complete growing season can be summarized through time-series analysis of NDVI data. The analysis of such time-series allow for extracting key phenological variables or metrics of a particular season. These characteristics may not necessarily correspond directly to conventional, ground-based phenological events, but do provide indications of ecosystem dynamics. A complete list of the phenological metrics that can be extracted from smoothed, time-series NDVI data is available in the USGS online resources (http://phenology.cr.usgs.gov/methods_deriving.php).This work aims to develop an open source application to automatically extract these phenological metrics from a set of satellite input data. The main advantage of QGIS for this specific application relies on the easiness and quickness in developing new plug-ins, using Python language, based on the experience of the research group in other related works. QGIS has its own application programming interface (API) with functionalities and programs to develop new features. The toolbar developed for this application was implemented using the plug-in NDVIToolbar.py. The user introduces the raster files as input and obtains a plot and a report with the metrics. The report includes the following eight metrics: SOST (Start Of Season - Time) corresponding to the day of the year identified as having a consistent upward trend in the NDVI time series; SOSN (Start Of Season - NDVI) corresponding to the NDVI value associated with SOST; EOST (End of Season - Time) which corresponds to the day of year identified at the end of a consistent downward trend in the NDVI time series; EOSN (End of Season - NDVI) corresponding to the NDVI value

  6. Open-source tool for automatic import of coded surveying data to multiple vector layers in GIS environment

    Directory of Open Access Journals (Sweden)

    Eva Stopková

    2016-12-01

    Full Text Available This paper deals with a tool that enables import of the coded data in a singletext file to more than one vector layers (including attribute tables, together withautomatic drawing of line and polygon objects and with optional conversion toCAD. Python script v.in.survey is available as an add-on for open-source softwareGRASS GIS (GRASS Development Team. The paper describes a case study basedon surveying at the archaeological mission at Tell-el Retaba (Egypt. Advantagesof the tool (e.g. significant optimization of surveying work and its limits (demandson keeping conventions for the points’ names coding are discussed here as well.Possibilities of future development are suggested (e.g. generalization of points’names coding or more complex attribute table creation.

  7. CoCoTools: open-source software for building connectomes using the CoCoMac anatomical database.

    Science.gov (United States)

    Blumenfeld, Robert S; Bliss, Daniel P; Perez, Fernando; D'Esposito, Mark

    2014-04-01

    Neuroanatomical tracer studies in the nonhuman primate macaque monkey are a valuable resource for cognitive neuroscience research. These data ground theories of cognitive function in anatomy, and with the emergence of graph theoretical analyses in neuroscience, there is high demand for these data to be consolidated into large-scale connection matrices ("macroconnectomes"). Because manual review of the anatomical literature is time consuming and error prone, computational solutions are needed to accomplish this task. Here we describe the "CoCoTools" open-source Python library, which automates collection and integration of macaque connectivity data for visualization and graph theory analysis. CoCoTools both interfaces with the CoCoMac database, which houses a vast amount of annotated tracer results from 100 years (1905-2005) of neuroanatomical research, and implements coordinate-free registration algorithms, which allow studies that use different parcellations of the brain to be translated into a single graph. We show that using CoCoTools to translate all of the data stored in CoCoMac produces graphs with properties consistent with what is known about global brain organization. Moreover, in addition to describing CoCoTools' processing pipeline, we provide worked examples, tutorials, links to on-line documentation, and detailed appendices to aid scientists interested in using CoCoTools to gather and analyze CoCoMac data.

  8. Penetration Tester's Open Source Toolkit

    CERN Document Server

    Faircloth, Jeremy

    2011-01-01

    Great commercial penetration testing tools can be very expensive and sometimes hard to use or of questionable accuracy. This book helps solve both of these problems. The open source, no-cost penetration testing tools presented do a great job and can be modified by the user for each situation. Many tools, even ones that cost thousands of dollars, do not come with any type of instruction on how and in which situations the penetration tester can best use them. Penetration Tester's Open Source Toolkit, Third Edition, expands upon existing instructions so that a professional can get the most accura

  9. NEV2lkit: a new open source tool for handling neuronal event files from multi-electrode recordings.

    Science.gov (United States)

    Bongard, Markus; Micol, Daniel; Fernández, Eduardo

    2014-06-01

    The analysis and discrimination of action potentials, or "spikes", is a central issue to systems neuroscience research. Here we introduce a free open source software for the analysis and discrimination of neural spikes based on principal component analysis and different clustering algorithms. The main objective is to supply a friendly user interface that links the experimental data to a basic set of routines for analysis, visualization and classification of spikes in a consistent framework. The tool has been tested on artificial data sets, on multi-electrode extracellular recordings from ganglion cell populations in isolated superfused mouse, rabbit and turtle retinas, and on electrophysiological recordings from mouse visual cortex. Our results show that NEV2lkit is very reliable and able to satisfy the experimental demands in terms of accuracy, efficiency and consistency across experiments. It performs fast unit sorting in single or multiple experiments and allows the extraction of spikes from over large time intervals in continuously recorded data streams. The tool is implemented in C++ and runs cross-platform on Linux, OS X and Windows systems. To facilitate the adaptation and extension as well as the addition of new routines, tools and algorithms for data analysis, the source code, binary distributions for different operating systems and documentation are all freely available at http://nev2lkit.sourceforge.net .

  10. 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.

  11. Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose-volume outcome relationships

    Energy Technology Data Exchange (ETDEWEB)

    Naqa, I El [Washington University, Saint Louis, MO (United States); Suneja, G [Brown Medical School, Providence, RI (United States); Lindsay, P E [Washington University, St. Louis, MO (United States); Hope, A J [Washington University, Saint Louis, MO (United States); Alaly, J R [Washington University, Saint Louis, MO (United States); Vicic, M [Washington University, Saint Louis, MO (United States); Bradley, J D [Washington University, Saint Louis, MO (United States); Apte, A [Washington University, Saint Louis, MO (United States); Deasy, J O [Washington University, Saint Louis, MO (United States)

    2006-11-21

    Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

  12. Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose volume outcome relationships

    Science.gov (United States)

    El Naqa, I.; Suneja, G.; Lindsay, P. E.; Hope, A. J.; Alaly, J. R.; Vicic, M.; Bradley, J. D.; Apte, A.; Deasy, J. O.

    2006-11-01

    Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

  13. STUDENT OPINION TOWARDS USING AN OPEN SOURCE LEARNING MANAGEMENT SYSTEM TOGETHER WITH A COLLABORATIVE TOOL

    Directory of Open Access Journals (Sweden)

    Nadire Cavus

    2008-12-01

    Full Text Available This paper is about a pilot study which has been carried out at the Near East University during the 2004/5 FallSemester using the Moodle LMS together with GREWPtool collaborative editor. The system has been tested with 36students taking the Java and the Pascal programming courses. The results of the pilot study showed that a LearningManagement System can be made more efficient if it is enhanced by a collaborative learning tool. Our results have alsoshown that programming languages such as Pascal and Java can be thought successfully in a web-based environment usingan LMS system together with a collaborative tool

  14. Creating Open Source Conversation

    Science.gov (United States)

    Sheehan, Kate

    2009-01-01

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

  15. 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...

  16. Creating Open Source Conversation

    Science.gov (United States)

    Sheehan, Kate

    2009-01-01

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

  17. Environmental and Landscape Remote Sensing Using Free and Open Source Image Processing Tools

    Science.gov (United States)

    As global climate change and human activities impact the environment, there is a growing need for scientific tools to monitor and measure environmental conditions that support human and ecological health. Remotely sensed imagery from satellite and airborne platforms provides a g...

  18. Testing an Open Source installation and server provisioning tool for the INFN CNAF Tierl Storage system

    Science.gov (United States)

    Pezzi, M.; Favaro, M.; Gregori, D.; Ricci, P. P.; Sapunenko, V.

    2014-06-01

    In large computing centers, such as the INFN CNAF Tier1 [1], is essential to be able to configure all the machines, depending on use, in an automated way. For several years at the Tier1 has been used Quattor[2], a server provisioning tool, which is currently used in production. Nevertheless we have recently started a comparison study involving other tools able to provide specific server installation and configuration features and also offer a proper full customizable solution as an alternative to Quattor. Our choice at the moment fell on integration between two tools: Cobbler [3] for the installation phase and Puppet [4] for the server provisioning and management operation. The tool should provide the following properties in order to replicate and gradually improve the current system features: implement a system check for storage specific constraints such as kernel modules black list at boot time to avoid undesired SAN (Storage Area Network) access during disk partitioning; a simple and effective mechanism for kernel upgrade and downgrade; the ability of setting package provider using yum, rpm or apt; easy to use Virtual Machine installation support including bonding and specific Ethernet configuration; scalability for managing thousands of nodes and parallel installations. This paper describes the results of the comparison and the tests carried out to verify the requirements and the new system suitability in the INFN-T1 environment.

  19. ThManager: An Open Source Tool for Creating and Visualizing SKOS

    Directory of Open Access Journals (Sweden)

    Javier Lacasta

    2007-09-01

    Full Text Available Knowledge organization systems denotes formally represented knowledge that is used within the context of digital libraries to improve data sharing and information retrieval. To increase their use, and to reuse them when possible, it is vital to manage them adequately and to provide them in a standard interchange format. Simple knowledge organization systems (SKOS seem to be the most promising representation for the type of knowledge models used in digital libraries, but there is a lack of tools that are able to properly manage it. This work presents a tool that fills this gap, facilitating their use in different environments and using SKOS as an interchange format.

  20. 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.

  1. Qualitative: Open Source Python Tool for Quality Estimation over Multiple Machine Translation Outputs

    Directory of Open Access Journals (Sweden)

    Eleftherios Avramidis

    2014-09-01

    Full Text Available “Qualitative” is a python toolkit for ranking and selection of sentence-level output by different MT systems using Quality Estimation. The toolkit implements a basic pipeline for annotating the given sentences with black-box features. Consequently, it applies a machine learning mechanism in order to rank data based on models pre-trained on human preferences. The preprocessing pipeline includes support for language models, PCFG parsing, language checking tools and various other pre-processors and feature generators. The code follows the principles of object-oriented programming to allow modularity and extensibility. The tool can operate by processing both batch-files and single sentences. An XML-RPC interface is provided for hooking up with web-services and a graphical animated web-based interface demonstrates its potential on-line use.

  2. A HTML5 open source tool to conduct studies based on Libet's clock paradigm.

    Science.gov (United States)

    Garaizar, Pablo; Cubillas, Carmelo P; Matute, Helena

    2016-09-13

    Libet's clock is a well-known procedure in experiments in psychology and neuroscience. Examples of its use include experiments exploring the subjective sense of agency, action-effect binding, and subjective timing of conscious decisions and perceptions. However, the technical details of the apparatus used to conduct these types of experiments are complex, and are rarely explained in sufficient detail as to guarantee an exact replication of the procedure. With this in mind, we developed Labclock Web, a web tool designed to conduct online and offline experiments using Libet's clock. After describing its technical features, we explain how to configure specific experiments using this tool. Its degree of accuracy and precision in the presentation of stimuli has been technically validated, including the use of two cognitive experiments conducted with voluntary participants who performed the experiment both in our laboratory and via the Internet. Labclock Web is distributed without charge under a free software license (GPLv3) since one of our main objectives is to facilitate the replication of experiments and hence the advancement of knowledge in this area.

  3. A HTML5 open source tool to conduct studies based on Libet’s clock paradigm

    Science.gov (United States)

    Garaizar, Pablo; Cubillas, Carmelo P.; Matute, Helena

    2016-01-01

    Libet’s clock is a well-known procedure in experiments in psychology and neuroscience. Examples of its use include experiments exploring the subjective sense of agency, action-effect binding, and subjective timing of conscious decisions and perceptions. However, the technical details of the apparatus used to conduct these types of experiments are complex, and are rarely explained in sufficient detail as to guarantee an exact replication of the procedure. With this in mind, we developed Labclock Web, a web tool designed to conduct online and offline experiments using Libet’s clock. After describing its technical features, we explain how to configure specific experiments using this tool. Its degree of accuracy and precision in the presentation of stimuli has been technically validated, including the use of two cognitive experiments conducted with voluntary participants who performed the experiment both in our laboratory and via the Internet. Labclock Web is distributed without charge under a free software license (GPLv3) since one of our main objectives is to facilitate the replication of experiments and hence the advancement of knowledge in this area. PMID:27623167

  4. Investigation and Evaluation of the open source ETL tools GeoKettle and Talend Open Studio in terms of their ability to process spatial data

    Science.gov (United States)

    Kuhnert, Kristin; Quedenau, Jörn

    2016-04-01

    Integration and harmonization of large spatial data sets is not only since the introduction of the spatial data infrastructure INSPIRE a big issue. The process of extracting and combining spatial data from heterogeneous source formats, transforming that data to obtain the required quality for particular purposes and loading it into a data store, are common tasks. The procedure of Extraction, Transformation and Loading of data is called ETL process. Geographic Information Systems (GIS) can take over many of these tasks but often they are not suitable for processing large datasets. ETL tools can make the implementation and execution of ETL processes convenient and efficient. One reason for choosing ETL tools for data integration is that they ease maintenance because of a clear (graphical) presentation of the transformation steps. Developers and administrators are provided with tools for identification of errors, analyzing processing performance and managing the execution of ETL processes. Another benefit of ETL tools is that for most tasks no or only little scripting skills are required so that also researchers without programming background can easily work with it. Investigations on ETL tools for business approaches are available for a long time. However, little work has been published on the capabilities of those tools to handle spatial data. In this work, we review and compare the open source ETL tools GeoKettle and Talend Open Studio in terms of processing spatial data sets of different formats. For evaluation, ETL processes are performed with both software packages based on air quality data measured during the BÄRLIN2014 Campaign initiated by the Institute for Advanced Sustainability Studies (IASS). The aim of the BÄRLIN2014 Campaign is to better understand the sources and distribution of particulate matter in Berlin. The air quality data are available in heterogeneous formats because they were measured with different instruments. For further data analysis

  5. Moose: An Open-Source Framework to Enable Rapid Development of Collaborative, Multi-Scale, Multi-Physics Simulation Tools

    Science.gov (United States)

    Slaughter, A. E.; Permann, C.; Peterson, J. W.; Gaston, D.; Andrs, D.; Miller, J.

    2014-12-01

    The Idaho National Laboratory (INL)-developed Multiphysics Object Oriented Simulation Environment (MOOSE; www.mooseframework.org), is an open-source, parallel computational framework for enabling the solution of complex, fully implicit multiphysics systems. MOOSE provides a set of computational tools that scientists and engineers can use to create sophisticated multiphysics simulations. Applications built using MOOSE have computed solutions for chemical reaction and transport equations, computational fluid dynamics, solid mechanics, heat conduction, mesoscale materials modeling, geomechanics, and others. To facilitate the coupling of diverse and highly-coupled physical systems, MOOSE employs the Jacobian-free Newton-Krylov (JFNK) method when solving the coupled nonlinear systems of equations arising in multiphysics applications. The MOOSE framework is written in C++, and leverages other high-quality, open-source scientific software packages such as LibMesh, Hypre, and PETSc. MOOSE uses a "hybrid parallel" model which combines both shared memory (thread-based) and distributed memory (MPI-based) parallelism to ensure efficient resource utilization on a wide range of computational hardware. MOOSE-based applications are inherently modular, which allows for simulation expansion (via coupling of additional physics modules) and the creation of multi-scale simulations. Any application developed with MOOSE supports running (in parallel) any other MOOSE-based application. Each application can be developed independently, yet easily communicate with other applications (e.g., conductivity in a slope-scale model could be a constant input, or a complete phase-field micro-structure simulation) without additional code being written. This method of development has proven effective at INL and expedites the development of sophisticated, sustainable, and collaborative simulation tools.

  6. Open Health Tools: Tooling for Interoperable Healthcare

    Directory of Open Access Journals (Sweden)

    Skip McGaughey

    2008-11-01

    Full Text Available The Open Health Tools initiative is creating an ecosystem focused on the production of software tooling that promotes the exchange of medical information across political, geographic, cultural, product, and technology lines. At its core, OHT believes that the availability of high-quality tooling that interoperates will propel the industry forward, enabling organizations and vendors to build products and systems that effectively work together. This will ?raise the interoperability bar? as a result of having tools that just work. To achieve these lofty goals, careful consideration must be made to the constituencies that will be most affected by an OHT-influenced world. This document outlines a vision of OHT?s impact to these stakeholders. It does not explain the OHT process itself or how the OHT community operates. Instead, we place emphasis on the impact of that process within the health industry. The catchphrase ?code is king? underpins this document, meaning that the manifestation of any open source community lies in the products and technology it produces.

  7. CrossCheck: an open-source web tool for high-throughput screen data analysis.

    Science.gov (United States)

    Najafov, Jamil; Najafov, Ayaz

    2017-07-19

    Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis. CrossCheck is a centralized database that allows effortless comparison of the user-entered list of gene symbols with 16,231 published datasets. These datasets include published data from genome-wide RNAi and CRISPR screens, interactome proteomics and phosphoproteomics screens, cancer mutation databases, low-throughput studies of major cell signaling mediators, such as kinases, E3 ubiquitin ligases and phosphatases, and gene ontological information. Moreover, CrossCheck includes a novel database of predicted protein kinase substrates, which was developed using proteome-wide consensus motif searches. CrossCheck dramatically simplifies high-throughput screen data analysis and enables researchers to dig deep into the published literature and streamline data-driven hypothesis generation. CrossCheck is freely accessible as a web-based application at http://proteinguru.com/crosscheck.

  8. The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data

    Directory of Open Access Journals (Sweden)

    Hyunseok P Kang

    2010-01-01

    Full Text Available Background: Tissue microarrays (TMAs are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF provides a flexible method to represent knowledge in triples, which take the form Subject- Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs, which are global in scope. We present an OWL (Web Ontology Language schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration. Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format. Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES to OWL. Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.

  9. 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.

  10. Steering Landsat-oriented, open-source risk-mapping tools towards Copernicus: tuning parameters on Sentinel-2 data

    Science.gov (United States)

    De Vecchi, Daniele; Dell'Acqua, Fabio

    2016-04-01

    consortium guarantees support and improvements to the proposed set of tools. Keywords: Vulnerability monitoring, exposure monitoring, remote sensing, optical imagery, Copernicus, Sentinel-2, open-source software tools

  11. The Wildland Fire Emissions Information System: Providing information for carbon cycle studies with open source geospatial tools

    Science.gov (United States)

    French, N. H.; Erickson, T.; McKenzie, D.

    2008-12-01

    A major goal of the North American Carbon Program is to resolve uncertainties in understanding and managing the carbon cycle of North America. As carbon modeling tools become more comprehensive and spatially oriented, accurate datasets to spatially quantify carbon emissions from fire are needed, and these data resources need to be accessible to users for decision-making. Under a new NASA Carbon Cycle Science project, Drs. Nancy French and Tyler Erickson, of the Michigan Technological University, Michigan Tech Research Institute (MTRI), are teaming with specialists with the USDA Forest Service Fire and Environmental Research Applications (FERA) team to provide information for mapping fire-derived carbon emissions to users. The project focus includes development of a web-based system to provide spatially resolved fire emissions estimates for North America in a user-friendly environment. The web-based Decision Support System will be based on a variety of open source technologies. The Fuel Characteristic Classification System (FCCS) raster map of fuels and MODIS-derived burned area vector maps will be processed using the Geographic Data Abstraction Library (GDAL) and OGR Simple Features Library. Tabular and spatial project data will be stored in a PostgreSQL/PostGIS, a spatially enabled relational database server. The browser-based user interface will be created using the Django web page framework to allow user input for the decision support system. The OpenLayers mapping framework will be used to provide users with interactive maps within the browser. In addition, the data products will be made available in standard open data formats such as KML, to allow for easy integration into other spatial models and data systems.

  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. SELENA - An open-source tool for seismic risk and loss assessment using a logic tree computation procedure

    Science.gov (United States)

    Molina, S.; Lang, D. H.; Lindholm, C. D.

    2010-03-01

    The era of earthquake risk and loss estimation basically began with the seminal paper on hazard by Allin Cornell in 1968. Following the 1971 San Fernando earthquake, the first studies placed strong emphasis on the prediction of human losses (number of casualties and injured used to estimate the needs in terms of health care and shelters in the immediate aftermath of a strong event). In contrast to these early risk modeling efforts, later studies have focused on the disruption of the serviceability of roads, telecommunications and other important lifeline systems. In the 1990s, the National Institute of Building Sciences (NIBS) developed a tool (HAZUS ®99) for the Federal Emergency Management Agency (FEMA), where the goal was to incorporate the best quantitative methodology in earthquake loss estimates. Herein, the current version of the open-source risk and loss estimation software SELENA v4.1 is presented. While using the spectral displacement-based approach (capacity spectrum method), this fully self-contained tool analytically computes the degree of damage on specific building typologies as well as the associated economic losses and number of casualties. The earthquake ground shaking estimates for SELENA v4.1 can be calculated or provided in three different ways: deterministic, probabilistic or based on near-real-time data. The main distinguishing feature of SELENA compared to other risk estimation software tools is that it is implemented in a 'logic tree' computation scheme which accounts for uncertainties of any input (e.g., scenario earthquake parameters, ground-motion prediction equations, soil models) or inventory data (e.g., building typology, capacity curves and fragility functions). The data used in the analysis is assigned with a decimal weighting factor defining the weight of the respective branch of the logic tree. The weighting of the input parameters accounts for the epistemic and aleatoric uncertainties that will always follow the necessary

  14. Open Source Telecommunication Companies

    Directory of Open Access Journals (Sweden)

    Peter Liu

    2007-08-01

    Full Text Available Little is known about companies whose core business is selling telecommunications products that lever open source projects. Open source telecommunications (OST companies operate in markets that are very different from typical software product markets. The telecommunications market is regulated, vertically integrated, and proprietary designs and special chips are widely used. For a telecommunications product to be useful, it must interact with both access network products and core network products. Due to specifications in Service Agreements Levels, penalties for failures of telecommunications products are very high. This article shares information that is not widely known, including a list of OST companies and the open source projects on which they depend, the size and diversity of venture capital investment in OST companies, the nature of the commercial product-open source software and company-project relationships, ways in which OST companies make money, benefits and risks of OST companies, and competition between OST companies. Analysis of this information provides insights into the ways in which companies can build business models around open source software. These findings will be of interest to entrepreneurs, top management teams of incumbent companies that sell telecommunications products, and those who care about Ontario's ability to compete globally.

  15. Open source systems security certification

    CERN Document Server

    Damiani, Ernesto; El Ioini, Nabil

    2009-01-01

    Open Source Advances in Computer Applications book series provides timely technological and business information for: Enabling Open Source Systems (OSS) to become an integral part of systems and devices produced by technology companies; Inserting OSS in the critical path of complex network development and embedded products, including methodologies and tools for domain-specific OSS testing (lab code available), plus certification of security, dependability and safety properties for complex systems; Ensuring integrated systems, including OSS, meet performance and security requirements as well as achieving the necessary certifications, according to the overall strategy of OSS usage on the part of the adopter

  16. Open source GIS based tools to improve hydrochemical water resources management in EU H2020 FREEWAT platform

    Science.gov (United States)

    Criollo, Rotman; Velasco, Violeta; Vázquez-Suñé, Enric; Nardi, Albert; Marazuela, Miguel A.; Rossetto, Rudy; Borsi, Iacopo; Foglia, Laura; Cannata, Massimiliano; De Filippis, Giovanna

    2017-04-01

    Due to the general increase of water scarcity (Steduto et al., 2012), water quantity and quality must be well known to ensure a proper access to water resources in compliance with local and regional directives. This circumstance can be supported by tools which facilitate process of data management and its analysis. Such analyses have to provide research/professionals, policy makers and users with the ability to improve the management of the water resources with standard regulatory guidelines. Compliance with the established standard regulatory guidelines (with a special focus on requirement deriving from the GWD) should have an effective monitoring, evaluation, and interpretation of a large number of physical and chemical parameters. These amounts of datasets have to be assessed and interpreted: (i) integrating data from different sources and gathered with different data access techniques and formats; (ii) managing data with varying temporal and spatial extent; (iii) integrating groundwater quality information with other relevant information such as further hydrogeological data (Velasco et al., 2014) and pre-processing these data generally for the realization of groundwater models. In this context, the Hydrochemical Analysis Tools, akvaGIS Tools, has been implemented within the H2020 FREEWAT project; which aims to manage water resources by modelling water resource management in an open source GIS platform (QGIS desktop). The main goal of AkvaGIS Tools is to improve water quality analysis through different capabilities to improve the case study conceptual model managing all data related into its geospatial database (implemented in Spatialite) and a set of tools for improving the harmonization, integration, standardization, visualization and interpretation of the hydrochemical data. To achieve that, different commands cover a wide range of methodologies for querying, interpreting, and comparing groundwater quality data and facilitate the pre-processing analysis for

  17. Development of a web GIS application for emissions inventory spatial allocation based on open source software tools

    Science.gov (United States)

    Gkatzoflias, Dimitrios; Mellios, Giorgos; Samaras, Zissis

    2013-03-01

    Combining emission inventory methods and geographic information systems (GIS) remains a key issue for environmental modelling and management purposes. This paper examines the development of a web GIS application as part of an emission inventory system that produces maps and files with spatial allocated emissions in a grid format. The study is not confined in the maps produced but also presents the features and capabilities of a web application that can be used by every user even without any prior knowledge of the GIS field. The development of the application was based on open source software tools such as MapServer for the GIS functions, PostgreSQL and PostGIS for the data management and HTML, PHP and JavaScript as programming languages. In addition, background processes are used in an innovative manner to handle the time consuming and computational costly procedures of the application. Furthermore, a web map service was created to provide maps to other clients such as the Google Maps API v3 that is used as part of the user interface. The output of the application includes maps in vector and raster format, maps with temporal resolution on daily and hourly basis, grid files that can be used by air quality management systems and grid files consistent with the European Monitoring and Evaluation Programme Grid. Although the system was developed and validated for the Republic of Cyprus covering a remarkable wide range of pollutant and emissions sources, it can be easily customized for use in other countries or smaller areas, as long as geospatial and activity data are available.

  18. 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...

  19. Open source development

    DEFF Research Database (Denmark)

    Ulhøi, John Parm

    2004-01-01

    This paper addresses innovations based on open source or non-proprietary knowledge. Viewed through the lens of private property theory, such agency appears to be a true anomaly. However, by a further turn of the theoretical kaleidoscope, we will show that there may be perfectly justifiable reason...

  20. 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…

  1. 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…

  2. 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.

  3. Open-Source Tools for Enhancing Full-Text Searching of OPACs: Use of Koha, Greenstone and Fedora

    Science.gov (United States)

    Anuradha, K. T.; Sivakaminathan, R.; Kumar, P. Arun

    2011-01-01

    Purpose: There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text…

  4. 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.

  5. Kinetic Analysis of Dynamic Positron Emission Tomography Data using Open-Source Image Processing and Statistical Inference Tools.

    Science.gov (United States)

    Hawe, David; Hernández Fernández, Francisco R; O'Suilleabháin, Liam; Huang, Jian; Wolsztynski, Eric; O'Sullivan, Finbarr

    2012-05-01

    In dynamic mode, positron emission tomography (PET) can be used to track the evolution of injected radio-labelled molecules in living tissue. This is a powerful diagnostic imaging technique that provides a unique opportunity to probe the status of healthy and pathological tissue by examining how it processes substrates. The spatial aspect of PET is well established in the computational statistics literature. This article focuses on its temporal aspect. The interpretation of PET time-course data is complicated because the measured signal is a combination of vascular delivery and tissue retention effects. If the arterial time-course is known, the tissue time-course can typically be expressed in terms of a linear convolution between the arterial time-course and the tissue residue. In statistical terms, the residue function is essentially a survival function - a familiar life-time data construct. Kinetic analysis of PET data is concerned with estimation of the residue and associated functionals such as flow, flux, volume of distribution and transit time summaries. This review emphasises a nonparametric approach to the estimation of the residue based on a piecewise linear form. Rapid implementation of this by quadratic programming is described. The approach provides a reference for statistical assessment of widely used one- and two-compartmental model forms. We illustrate the method with data from two of the most well-established PET radiotracers, (15)O-H(2)O and (18)F-fluorodeoxyglucose, used for assessment of blood perfusion and glucose metabolism respectively. The presentation illustrates the use of two open-source tools, AMIDE and R, for PET scan manipulation and model inference.

  6. 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.

  7. 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.

  8. Open source MySQL Browser for Open Innovation

    Directory of Open Access Journals (Sweden)

    Radu Bucea-Manea-Tonis

    2014-07-01

    Full Text Available Abstract. Our purpose is to cross-compile MySQL driver source code for Linux on Windows architecture using a tool chain in order to build a neutral valid graphic interface on 32 bits. Once achieving this goal we could say that every possible Open source application can be built and run on Windows with maximum efficiency concerning costs and resource. This browser is an example of open innovation because its source code is free for anybody willing to develop new software apps for business and uses only Open source tools.

  9. The Seismic Tool-Kit (STK): An Open Source Software For Learning the Basis of Signal Processing and Seismology.

    Science.gov (United States)

    Reymond, D.

    2016-12-01

    We present an open source software project (GNU public license), named STK: Seismic Tool-Kit, that is dedicated mainly for learning signal processing and seismology. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 20000 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 passage in the frequency domain via the Fourier transform is used to introduce the estimation of spectral density of the signal , 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 noise), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. STK has been used in some schools for viewing and plotting seismic records provided by IRIS, and it has been used as a practical support for teaching the basis of signal processing. Useful links:http://sourceforge.net

  10. Linking the open source, spatial electrification tool (ONSSET) and the open source energy modelling system (OSeMOSYS), with a focus on Sub-Saharan Africa

    Science.gov (United States)

    Mentis, Dimitrios; Howells, Mark; Rogner, Holger; Korkovelos, Alexandros; Arderne, Christopher; Siyal, Shahid; Zepeda, Eduardo; Taliotis, Constantinos; Bazilian, Morgan; de Roo, Ad; Tanvez, Yann; Oudalov, Alexandre; Scholtz, Ernst

    2017-04-01

    In September 2015, the United Nations General Assembly adopted Agenda 2030, which comprises a set of 17 Sustainable Development Goals (SDGs) defined by 169 targets. "Ensuring access to affordable, reliable, sustainable and modern energy for all by 2030" is the seventh goal (SDG7). While access to energy refers to more than electricity, the latter is the central focus of this work. According to the World Bank's 2015 Global Tracking Framework, roughly 15% of world population (or 1.1 billion people) lack access to electricity, and many more rely on poor quality electricity services. The majority of those without access (87%) reside in rural areas. This paper presents results of a Geographic Information Systems (GIS) approach coupled with open access data and linked to the Electricity Model Base for Africa (TEMBA), a model that represents each continental African country's electricity supply system. We present least-cost electrification strategies on a country-by-country basis for Sub-Saharan Africa. The electrification options include grid extension, mini-grid and stand-alone systems for rural, peri-urban, and urban contexts across the economy. At low levels of electricity demand there is a strong penetration of standalone technologies. However, higher electricity demand levels move the favourable electrification option from stand-alone systems to mini grid and to grid extensions.

  11. 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...

  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. Een boekje open over Open Source ERP

    NARCIS (Netherlands)

    Sneller, A.C.W.(L.)

    2009-01-01

    Er zijn vele ERP-systemen die met behulp van open source worden ontwikkeld. Organisaties die open source ERP willen implementeren staan voor twee strategische keuzes: hoe zit het met de continuïteit en wie gaat het systeem onderhouden?

  14. 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.

  15. 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

  16. Design and Development of a Nanoscale Multi Probe System Using Open Source SPM Controller and GXSM Software: A Tool of Nanotechnology

    CERN Document Server

    Babu, S K Suresh; Moni, D Jackuline; Devaprakasam, D

    2014-01-01

    We report our design, development, installation and troubleshooting of an open source Gnome X Scanning Microscopy (GXSM) software package for controlling and processing of modern Scanning Probe Microscopy (SPM) system as a development tool of Nanotechnology. GXSM is a full featured analysis tool for the characterization of nanomaterials with different controlling tools like Atomic Force Microscopy (AFM), Scanning Tunneling Spectroscopy (STS), scanning tunneling microscopy (STM), Nanoindentation and etc.,. This developed package tool consists of Digital Signal Processing (DSP) and image processing system of SPM. A digital signal processor (DSP) subsystem runs the feedback loop, generates the scanning signals and acquires the data during SPM measurements. With installed SR-Hwl plug-in this developed package was tested in no hardware mode.

  17. Open access and open source in chemistry

    Directory of Open Access Journals (Sweden)

    Todd Matthew H

    2007-02-01

    Full Text Available Abstract Scientific data are being generated and shared at ever-increasing rates. Two new mechanisms for doing this have developed: open access publishing and open source research. We discuss both, with recent examples, highlighting the differences between the two, and the strengths of both.

  18. The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data

    Directory of Open Access Journals (Sweden)

    Edgerton Mary E

    2003-05-01

    Full Text Available Abstract Background Tissue Microarrays (TMAs allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1 Header, containing the specification Dublin Core identifiers, 2 Block, describing the paraffin-embedded array of tissues, 3Slide, describing the glass slides produced from the Block, and 4 Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange

  19. Defining Open Source

    Directory of Open Access Journals (Sweden)

    Russ Nelson

    2007-09-01

    Full Text Available The Open Source Initiative and the Free Software Foundation share a common goal: that everyone should be free to modify and redistribute the software they commonly use. 'Should' is of course a normative word. For the FSF, 'should' is a moral imperative. Anything else is an immoral restriction on people's activities, just as are restrictions on speech, press, movement, and religion. For the OSI, freedom is a necessary precondition for a world where "software doesn't suck", in the words of a founder of the OSI. The FSF started from its founder's GNU Manifesto widely published in 1985. Given the manifesto's hostility to copyright, and given the failure of the Free Software Foundation to gain any traction amongst commercial users of software even with a 13-year head start, a group of people gathered together in 1998 to talk about a new strategy to get the corporate world to listen to hackers. They were impressed by Eric Raymond's Cathedral and the Bazaar's take-up among business leaders.

  20. jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

    Directory of Open Access Journals (Sweden)

    Hinselmann Georg

    2011-01-01

    Full Text Available Abstract Background The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints, only a few open source implementations are available. The aim of this work is to introduce a library for exactly defined molecular decompositions, with a strong focus on the application of these features in machine learning and data mining. It provides several options such as search depth, distance cut-offs, atom- and pharmacophore typing. Furthermore, it provides the functionality to combine, to compare, or to export the fingerprints into several formats. Results We provide a Java 1.6 library for the decomposition of chemical graphs based on the open source Chemistry Development Kit toolkit. We reimplemented popular fingerprinting algorithms such as depth-first search fingerprints, extended connectivity fingerprints, autocorrelation fingerprints (e.g. CATS2D, radial fingerprints (e.g. Molprint2D, geometrical Molprint, atom pairs, and pharmacophore fingerprints. We also implemented custom fingerprints such as the all-shortest path fingerprint that only includes the subset of shortest paths from the full set of paths of the depth-first search fingerprint. As an application of jCompoundMapper, we provide a command-line executable binary. We measured the conversion speed and number of features for each encoding and described the composition of the features in detail. The quality of the encodings was tested using the default parametrizations in combination with a support vector machine on the Sutherland QSAR data sets. Additionally, we benchmarked the fingerprint encodings on the large-scale Ames toxicity benchmark using a large-scale linear support vector machine. The results were promising and could often compete with literature results. On the large Ames benchmark, for example, we obtained an AUC ROC performance of 0

  1. DKIE: Open Source Information Extraction for Danish

    DEFF Research Database (Denmark)

    Derczynski, Leon; Field, Camilla Vilhelmsen; Bøgh, Kenneth Sejdenfaden

    2014-01-01

    Danish is a major Scandinavian language spoken daily by around six million people. However, it lacks a unified, open set of NLP tools. This demonstration will introduce DKIE, an extensible open-source toolkit for processing Danish text. We implement an information extraction architecture for Danish...

  2. DKIE: Open Source Information Extraction for Danish

    DEFF Research Database (Denmark)

    Derczynski, Leon; Field, Camilla Vilhelmsen; Bøgh, Kenneth Sejdenfaden

    2014-01-01

    Danish is a major Scandinavian language spoken daily by around six million people. However, it lacks a unified, open set of NLP tools. This demonstration will introduce DKIE, an extensible open-source toolkit for processing Danish text. We implement an information extraction architecture for Danish...... independently or with the Stanford NLP toolkit....

  3. Editorial: Open Source in Government

    Directory of Open Access Journals (Sweden)

    Dru Lavigne

    2009-04-01

    Full Text Available Last summer, the Center for Strategic and International Studies published the sixth update to their Open Source Policy survey. The survey "tracks governmental policies on the use of open source software as reported in the press or other media." The report lists 275 open source policy initiatives. It also breaks down by country and by government level whether the policy on the use of open source is considered to be advisory, preferential, or mandatory. The editorial theme for the May issue of the OSBR is "open source in government" and we are pleased that the authors have drawn upon their experiences to provide insight into public policy regarding open source for many parts of the world.

  4. SU-F-BRB-16: A Spreadsheet Based Automatic Trajectory GEnerator (SAGE): An Open Source Tool for Automatic Creation of TrueBeam Developer Mode Robotic Trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Etmektzoglou, A; Mishra, P; Svatos, M [Varian Medical Systems, Palo Alto, CA (United States)

    2015-06-15

    Purpose: To automate creation and delivery of robotic linac trajectories with TrueBeam Developer Mode, an open source spreadsheet-based trajectory generation tool has been developed, tested and made freely available. The computing power inherent in a spreadsheet environment plus additional functions programmed into the tool insulate users from the underlying schema tedium and allow easy calculation, parameterization, graphical visualization, validation and finally automatic generation of Developer Mode XML scripts which are directly loadable on a TrueBeam linac. Methods: The robotic control system platform that allows total coordination of potentially all linac moving axes with beam (continuous, step-and-shoot, or combination thereof) becomes available in TrueBeam Developer Mode. Many complex trajectories are either geometric or can be described in analytical form, making the computational power, graphing and programmability available in a spreadsheet environment an easy and ideal vehicle for automatic trajectory generation. The spreadsheet environment allows also for parameterization of trajectories thus enabling the creation of entire families of trajectories using only a few variables. Standard spreadsheet functionality has been extended for powerful movie-like dynamic graphic visualization of the gantry, table, MLC, room, lasers, 3D observer placement and beam centerline all as a function of MU or time, for analysis of the motions before requiring actual linac time. Results: We used the tool to generate and deliver extended SAD “virtual isocenter” trajectories of various shapes such as parameterized circles and ellipses. We also demonstrated use of the tool in generating linac couch motions that simulate respiratory motion using analytical parameterized functions. Conclusion: The SAGE tool is a valuable resource to experiment with families of complex geometric trajectories for a TrueBeam Linac. It makes Developer Mode more accessible as a vehicle to quickly

  5. Open Source, Open Access, Open Review, Open Data. Initiativen zu mehr Offenheit in der digitalen Welt

    OpenAIRE

    Herb, Ulrich

    2011-01-01

    The article discusses the principles of openess, open access and open availability of information based on the examples of open access to scientific information, open government data, open geographical data and open source software.

  6. Open Source, Open Access, Open Review, Open Data. Initiativen zu mehr Offenheit in der digitalen Welt

    OpenAIRE

    Herb, Ulrich

    2011-01-01

    The article discusses the principles of openess, open access and open availability of information based on the examples of open access to scientific information, open government data, open geographical data and open source software.

  7. Computer Forensics Education - the Open Source Approach

    Science.gov (United States)

    Huebner, Ewa; Bem, Derek; Cheung, Hon

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

  8. Open source bioimage informatics for cell biology.

    Science.gov (United States)

    Swedlow, Jason R; Eliceiri, Kevin W

    2009-11-01

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

  9. Earth-Observation based mapping and monitoring of exposure change in the megacity of Istanbul: open-source tools from the MARSITE project

    Science.gov (United States)

    De Vecchi, Daniele; Dell'Acqua, Fabio

    2016-04-01

    The EU FP7 MARSITE project aims at assessing the "state of the art" of seismic risk evaluation and management at European level, as a starting point to move a "step forward" towards new concepts of risk mitigation and management by long-term monitoring activities carried out both on land and at sea. Spaceborne Earth Observation (EO) is one of the means through which MARSITE is accomplishing this commitment, whose importance is growing as a consequence of the operational unfolding of the Copernicus initiative. Sentinel-2 data, with its open-data policy, represents an unprecedented opportunity to access global spaceborne multispectral data for various purposes including risk monitoring. In the framework of EU FP7 projects MARSITE, RASOR and SENSUM, our group has developed a suite of geospatial software tools to automatically extract risk-related features from EO data, especially on the exposure and vulnerability side of the "risk equation" [1]. These are for example the extension of a built-up area or the distribution of building density. These tools are available open-source as QGIS plug-ins [2] and their source code can be freely downloaded from GitHub [3]. A test case on the risk-prone mega city of Istanbul has been set up, and preliminary results will be presented in this paper. The output of the algorithms can be incorporated into a risk modeling process, whose output is very useful to stakeholders and decision makers who intend to assess and mitigate the risk level across the giant urban agglomerate. Keywords - Remote Sensing, Copernicus, Istanbul megacity, seismic risk, multi-risk, exposure, open-source References [1] Harb, M.M.; De Vecchi, D.; Dell'Acqua, F., "Physical Vulnerability Proxies from Remotes Sensing: Reviewing, Implementing and Disseminating Selected Techniques," Geoscience and Remote Sensing Magazine, IEEE , vol.3, no.1, pp.20,33, March 2015. doi: 10.1109/MGRS.2015.2398672 [2] SENSUM QGIS plugin, 2016, available online at: https://plugins.qgis.org/plugins/sensum_eo_tools

  10. Open Source Vulnerability Database Project

    Directory of Open Access Journals (Sweden)

    Jake Kouns

    2008-06-01

    Full Text Available This article introduces the Open Source Vulnerability Database (OSVDB project which manages a global collection of computer security vulnerabilities, available for free use by the information security community. This collection contains information on known security weaknesses in operating systems, software products, protocols, hardware devices, and other infrastructure elements of information technology. The OSVDB project is intended to be the centralized global open source vulnerability collection on the Internet.

  11. Generation of realistic nonwoven and foam filter geometry and mesh for filtration simulation using open-source tools

    OpenAIRE

    Abishek, S.; Mullins, B; King, A.; Kasper, G; Heikamp, W.

    2016-01-01

    Recovery of liquid aerosols (mists) from industrial processes is typically accomplished through coalescence filtration, employing highly porous nonwoven (fibrous), knitted or foam media which are regarded to potentially provide high collection efficiencies. Highly resolved pore-scale computational fluid dynamics (CFD) analysis of mist filtration processes is increasingly becoming an important tool for design and optimization of such filter media. A key to efficient application-specific optimi...

  12. Using an open source observational tool to measure the influence of the doctor's consulting style and the computer system on the outcomes of the clinical consultation.

    Science.gov (United States)

    De Lusignan, Simon; Kumarapeli, Pushpa; Debar, Safia; Kushniruk, Andre W; Pearce, Chris

    2009-01-01

    Computerization of general practice is an international phenomenon. Many of the Electronic Patient Record (EPR) systems have developed organically with considerable variation in their interface and functionality. Consequently they have differing impact on the clinical consultation. There is a dearth of tools available to study their impact on the consultation. The objective is to use ALFA to film and analyze a simulated clinical consultation. We used the ALFA (Activity Log File Aggregation) open source toolkit, to make video based observation and analysis of the computer mediated consultation. ALFA enables precise comparison of core elements of EPR systems. It allows multiple video channels including screen capture, data about computer use, and verbal interactions to be synchronized, timed and navigated through for analysis. The toolkit is free and can be downloaded under an open source license from www.biomedicalinformatics.info/alfa/. Its outputs, which include Unified Modelling Language (UML), provide the evidence-base for assessing the impact of the computer on the consultation the designing of EPR systems. ALFA has been used to compare different brands of primary care computer systems; nurse case-load selection and consultation in psychiatry.

  13. Open Source GIS based integrated watershed management

    Science.gov (United States)

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

    2013-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-20

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

  15. Preliminary Verification and Validation of WEC-Sim, an Open-Source Wave Energy Converter Design Tool: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Ruehl, K.; Michelen, C.; Kanner, S.; Lawson, M.; Yu, Y. H.

    2014-03-01

    To promote and support the wave energy industry, a wave energy converter (WEC) design tool, WEC-Sim, is being developed by Sandia National Laboratories and the National Renewable Energy Laboratory. In this paper, the WEC-Sim code is used to model a point absorber WEC designed by the U.S. Department of Energy's reference model project. Preliminary verification was performed by comparing results of the WEC-Sim simulation through a code-to-code comparison, utilizing the commercial codes ANSYS-AQWA, WaveDyn, and OrcaFlex. A preliminary validation of the code was also performed by comparing WEC-Sim simulation results to experimental wave tank tests.

  16. Open Source Fundamental Industry Classification

    OpenAIRE

    Kakushadze, Zura; Yu, Willie

    2017-01-01

    We provide complete source code for building a fundamental industry classification based on publically available and freely downloadable data. We compare various fundamental industry classifications by running a horserace of short-horizon trading signals (alphas) utilizing open source heterotic risk models (https://ssrn.com/abstract=2600798) built using such industry classifications. Our source code includes various stand-alone and portable modules, e.g., for downloading/parsing web data, etc.

  17. SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data

    Directory of Open Access Journals (Sweden)

    Diaz-Uriarte Ramon

    2008-01-01

    Full Text Available Abstract Background Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods, however, are not available to biomedical researchers, leading to many re-implementations from scratch of ad-hoc, and suboptimal, approaches with survival data. Results We have developed SignS (Signatures for Survival data, an open-source, freely-available, web-based tool and R package for gene selection, building molecular signatures, and prediction with survival data. SignS implements four methods which, according to existing reviews, perform well and, by being of a very different nature, offer complementary approaches. We use parallel computing via MPI, leading to large decreases in user waiting time. Cross-validation is used to asses predictive performance and stability of solutions, the latter an issue of increasing concern given that there are often several solutions with similar predictive performance. Biological interpretation of results is enhanced because genes and signatures in models can be sent to other freely-available on-line tools for examination of PubMed references, GO terms, and KEGG and Reactome pathways of selected genes. Conclusion SignS is the first web-based tool for survival analysis of expression data, and one of the very few with biomedical researchers as target users. SignS is also one of the few bioinformatics web-based applications to extensively use parallelization, including fault tolerance and crash recovery. Because of its combination of methods implemented, usage of parallel computing, code availability, and links to additional data bases, SignS is a unique tool, and will be of immediate relevance to biomedical researchers, biostatisticians and bioinformaticians.

  18. 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...

  19. DensToolKit: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

    Science.gov (United States)

    Solano-Altamirano, J. M.; Hernández-Pérez, Julio M.

    2015-11-01

    DensToolKit is a suite of cross-platform, optionally parallelized, programs for analyzing the molecular electron density (ρ) and several fields derived from it. Scalar and vector fields, such as the gradient of the electron density (∇ρ), electron localization function (ELF) and its gradient, localized orbital locator (LOL), region of slow electrons (RoSE), reduced density gradient, localized electrons detector (LED), information entropy, molecular electrostatic potential, kinetic energy densities K and G, among others, can be evaluated on zero, one, two, and three dimensional grids. The suite includes a program for searching critical points and bond paths of the electron density, under the framework of Quantum Theory of Atoms in Molecules. DensToolKit also evaluates the momentum space electron density on spatial grids, and the reduced density matrix of order one along lines joining two arbitrary atoms of a molecule. The source code is distributed under the GNU-GPLv3 license, and we release the code with the intent of establishing an open-source collaborative project. The style of DensToolKit's code follows some of the guidelines of an object-oriented program. This allows us to supply the user with a simple manner for easily implement new scalar or vector fields, provided they are derived from any of the fields already implemented in the code. In this paper, we present some of the most salient features of the programs contained in the suite, some examples of how to run them, and the mathematical definitions of the implemented fields along with hints of how we optimized their evaluation. We benchmarked our suite against both a freely-available program and a commercial package. Speed-ups of ˜2×, and up to 12× were obtained using a non-parallel compilation of DensToolKit for the evaluation of fields. DensToolKit takes similar times for finding critical points, compared to a commercial package. Finally, we present some perspectives for the future development and

  20. The Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT): An Open-source Tool for Efficient Fitting of Astrometric and Radial Velocity Data

    Science.gov (United States)

    Mede, Kyle; Brandt, Timothy D.

    2017-03-01

    We present the Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT), a new, open-source suite to fit the orbital elements of planetary or stellar-mass companions to any combination of radial velocity and astrometric data. To explore the parameter space of Keplerian models, ExoSOFT may be operated with its own multistage sampling approach or interfaced with third-party tools such as emcee. In addition, ExoSOFT is packaged with a collection of post-processing tools to analyze and summarize the results. Although only a few systems have been observed with both radial velocity and direct imaging techniques, this number will increase, thanks to upcoming spacecraft and ground-based surveys. Providing both forms of data enables simultaneous fitting that can help break degeneracies in the orbital elements that arise when only one data type is available. The dynamical mass estimates this approach can produce are important when investigating the formation mechanisms and subsequent evolution of substellar companions. ExoSOFT was verified through fitting to artificial data and was implemented using the Python and Cython programming languages; it is available for public download at https://github.com/kylemede/ExoSOFT under GNU General Public License v3.

  1. Open Source Live Distributions for Computer Forensics

    Science.gov (United States)

    Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

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

  2. 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

  3. The Open Source Stochastic Building Simulation Tool SLBM and Its Capabilities to Capture Uncertainty of Policymaking in the U.S. Building Sector

    Energy Technology Data Exchange (ETDEWEB)

    Stadler, Michael; Marnay, Chris; Azevedo, Ines Lima; Komiyama, Ryoichi; Lai, Judy

    2009-05-14

    The increasing concern about climate change as well as the expected direct environmental economic impacts of global warming will put considerable constraints on the US building sector, which consumes roughly 48percent of the total primary energy, making it the biggest single source of CO2 emissions. It is obvious that the battle against climate change can only be won by considering innovative building approaches and consumer behaviors and bringing new, effective low carbon technologies to the building / consumer market. However, the limited time given to mitigate climate change is unforgiving to misled research and / or policy. This is the reason why Lawrence Berkeley National Lab is working on an open source long range Stochastic Lite Building Module (SLBM) to estimate the impact of different policies and consumer behavior on the market penetration of low carbon building technologies. SLBM is designed to be a fast running, user-friendly model that analysts can readily run and modify in its entirety through a visual interface. The tool is fundamentally an engineering-economic model with technology adoption decisions based on cost and energy performance characteristics of competing technologies. It also incorporates consumer preferences and passive building systems as well as interactions between technologies (such as internal heat gains). Furthermore, everything is based on service demand, e.g. a certain temperature or luminous intensity, instead of energy intensities. The core objectives of this paper are to demonstrate the practical approach used, to start a discussion process between relevant stakeholders and to build collaborations.

  4. THE OPEN SOURCING OF EPANET

    Science.gov (United States)

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

  5. Open Source Wifi Hotspot Implementation

    Directory of Open Access Journals (Sweden)

    Tyler Sondag

    2007-06-01

    Full Text Available The goal of this paper is to describe a design—including the hardware, software, and configuration––for an open source wireless network. The network designed will require authentication. While care will be taken to keep the authentication exchange secure, the network will otherwise transmit data without encryption.

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

    Science.gov (United States)

    Committee for Economic Development, 2006

    2006-01-01

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

  7. From HYSOMA to ENSOMAP - A new open source tool for quantitative soil properties mapping based on hyperspectral imagery from airborne to spaceborne applications

    Science.gov (United States)

    Chabrillat, Sabine; Guillaso, Stephane; Rabe, Andreas; Foerster, Saskia; Guanter, Luis

    2016-04-01

    , HYSOMA has allowed non-experienced hyperspectral imagery users that have access to ground-truth data to develop fully quantitative maps of common soil properties after few button-clicks. Currently for more applicability to global spaceborne applications, soil algorithms are being further developed in the context of the EnMAP satellite mission, for the HYSOMA extension and implementation in the EnMAP Box. The EnMAP Box is a freely available, platform-independent open source software designed to process hyperspectral remote sensing data, and particularly developed to handle data from the EnMAP sensor. The soil masking and mapping functions and soil analyses tools of the HYSOMA software were now implemented in EnMAP Box applications tools as EnSOMAP suite (Environmental Soil Mapping) and further extended to include new soil parameters such as salt and hydrocarbon mapping. In this paper, we will present an update of the status of the soil algorithms developed at GFZ from HYSOMA to open source ENSOMAP and additional soil mapping functions.

  8. LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

    Science.gov (United States)

    Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

    2016-09-02

    Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNP(xl) for UV-induced peptide-RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark ( Ramus, C.; J. Proteomics 2016 , 132 , 51 - 62 ). The second workflow, RNP(xl), represents the first software solution to date for identification of peptide-RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results.

  9. Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders.

    Science.gov (United States)

    G C C L Cardenas, Raony; D Linhares, Natália; L Ferreira, Raquel; Pena, Sérgio D J

    2017-06-01

    Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the "1-click" method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE-Núcleo de Genética Médica in Brazil and at the Children's University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org.

  10. An 'open source' networked identity

    DEFF Research Database (Denmark)

    Larsen, Malene Charlotte

    2013-01-01

    , but also an important part of their self-presentation online. It is discussed why these emotional statements are almost always publically available – or even strategically, intentionally placed on the young people's profiles. In relation to this, it is argued that young people – through their emotional...... communicative actions – are not only performing their own identity, but are becoming co-constructors of each other's identities, which the author characterizes as an 'open source' networked identity....

  11. The Open Source Hardening Project

    Science.gov (United States)

    2009-07-01

    code on a recurring basis from more than 250 open popular source projects such as Firefox, Linux, and PHP . This represents 14,238 individual project...gcc) greatly simplifies debugging and error reporting. For exam- ple, all COREUTILS bugs were confirmed and fixed within two days and versions of the...making system calls fail outside of KLEE — we built a simple utility that uses the ptrace debugging interface to skip the system calls that were

  12. Reliability methods in OpenEarthTools

    NARCIS (Netherlands)

    Den Heijer, C.

    2012-01-01

    OpenEarthTools contains, apart from a lot of other tools in various programming languages, the probabilistic reliability methods FORM and Monte Carlo. This document aims at describing and providing background information and examples on the FORM and Monte Carlo implementation available in OpenEarthT

  13. 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.

  14. Enabling Open Hardware through FOSS tools

    CERN Document Server

    CERN. Geneva

    2016-01-01

    Software developers often take open file formats and tools for granted. When you publish code on github, you do not ask yourself if somebody will be able to open it and modify it. We need the same freedom in the open hardware world, to make it truly accessible for everyone.

  15. 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

  16. Research on OpenStack of open source cloud computing in colleges and universities’ computer room

    Science.gov (United States)

    Wang, Lei; Zhang, Dandan

    2017-06-01

    In recent years, the cloud computing technology has a rapid development, especially open source cloud computing. Open source cloud computing has attracted a large number of user groups by the advantages of open source and low cost, have now become a large-scale promotion and application. In this paper, firstly we briefly introduced the main functions and architecture of the open source cloud computing OpenStack tools, and then discussed deeply the core problems of computer labs in colleges and universities. Combining with this research, it is not that the specific application and deployment of university computer rooms with OpenStack tool. The experimental results show that the application of OpenStack tool can efficiently and conveniently deploy cloud of university computer room, and its performance is stable and the functional value is good.

  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. Open Source Initiative Powers Real-Time Data Streams

    Science.gov (United States)

    2014-01-01

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

  19. Editorial: Humanitarian Open Source (December 2010

    Directory of Open Access Journals (Sweden)

    Leslie Hawthorn

    2010-11-01

    Full Text Available In recent years, our increasingly connected world has provided us with a greater understanding of the needs of our fellow global citizens. The devastating worldwide impact of natural disasters, disease, and poverty has been raised in our collective awareness and our ability to collectively alleviate this suffering has been brought to the fore. While many of us are familiar with donating our funds to better the lives of those less fortunate than ourselves, it is often easy to overlook a core component of facing these global challenges: information technology. The humanitarian open source movement seeks to ameliorate these sufferings through the creation of IT infrastructure to support a wide array of goals for the public good, such as providing effective healthcare or microloans to the poorest of the poor. Achieving these goals requires a sophisticated set of software and hardware tools, all of which work to save and improve lives in some of the most difficult of situations where the availability of electricity, data, IT knowledge, etc. may be low or lacking altogether. It should come as no surprise that the humanitarian open source domain attracts a great deal of attention from software developers, engineers, and others who find that they are able to both solve intense technical challenges while helping to improve the lives of others. However, to support ongoing humanitarian needs, the communities who produce humanitarian free and open source software (HFOSS and hardware have increasingly identified the need for business models to support their efforts. While the lower cost of using open source software and hardware solutions means that more funds can be directed to aid and comfort those in need, the goodwill of developer communities and the funds of grantees alone cannot grow the ecosystem sufficiently to meet ever-growing global needs. To face these challenges - poverty, global health crises, disaster relief, etc. - humanitarian open source

  20. From open source communications to knowledge

    Science.gov (United States)

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

    2016-05-01

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

  1. 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...

  2. The successes and challenges of open-source biopharmaceutical innovation.

    Science.gov (United States)

    Allarakhia, Minna

    2014-05-01

    Increasingly, open-source-based alliances seek to provide broad access to data, research-based tools, preclinical samples and downstream compounds. The challenge is how to create value from open-source biopharmaceutical innovation. This value creation may occur via transparency and usage of data across the biopharmaceutical value chain as stakeholders move dynamically between open source and open innovation. In this article, several examples are used to trace the evolution of biopharmaceutical open-source initiatives. The article specifically discusses the technological challenges associated with the integration and standardization of big data; the human capacity development challenges associated with skill development around big data usage; and the data-material access challenge associated with data and material access and usage rights, particularly as the boundary between open source and open innovation becomes more fluid. It is the author's opinion that the assessment of when and how value creation will occur, through open-source biopharmaceutical innovation, is paramount. The key is to determine the metrics of value creation and the necessary technological, educational and legal frameworks to support the downstream outcomes of now big data-based open-source initiatives. The continued focus on the early-stage value creation is not advisable. Instead, it would be more advisable to adopt an approach where stakeholders transform open-source initiatives into open-source discovery, crowdsourcing and open product development partnerships on the same platform.

  3. Leveraging on Easy Java Simulation tool and open source computer simulation library to create interactive digital media for mass customization of high school physics curriculum

    OpenAIRE

    Wee, Loo Kang; Mak, Wai Keong

    2012-01-01

    This paper highlights the diverse possibilities in the rich community of educators from the Conceptual Learning of Science (CoLoS) and Open Source Physics (OSP) movement to engage, enable and empower educators and students, to create interactive digital media through computer modeling. This concept revolves around a paradigmatic shift towards participatory learning through immersive computer modeling, as opposed to using technology for information transmission. We aim to engage high school ed...

  4. Evolution of open source networks in industry

    NARCIS (Netherlands)

    de Laat, P.B.

    2004-01-01

    The open source software movement has become a threat to corporate software development. In response, companies started to develop products and services related to open source software. Subsequently, they also tried to come to terms with the processes that are characteristic of open source software

  5. Future of Open Source systems

    Directory of Open Access Journals (Sweden)

    Karel Charvát

    2010-02-01

    Full Text Available Software distribution strategies have many aspects and can be analysed by reviewing different incisions of a strategy. The focus of this paper is on Licensing aspect involves licensing strategy, licensing risks, licensing enforcement costs. Furthermore, by formulating licensing strategy main technical and logistical aspects are predicted also. The key issues of this paper are different business modes for FOSS software and also SWOT analysis of usage and development of FOSS software from point of view of different user groups. This analysis was provided as part of work of Humboldt IP and collaborative@rural IP. Currently this strategy are important issue of members of Czech Centre for Science and Society and WirelessInfo Living Lab, where the models based on dual licensing are key strategy.Keywords: Open Source, Licensing, FOSS base business models. SWOT analysis, Knowledge society, Knowledge economy

  6. 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...

  7. Leveraging on Easy Java Simulation tool and open source computer simulation library to create interactive digital media for mass customization of high school physics curriculum

    CERN Document Server

    Wee, Loo Kang

    2012-01-01

    This paper highlights the diverse possibilities in the rich community of educators from the Conceptual Learning of Science (CoLoS) and Open Source Physics (OSP) movement to engage, enable and empower educators and students, to create interactive digital media through computer modeling. This concept revolves around a paradigmatic shift towards participatory learning through immersive computer modeling, as opposed to using technology for information transmission. We aim to engage high school educators to professionally develop themselves by creating and customizing simulations possible through Easy Java Simulation (Ejs) and its learning community. Ejs allows educators to be designers of learning environments through modifying source codes of the simulation. Educators can conduct lessons with students' using these interactive digital simulations and rapidly enhance the simulation through changing the source codes personally. Ejs toolkit, its library of simulations and growing community contributed simulation cod...

  8. The Commercial Open Source Business Model

    Science.gov (United States)

    Riehle, Dirk

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

  9. Open Source Testing Capability for Geospatial Software

    Science.gov (United States)

    Bermudez, L. E.

    2013-12-01

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

  10. Your Personal Analysis Toolkit - An Open Source Solution

    Science.gov (United States)

    Mitchell, T.

    2009-12-01

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

  11. OpenDOAR Policy tools and applications

    CERN Document Server

    CERN. Geneva

    2007-01-01

    OpenDOAR conducted a survey of the world's repositories that showed 2/3 as having unusable or missing policies for content re-use and other issues. Such policies are essential for service providers to be able to develop innovative services that use the full potential of open access. OpenDOAR has developed a set of policy generator tools for repository administrators and is contacting administrators to advocate policy development. It is hoped that one outcome from this work will be some standardisation of policies in vocabulary and intent. Other developments include an OpenDOAR API. This presentation looks at the way that the tools and API have been developed and the implcations for their use. View Bill Hubbard's biography

  12. Open Genetic Code: on open source in the life sciences

    NARCIS (Netherlands)

    Deibel, E.

    2014-01-01

    The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life

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

    Science.gov (United States)

    Erdemir, Ahmet

    2016-02-01

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

  14. The Open Source Snowpack modelling ecosystem

    Science.gov (United States)

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

    2016-04-01

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

  15. Phenomena of Open Source and Slovenia's Adaption

    Directory of Open Access Journals (Sweden)

    Matej Mertik

    2011-06-01

    Full Text Available Although free open source libre (FLOSS software is increasing its presence in the media and in debates between IT professionals, and although even citizens in general are starting to talk about it, FLOSS is still in general quite an unknown quantity. But this is changing. There is more and more interest in open source software by general users and also its influence on the public and business sector is undeniable. What is open source? Where did it all start? How is Slovenia using open source? What have we learned? Where are the opportunities for FLOSS? These are the sort of questions we will try to answer in this document. Slovenia implemented some of the important steps in introducing open source, however we are still far behind in terms of open source adoption and great opportunities exist for its better use in future.

  16. Open source innovation phenomenon, participant behaviour, impact

    CERN Document Server

    Herstatt, Cornelius

    2015-01-01

    Open Source Innovation (OSI) has gained considerable momentum within the last years. Academic and management practice interest grows as more and more end-users consider and even participate in Open Source product development like Linux, Android, or Wikipedia. Open Source Innovation: Phenomenon, Participant Behaviour, Impact brings together rigorous academic research and business importance in scrutinizing OCI from three perspectives: The Phenomenon, Participants' Behavior, and Business Implications. The first section introduces OCI artefacts, including who is participating and why, and provide

  17. 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…

  18. 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…

  19. Deep Learning in Open Source Learning Streams

    DEFF Research Database (Denmark)

    Kjærgaard, Thomas

    2016-01-01

    and contrasted to the notion of functionalistic learning in a digital context. The mechanism that enables deep learning in this context is ‘The Open Source Learning Stream’. ‘The Open Source Learning Stream’ is the notion of sharing ‘learning instances’ in a digital space (discussion board, Facebook group......, unistructural, multistructural or relational learning. The research concludes that ‘The Open Source Learning Stream’ can catalyze deep learning and that there are four types of ‘Open Source Learning streams’; individual/ asynchronous, individual/synchronous, shared/asynchronous and shared...

  20. Open-source hardware for medical devices.

    Science.gov (United States)

    Niezen, Gerrit; Eslambolchilar, Parisa; Thimbleby, Harold

    2016-04-01

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

  1. 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.

  2. Open Source Data Warehousing and Business Intelligence

    CERN Document Server

    Bulusu, Lakshman

    2012-01-01

    Open Source Data Warehousing and Business Intelligence is an all-in-one reference for developing open source based data warehousing (DW) and business intelligence (BI) solutions that are business-centric, cross-customer viable, cross-functional, cross-technology based, and enterprise-wide. Considering the entire lifecycle of an open source DW & BI implementation, its comprehensive coverage spans from basic concepts all the way through to customization. Highlighting the key differences between open source and vendor DW and BI technologies, the book identifies end-to-end solutions that are scala

  3. Open Genetic Code: on open source in the life sciences.

    Science.gov (United States)

    Deibel, Eric

    2014-01-01

    The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.

  4. Physics of non-steady state diffusion of lightweight atoms in a heavy atom matrix. Introducing an open-source tool for simulated-experiments in fluid mechanics

    CERN Document Server

    Serrano-López, Roberto; Tapia-Júdez, Oscar; Fradera, Jorge

    2013-01-01

    The practice-based learning methodologies offer to undergraduate professors different ways to illustrate certain general physic principles. Traditional experimental workbenches have been extensively used during decades for academic lessons in order to complete theoretical dissertations or lectures, aiming at assuring an adequate understanding. The high cost of materials and laboratory equipment, the excessive preparation time, and the difficulty for carrying out offsite-campus replications by students, are disadvantages that can discourage of trying new kinds of experimental tasks. This paper gives insight of simulated experiment possibilities through an open-source-based computational suite in teaching fluid mechanics. Physics underlying diffusion of a light specie in a heavier atom matrix, as function of time and position, were explained to students as an example to teach them the Fick's Second Law expression. We present a docent step-by-step programme, scheduled in three sessions. The expected solution is ...

  5. 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

  6. Open Government: A Tool for Democracy?

    Directory of Open Access Journals (Sweden)

    Emiliana De Blasio

    2016-12-01

    Full Text Available The growing disconnection between citizens and decision-makers is pushing politics towards a re-shaping of institutional design. New spaces of political participation are sustained and even reinforced by communication, especially by digital communication. Governments and public administrations can find and use different models to facilitate citizens’ participation; e-government, open government and a specific design of digital democracy. In this respect, open government can constitute a way to re-connect citizens and political institutions, but at the same time, it can also be an “appealing” tool to institutionalize bottom-up participation and so anesthetizing it. The aim of this article is to present the first findings of an international research project about open government and participatory platforms in four European countries (France, Italy, Spain, the UK. The study tries to understand if participatory platforms can improve the quality of democracy, and if open government can contribute to democratizing democracy.

  7. Open Source CRM Systems for SMEs

    CERN Document Server

    Tereso, Marco

    2011-01-01

    Customer Relationship Management (CRM) systems are very common in large companies. However, CRM systems are not very common in Small and Medium Enterprises (SMEs). Most SMEs do not implement CRM systems due to several reasons, such as lack of knowledge about CRM or lack of financial resources to implement CRM systems. SMEs have to start implementing Information Systems (IS) technology into their business operations in order to improve business values and gain more competitive advantage over rivals. CRM system has the potential to help improve the business value and competitive capabilities of SMEs. Given the high fixed costs of normal activity of companies, we intend to promote free and viable solutions for small and medium businesses. In this paper, we explain the reasons why SMEs do not implement CRM system and the benefits of using open source CRM system in SMEs. We also describe the functionalities of top open source CRM systems, examining the applicability of these tools in fitting the needs of SMEs.

  8. The open-source neuroimaging research enterprise.

    Science.gov (United States)

    Marcus, Daniel S; Archie, Kevin A; Olsen, Timothy R; Ramaratnam, Mohana

    2007-11-01

    While brain imaging in the clinical setting is largely a practice of looking at images, research neuroimaging is a quantitative and integrative enterprise. Images are run through complex batteries of processing and analysis routines to generate numeric measures of brain characteristics. Other measures potentially related to brain function - demographics, genetics, behavioral tests, neuropsychological tests - are key components of most research studies. The canonical scanner - PACS - viewing station axis used in clinical practice is therefore inadequate for supporting neuroimaging research. Here, we model the neuroimaging research enterprise as a workflow. The principal components of the workflow include data acquisition, data archiving, data processing and analysis, and data utilization. We also describe a set of open-source applications to support each step of the workflow and the transitions between these steps. These applications include DIGITAL IMAGING AND COMMUNICATIONS IN MEDICINE viewing and storage tools, the EXTENSIBLE NEUROIMAGING ARCHIVE TOOLKIT data archiving and exploration platform, and an engine for running processing/analysis pipelines. The overall picture presented is aimed to motivate open-source developers to identify key integration and communication points for interoperating with complimentary applications.

  9. HERAFitter, Open Source QCD Fit Project

    CERN Document Server

    Alekhin, S.; Belov, P.; Borroni, S.; Botje, M.; Britzger, D.; Camarda, S.; Cooper-Sarkar, A.M.; Daum, K.; Diaconu, C.; Feltesse, J.; Gizhko, A.; Glazov, A.; Guffanti, A.; Guzzi, M.; Hautmann, F.; Jung, A.; Jung, H.; Kolesnikov, V.; Kowalski, H.; Kuprash, O.; Kusina, A.; Levonian, S.; Lipka, K.; Lobodzinski, B.; Lohwasser, K.; Luszczak, A.; Malaescu, B.; McNulty, R.; Myronenko, V.; Naumann-Emme, S.; Nowak, K.; Olness, F.; Perez, E.; Pirumov, H.; Plačakytė, R.; Rabbertz, K.; Radescu, V.; Sadykov, R.; Salam, G.P.; Sapronov, A.; Schöning, A.; Schörner-Sadenius, T.; Shushkevich, S.; Slominski, W.; Spiesberger, H.; Starovoitov, P.; Sutton, M.; Tomaszewska, J.; Turkot, O.; Vargas, A.; Watt, G.; Wichmann, K.

    2015-07-02

    HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton-proton deep inelastic scattering and proton-proton (proton-antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodological options for carrying out PDF fits and plotting tools to help visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study t...

  10. HERAFitter, Open Source QCD Fit Project

    CERN Document Server

    Alekhin, S; Belov, P; Borroni, S; Botje, M; Britzger, D; Camarda, S; Cooper-Sarkar, A M; Daum, K; Diaconu, C; Feltesse, J; Gizhko, A; Glazov, A; Guffanti, A; Guzzi, M; Hautmann, F; Jung, A; Jung, H; Kolesnikov, V; Kowalski, H; Kuprash, O; Kusina, A; Levonian, S; Lipka, K; Lobodzinski, B; Lohwasser, K; Luszczak, A; Malaescu, B; McNulty, R; Myronenko, V; Naumann-Emme, S; Nowak, K; Olness, F; Perez, E; Pirumov, H; Plačakytė, R; Rabbertz, K; Radescu, V; Sadykov, R; Salam, G P; Sapronov, A; Schöning, A; Schörner-Sadenius, T; Shushkevich, S; Slominski, W; Spiesberger, H; Starovoitov, P; Sutton, M; Tomaszewska, J; Turkot, O; Vargas, A; Watt, G; Wichmann, K

    2015-01-01

    HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton-proton deep inelastic scattering and proton-proton (proton-antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodological options for carrying out PDF fits and plotting tools to help visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study t...

  11. 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...

  12. 7 Questions to Ask Open Source Vendors

    Science.gov (United States)

    Raths, David

    2012-01-01

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

  13. Scalable Open Source Smart Grid Simulator (SGSim)

    DEFF Research Database (Denmark)

    Ebeid, Emad Samuel Malki; Jacobsen, Rune Hylsberg; Quaglia, Davide

    2017-01-01

    . This paper presents an open source smart grid simulator (SGSim). The simulator is based on open source SystemC Network Simulation Library (SCNSL) and aims to model scalable smart grid applications. SGSim has been tested under different smart grid scenarios that contain hundreds of thousands of households...

  14. Open source and open standards in e-learning research

    NARCIS (Netherlands)

    Koper, Rob

    2007-01-01

    Presentation at the TENCompetence Winterschool directed at Ph.D. students to position e-learning research and the role of open source and open standards to facilitate the research process in a methodological sense. The presentation is based on the paper: http://hdl.handle.net/1820/780

  15. Open source and open standards in e-learning research

    NARCIS (Netherlands)

    Koper, Rob

    2007-01-01

    Presentation at the TENCompetence Winterschool directed at Ph.D. students to position e-learning research and the role of open source and open standards to facilitate the research process in a methodological sense. The presentation is based on the paper: http://hdl.handle.net/1820/780

  16. "Open-Sourcing" Personal Learning

    Science.gov (United States)

    Fiedler, Sebastian H.D.

    2014-01-01

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

  17. Open Source And New Media Artists

    Directory of Open Access Journals (Sweden)

    Katri Halonen

    2007-01-01

    Full Text Available This paper deals with the open source method practiced within the new media art context. I present a case study on an international festival, PixelACHE 2005, which was organized by and for new media artists and served as a platform for demonstrations of new media projects and as a meeting place for experimental new media artists. In this article I discuss how new media artists adapted the open source ideology. Open source is seen both as a more liberal method of distribution and as an open joint creative process. I was particularly interested in what kind of motives the new media artists had for taking part in the PixelACHE festival and the joint artistic creative process. In my analysis, I found four different groups that have diverse motives for participating in open source art projects. One group contains the key persons who use the open source network as an important reference in their professional image. Members of the second and third group are new media artists who earn their main income in either the public or corporate sector and use open source projects as a learning platform. The fourth group comprises young enthusiasts who are seeking jobs and professional networking opportunities in the open source network.

  18. OMPC: an open-source MATLAB®-to-Python compiler

    Directory of Open Access Journals (Sweden)

    Peter Jurica

    2009-02-01

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

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

    Science.gov (United States)

    Jurica, Peter; van Leeuwen, Cees

    2009-01-01

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

  20. OMPC: an Open-Source MATLAB®-to-Python Compiler

    Science.gov (United States)

    Jurica, Peter; van Leeuwen, Cees

    2008-01-01

    Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

  1. The Efficient Utilization of Open Source Information

    Energy Technology Data Exchange (ETDEWEB)

    Baty, Samuel R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Intelligence and Systems Analysis

    2016-08-11

    These are a set of slides on the efficient utilization of open source information. Open source information consists of a vast set of information from a variety of sources. Not only does the quantity of open source information pose a problem, the quality of such information can hinder efforts. To show this, two case studies are mentioned: Iran and North Korea, in order to see how open source information can be utilized. The huge breadth and depth of open source information can complicate an analysis, especially because open information has no guarantee of accuracy. Open source information can provide key insights either directly or indirectly: looking at supporting factors (flow of scientists, products and waste from mines, government budgets, etc.); direct factors (statements, tests, deployments). Fundamentally, it is the independent verification of information that allows for a more complete picture to be formed. Overlapping sources allow for more precise bounds on times, weights, temperatures, yields or other issues of interest in order to determine capability. Ultimately, a "good" answer almost never comes from an individual, but rather requires the utilization of a wide range of skill sets held by a team of people.

  2. 'Open-sourcing' personal learning

    OpenAIRE

    Fiedler, Sebastian H. D.

    2014-01-01

    This article offers a critical reflection on the contemporary Open Educational Resource (OER) movement, its unquestioned investment in a collective 'content fetish' and an educational 'problem description' that focuses on issues of scarcity, access, and availability of quality materials. It also argues that OER proponents fail to take notice of historically new forms of learning activity emerging within the unfolding digital transformation of our global society. The article reviews some descr...

  3. An 'open source' networked identity

    DEFF Research Database (Denmark)

    Larsen, Malene Charlotte

    2016-01-01

    friendship, but also an important part of their self-presentation online. It examines why these emotional statements are almost always publicly available – or even strategically and intentionally placed on the young people’s profiles. In relation to this, it is argued that young people – through...... their emotional communicative actions – are not only staging their own identity, but are co-constructors of each other’s identities, which the author characterises as an “open source”, networked identity....

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  5. 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.

  6. Closed-loop, open-source electrophysiology

    Directory of Open Access Journals (Sweden)

    John D Rolston

    2010-09-01

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

  7. Lessons from an Open Source Business

    Directory of Open Access Journals (Sweden)

    Fred Dixon

    2011-04-01

    Full Text Available Creating a successful company is difficult; but creating a successful company, a successful open source project, and a successful ecosystem all at the same time is much more difficult. This article takes a retrospective look at some of the lessons we have learned in building BigBlueButton, an open source web conferencing system for distance education, and in building Blindside Networks, a company following the traditional business model of providing support and services to paying customers. Our main message is that the focus must be on creating a successful open source project first, for without it, no company in the ecosystem can flourish.

  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. Freeing Worldview's development process: Open source everything!

    Science.gov (United States)

    Gunnoe, T.

    2016-12-01

    Freeing your code and your project are important steps for creating an inviting environment for collaboration, with the added side effect of keeping a good relationship with your users. NASA Worldview's codebase was released with the open source NOSA (NASA Open Source Agreement) license in 2014, but this is only the first step. We also have to free our ideas, empower our users by involving them in the development process, and open channels that lead to the creation of a community project. There are many highly successful examples of Free and Open Source Software (FOSS) projects of which we can take note: the Linux kernel, Debian, GNOME, etc. These projects owe much of their success to having a passionate mix of developers/users with a great community and a common goal in mind. This presentation will describe the scope of this openness and how Worldview plans to move forward with a more community-inclusive approach.

  10. On the Ambiguity of Commercial Open Source

    Directory of Open Access Journals (Sweden)

    Lucian Luca

    2006-01-01

    Full Text Available . Open source and commercial applications used to be two separate worlds. The former was the work of amateurs who had little interest in making a profit, while the latter was only profit oriented and was produced by big companies. Nowadays open source is a threat and an opportunity to serious businesses of all kinds, generating good profits while delivering low costs products to customers. The competition between commercial and open source software has impacted the industry and the society as a whole. But in the last years, the markets for commercial and open source software are converging rapidly and it is interesting to resume and discuss the implications of this new paradigm, taking into account arguments pro and against it.

  11. Deep Learning in Open Source Learning Streams

    DEFF Research Database (Denmark)

    Kjærgaard, Thomas

    2016-01-01

    This chapter presents research on deep learning in a digital learning environment and raises the question if digital instructional designs can catalyze deeper learning than traditional classroom teaching. As a theoretical point of departure the notion of ‘situated learning’ is utilized...... and contrasted to the notion of functionalistic learning in a digital context. The mechanism that enables deep learning in this context is ‘The Open Source Learning Stream’. ‘The Open Source Learning Stream’ is the notion of sharing ‘learning instances’ in a digital space (discussion board, Facebook group......, unistructural, multistructural or relational learning. The research concludes that ‘The Open Source Learning Stream’ can catalyze deep learning and that there are four types of ‘Open Source Learning streams’; individual/ asynchronous, individual/synchronous, shared/asynchronous and shared...

  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. The Spaces of Open-Source Politics

    DEFF Research Database (Denmark)

    Husted, Emil; Plesner, Ursula

    constructed by the Alternative as techniques for practicing open-source politics, and observe that physical and digital spaces create a vacillation between openness and closure. This vacillation produces a dialectic relationship between practices of imagination and affirmation. Curiously, it seems...

  14. Open Source Interoperability: It's More than Technology

    Directory of Open Access Journals (Sweden)

    Dominic Sartorio

    2008-01-01

    Full Text Available The Open Solutions Alliance is a consortium of leading commercial open source vendors, integrators and end users dedicated to the growth of open source based solutions in the enterprise. We believe Linux and other infrastructure software, such as Apache, has become mainstream, and packaged solutions represent the next great growth opportunity. However some unique challenges can temper that opportunity. These challenges include getting the word out about the maturity and enterprise-readiness of those solutions, ensuring interoperability both with each other and with other proprietary and legacy solutions, and ensuring healthy collaboration between vendors and their respective customer and developer communities.

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

    Science.gov (United States)

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

    2014-10-03

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

  16. [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).

  17. Open-source intelligence and privacy by design

    NARCIS (Netherlands)

    Koops, B.J.; Hoepman, J.H.; Leenes, R.

    2013-01-01

    As demonstrated by other papers on this issue, open-source intelligence (OSINT) by state authorities poses challenges for privacy protection and intellectual-property enforcement. A possible strategy to address these challenges is to adapt the design of OSINT tools to embed normative requirements, i

  18. Virtual Machine for Computer Forensics - the Open Source Perspective

    Science.gov (United States)

    Bem, Derek

    In this paper we discuss the potential role of virtual environments in the analysis phase of computer forensics investigations. We argue that commercial closed source computer forensics software has certain limitations, and we propose a method which may lead to gradual shift to open source software (OSS). A brief overview of virtual environments and open source software tools is presented and discussed. Further we identify current limitations of virtual environments leading to the conclusion that the method is very promising, but at this point in time it can not replace conventional techniques of computer forensics analysis. We demonstrate that using Virtual Machines (VM) in Linux environments can complement the conventional techniques, and often can bring faster and verifiable results not dependent on proprietary, close source tools.

  19. HERAFitter. Open source QCD fit project

    Energy Technology Data Exchange (ETDEWEB)

    Alekhin, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Institute for High Energy Physics, Protvino, Moscow Region (Russian Federation); Behnke, O.; Borroni, S.; Britzger, D.; Camarda, S.; Gizhko, A.; Glazov, A.; Guzzi, M.; Kowalski, H.; Kuprash, O.; Levonian, S.; Lipka, K.; Myronenko, V.; Naumann-Emme, S.; Pirumov, H.; Placakyte, R.; Radescu, V.; Schoerner-Sadenius, T.; Shushkevich, S.; Starovoitov, P.; Turkot, O.; Vargas, A.; Wichmann, K. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Belov, P. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); St. Petersburg State University, Department of Physics, St. Petersburg (Russian Federation); Botje, M. [Nikhef, Amsterdam (Netherlands); Cooper-Sarkar, A.M. [University of Oxford, Department of Physics, Oxford (United Kingdom); Daum, K. [Universitaet Wuppertal, Fachbereich C, Wuppertal (Germany); Universitaet Wuppertal, Rechenzentrum, Wuppertal (Germany); Diaconu, C. [Aix Marseille Universite, CNRS/IN2P3, CPPM UMR 7346, Marseille (France); Feltesse, J. [CEA, DSM/Irfu, CE-Saclay, Gif-sur-Yvette (France); Guffanti, A. [University of Copenhagen, Niels Bohr International Academy and Discovery Center, Niels Bohr Institute, Copenhagen (Denmark); Hautmann, F. [University of Southampton, School of Physics and Astronomy, Southampton (United Kingdom); Rutherford Appleton Laboratory, Chilton (United Kingdom); University of Oxford, Department of Theoretical Physics, Oxford (United Kingdom); Jung, A. [FERMILAB, Batavia, IL (United States); Jung, H. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Universiteit Antwerpen, Elementaire Deeltjes Fysica, Antwerp (Belgium); Kolesnikov, V.; Sadykov, R.; Sapronov, A. [Joint Institute for Nuclear Research (JINR), Dubna, Moscow Region (Russian Federation); Kusina, A.; Olness, F. [Southern Methodist University, Dallas, TX (United States); Lobodzinski, B. [Werner Heisenberg Institut, Max Planck Institut fuer Physik, Muenchen (Germany); Lohwasser, K. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Luszczak, A. [T. Kosciuszko University of Technology, Krakow (Poland); Malaescu, B. [UPMC and Universite, Paris-Diderot and CNRS/IN2P3, Laboratoire de Physique Nucleaire et de Hautes Energies, Paris (France); McNulty, R. [University College Dublin, Dublin 4 (Ireland); Nowak, K. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); University of Oxford, Department of Physics, Oxford (United Kingdom); Perez, E. [CERN, European Organization for Nuclear Research, Geneva (Switzerland); Rabbertz, K. [Institut fuer Experimentelle Kernphysik, Karlsruhe (Germany); Salam, G.P. [CERN, PH-TH, Geneva 23 (Switzerland); Leave from LPTHE, CNRS UMR 7589, UPMC Univ. Paris 6, Paris (France); Schoening, A. [Universitaet Heidelberg, Physikalisches Institut, Heidelberg (Germany); Slominski, W. [Jagiellonian University, Institute of Physics, Krakow (Poland); Spiesberger, H. [Johannes-Gutenberg-Universitaet, PRISMA Cluster of Excellence, Institut fuer Physik (WA THEP), Mainz (Germany); Sutton, M. [University of Sussex, Department of Physics and Astronomy, Brighton (United Kingdom); Tomaszewska, J. [Warsaw University of Technology, Faculty of Physics, Warsaw (Poland); Watt, G. [Durham University, Institute for Particle Physics Phenomenology, Durham (United Kingdom)

    2015-07-15

    HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton-proton deep inelastic scattering and proton-proton (proton-antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodological options for carrying out PDF fits and plotting tools to help to visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study the impact of new precise measurements from hadron colliders. This paper describes the general structure of HERAFitter and its wide choice of options. (orig.)

  20. XNAT Central: Open sourcing imaging research data.

    Science.gov (United States)

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

    2016-01-01

    XNAT Central is a publicly accessible medical imaging data repository based on the XNAT open-source imaging informatics platform. It hosts a wide variety of research imaging data sets. The primary motivation for creating XNAT Central was to provide a central repository to host and provide access to a wide variety of neuroimaging data. In this capacity, XNAT Central hosts a number of data sets from research labs and investigative efforts from around the world, including the OASIS Brains imaging studies, the NUSDAST study of schizophrenia, and more. Over time, XNAT Central has expanded to include imaging data from many different fields of research, including oncology, orthopedics, cardiology, and animal studies, but continues to emphasize neuroimaging data. Through the use of XNAT's DICOM metadata extraction capabilities, XNAT Central provides a searchable repository of imaging data that can be referenced by groups, labs, or individuals working in many different areas of research. The future development of XNAT Central will be geared towards greater ease of use as a reference library of heterogeneous neuroimaging data and associated synthetic data. It will also become a tool for making data available supporting published research and academic articles. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. 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…

  2. Making a Business out of Open Source

    CERN Document Server

    CERN. Geneva

    2007-01-01

    Marc Fleury, a physicist by training, retired in his thirties after selling the company JBoss, which made an open-source application server, to Red Hat. He will talk about the various business models of open source software. From leveraging available open source software and casual contributions, to on-ramp models and subscription models, various business models have been explored and function. Not all models work for all software fields and business types. He will review those business models in context and survey "state-of-the-art" economic models for open source software production. Speaker Bio: Marc Fleury is the creator of JBoss, an open-source Java application server. Fleury holds a degree in mathematics and a Doctorate in physics from the École Polytechnique in Paris and a Master in Theoretical Physics from the École Normale. He worked in France for Sun Microsystems before moving to the United States where he has worked on various Java projects. Fleury's research interest focused on middleware, a...

  3. 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.

  4. A prospective international cooperative information technology platform built using open-source tools for improving the access to and safety of bone marrow transplantation in low- and middle-income countries.

    Science.gov (United States)

    Agarwal, Rajat Kumar; Sedai, Amit; Dhimal, Sunil; Ankita, Kumari; Clemente, Luigi; Siddique, Sulman; Yaqub, Naila; Khalid, Sadaf; Itrat, Fatima; Khan, Anwar; Gilani, Sarah Khan; Marwah, Priya; Soni, Rajpreet; Missiry, Mohamed El; Hussain, Mohamed Hamed; Uderzo, Cornelio; Faulkner, Lawrence

    2014-01-01

    Jagriti Innovations developed a collaboration tool in partnership with the Cure2Children Foundation that has been used by health professionals in Italy, Pakistan, and India for the collaborative management of patients undergoing bone marrow transplantation (BMT) for thalassemia major since August 2008. This online open-access database covers data recording, analyzing, and reporting besides enabling knowledge exchange, telemedicine, capacity building, and quality assurance. As of February 2014, over 2400 patients have been registered and 112 BMTs have been performed with outcomes comparable to international standards, but at a fraction of the cost. This approach avoids medical emigration and contributes to local healthcare strengthening and competitiveness. This paper presents the experience and clinical outcomes associated with the use of this platform built using open-source tools and focusing on a locally pertinent tertiary care procedure-BMT. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  5. Open source intelligence, open social intelligence and privacy by design

    OpenAIRE

    Casanovas, Pompeu; Royal Melbourne Institute of Technology (Austràlia). Centre for Applied Social Research

    2014-01-01

    Ponència presentada a European Conference on Social Intelligence (ECSI-2014) OSINT stands for Open Source Intelligence, (O)SI for (Open) Social Intelligence, PbD for Privacy by Design. The CAPER project has built an OSINT solution oriented to the prevention of organized crime. How to balance freedom and security? This position paper describes a way to embed the legal and ethical issues raised by the General Data Reform Package (GDRP) in Europe into this kind of surveillance platforms. It f...

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Chenlong Zhang

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  10. Pioneering SESAME light source officially opened

    CERN Multimedia

    Caraban Gonzalez, Noemi

    2017-01-01

    Allan, Jordan, 16 May 2017. The SESAME light source was today officially opened by His Majesty King Abdullah II. An intergovernmental organization, SESAME is the first regional laboratory for the Middle East and neighbouring regions The laboratory’s official opening ushers in a new era of research covering fields ranging from medicine and biology, through materials science, physics and chemistry to healthcare, the environment, agriculture and archaeology.

  11. Developing a Successful Open Source Training Model

    Directory of Open Access Journals (Sweden)

    Belinda Lopez

    2010-01-01

    Full Text Available Training programs for open source software provide a tangible, and sellable, product. A successful training program not only builds revenue, it also adds to the overall body of knowledge available for the open source project. By gathering best practices and taking advantage of the collective expertise within a community, it may be possible for a business to partner with an open source project to build a curriculum that promotes the project and supports the needs of the company's training customers. This article describes the initial approach used by Canonical, the commercial sponsor of the Ubuntu Linux operating system, to engage the community in the creation of its training offerings. We then discuss alternate curriculum creation models and some of the conditions that are necessary for successful collaboration between creators of existing documentation and commercial training providers.

  12. 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 ...

  13. 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.

  14. Open Source in Canada's Public Sector

    Directory of Open Access Journals (Sweden)

    Evan Leibovitch

    2008-03-01

    Full Text Available The story of the growth of open source use in Canada has been far more a matter of evolution than revolution, so quiet in its pace that its progress has been difficult to measure. This has posed many challenges to Canadian open source advocates in their efforts to ensure that their country does not lag behind the rest of the world in understanding the social and business benefits open source provides. Perhaps some of the leading soldiers in the trenches might be our civil servants who protect the public purse. In addition to managing and minimizing the costs of delivering necessary services, public sector projects should also advance the social good through the delicate balance of transparency and efficiency.

  15. Open Source Development of Tangible Products - from a business perspective

    DEFF Research Database (Denmark)

    Fjeldsted, Asta S.; Adalsteinsdottir, Gudrun; Howard, Thomas J.

    This article’s objective is to set up some foundational theory and practices for Open Source Development (OSD) of tangible products, a novel and emerging approach derived from the well-known open source software movement. As a contribution to the first steps of research in this discipline a clear...... definition for OSD is proposed and used to describe the key elements of a suggested OSD Process model. Several case studies are analysed to create an Archetypal Business Model characterising OSD of tangible products and the possibilities and delimitations within. Furthermore, strategic tools are suggested...

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

    Directory of Open Access Journals (Sweden)

    O'Boyle Noel M

    2011-10-01

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

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

    Science.gov (United States)

    2011-01-01

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

  18. 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

  19. DEIMOS – an Open Source Image Database

    Directory of Open Access Journals (Sweden)

    M. Blazek

    2011-12-01

    Full Text Available The DEIMOS (DatabasE of Images: Open Source is created as an open-source database of images and videos for testing, verification and comparing of various image and/or video processing techniques such as enhancing, compression and reconstruction. The main advantage of DEIMOS is its orientation to various application fields – multimedia, television, security, assistive technology, biomedicine, astronomy etc. The DEIMOS is/will be created gradually step-by-step based upon the contributions of team members. The paper is describing basic parameters of DEIMOS database including application examples.

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

    Science.gov (United States)

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

    2013-12-01

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

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

    Science.gov (United States)

    2011-01-01

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

  2. Open source, open standards, and health care information systems.

    Science.gov (United States)

    Reynolds, Carl J; Wyatt, Jeremy C

    2011-02-17

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

  3. The SAMI2 Open Source Project

    Science.gov (United States)

    Huba, J. D.; Joyce, G.

    2001-05-01

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

  4. 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.

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

    Science.gov (United States)

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

    2015-12-01

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

  6. FlowCal: A User-Friendly, Open Source Software Tool for Automatically Converting Flow Cytometry Data from Arbitrary to Calibrated Units.

    Science.gov (United States)

    Castillo-Hair, Sebastian M; Sexton, John T; Landry, Brian P; Olson, Evan J; Igoshin, Oleg A; Tabor, Jeffrey J

    2016-07-15

    Flow cytometry is widely used to measure gene expression and other molecular biological processes with single cell resolution via fluorescent probes. Flow cytometers output data in arbitrary units (a.u.) that vary with the probe, instrument, and settings. Arbitrary units can be converted to the calibrated unit molecules of equivalent fluorophore (MEF) using commercially available calibration particles. However, there is no convenient, nonproprietary tool available to perform this calibration. Consequently, most researchers report data in a.u., limiting interpretation. Here, we report a software tool named FlowCal to overcome current limitations. FlowCal can be run using an intuitive Microsoft Excel interface, or customizable Python scripts. The software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Additionally, FlowCal automatically gates data, calculates common statistics, and produces publication quality plots. We validate FlowCal by calibrating a.u. measurements of E. coli expressing superfolder GFP (sfGFP) collected at 10 different detector sensitivity (gain) settings to a single MEF value. Additionally, we reduce day-to-day variability in replicate E. coli sfGFP expression measurements due to instrument drift by 33%, and calibrate S. cerevisiae Venus expression data to MEF units. Finally, we demonstrate a simple method for using FlowCal to calibrate fluorescence units across different cytometers. FlowCal should ease the quantitative analysis of flow cytometry data within and across laboratories and facilitate the adoption of standard fluorescence units in synthetic biology and beyond.

  7. Web Server Security on Open Source Environments

    Science.gov (United States)

    Gkoutzelis, Dimitrios X.; Sardis, Manolis S.

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

  8. Lighting the World: the first application of an open source, spatial electrification tool (OnSSET) on Sub-Saharan Africa

    Science.gov (United States)

    Mentis, Dimitrios; Howells, Mark; Rogner, Holger; Korkovelos, Alexandros; Arderne, Christopher; Zepeda, Eduardo; Siyal, Shahid; Taliotis, Costantinos; Bazilian, Morgan; de Roo, Ad; Tanvez, Yann; Oudalov, Alexandre; Scholtz, Ernst

    2017-08-01

    In September 2015, the United Nations General Assembly adopted Agenda 2030, which comprises a set of 17 Sustainable Development Goals (SDGs) defined by 169 targets. ‘Ensuring access to affordable, reliable, sustainable and modern energy for all by 2030’ is the seventh goal (SDG7). While access to energy refers to more than electricity, the latter is the central focus of this work. According to the World Bank’s 2015 Global Tracking Framework, roughly 15% of the world’s population (or 1.1 billion people) lack access to electricity, and many more rely on poor quality electricity services. The majority of those without access (87%) reside in rural areas. This paper presents results of a geographic information systems approach coupled with open access data. We present least-cost electrification strategies on a country-by-country basis for Sub-Saharan Africa. The electrification options include grid extension, mini-grid and stand-alone systems for rural, peri-urban, and urban contexts across the economy. At low levels of electricity demand there is a strong penetration of standalone technologies. However, higher electricity demand levels move the favourable electrification option from stand-alone systems to mini grid and to grid extensions.

  9. 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...

  10. Crime analysis using open source information

    DEFF Research Database (Denmark)

    Nizamani, Sarwat; Memon, Nasrullah; Shah, Azhar Ali;

    2015-01-01

    In this paper, we present a method of crime analysis from open source information. We employed un-supervised methods of data mining to explore the facts regarding the crimes of an area of interest. The analysis is based on well known clustering and association techniques. The results show...

  11. Of Birkenstocks and Wingtips: Open Source Licenses

    Science.gov (United States)

    Gandel, Paul B.; Wheeler, Brad

    2005-01-01

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

  12. 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...

  13. 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…

  14. Scribus – Open Source Desktop Publishing

    Directory of Open Access Journals (Sweden)

    Christoph Kaindel

    2010-12-01

    Full Text Available Professionelle Layout-Programme wie Quark XPress oder Adobe InDesign sind unerschwinglich teuer und daher im privaten oder Schulbereich kaum legal verfügbar. Das Open Source Programm Scribus stellt hier eine brauchbare Alternative dar.

  15. CONTENT MANAGEMENT SYSTEMS (CMS OPEN SOURCE WEBSITES

    Directory of Open Access Journals (Sweden)

    Marinela Lăzărică

    2013-01-01

    Full Text Available Firms need flexible software applications, which may be adaptable to dynamic changes of the modern business environment; they also need more control over their software costs, security and trust in purchased and implemented software. Moreover, they need to be free of individual software vendors and license costs for the software, etc. The solution of this problem consisted in open source applications and open source technology has proven that it can often provide high-quality software being a challenge for old models of software development and maintenance. The first content management system was announced in the late 90s. The offer of such software systems is varied and each of them has its own characteristics. This requires a comparative analysis of viable open-source systems in order to choose the most appropriate imposed goals. In this context, the paper illustrates the use of an open source content management system, like WordPress, to develop a content site in design of websites and analyzeits characteristics.

  16. Understanding open source communities: an organizational perspective

    NARCIS (Netherlands)

    Van Wendel de Joode, R.

    2005-01-01

    Open source communities are groups of sometimes hundreds if not thousands of individuals with different interests, backgrounds and motives. Many participants are volunteers, who are not paid to take part in the communities. Furthermore, many never get to meet each other in real life. They meet virtu

  17. 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...

  18. Crime analysis using open source information

    DEFF Research Database (Denmark)

    Nizamani, Sarwat; Memon, Nasrullah; Shah, Azhar Ali

    2015-01-01

    In this paper, we present a method of crime analysis from open source information. We employed un-supervised methods of data mining to explore the facts regarding the crimes of an area of interest. The analysis is based on well known clustering and association techniques. The results show...

  19. Open-source syringe pump library.

    Science.gov (United States)

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

    2014-01-01

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

  20. Open-source syringe pump library.

    Directory of Open Access Journals (Sweden)

    Bas Wijnen

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

  1. Open source OCR framework using mobile devices

    Science.gov (United States)

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

    2008-02-01

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

  2. Comparison of open-source linear programming solvers.

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-01

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

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

    Science.gov (United States)

    Krishnamurthy, M.

    2008-01-01

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

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

    Science.gov (United States)

    Krishnamurthy, M.

    2008-01-01

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

  5. Connecting UML and VDM++ with Open Tool Support

    DEFF Research Database (Denmark)

    Lausdahl, Kenneth; Listrup, Hans Kristian; Larsen, Peter Gorm

    2009-01-01

    Most formal method notations are text based, while tools used in industry often use graphical notations, such as UML. This paper demonstrates how the power of both approaches can be combined by providing the automatic translation of VDM++ models to and from UML. The translation is implemented as ...... as a plugin for the popular Eclipse development environment by the open-source Overture initiative. Both UML class diagrams and sequence diagrams can be translated, the latter enabling the novel ability to link with the combinatorial test facility of Overture....

  6. Measuring Modularity in Open Source Code Bases

    Directory of Open Access Journals (Sweden)

    Roberto Milev

    2009-03-01

    Full Text Available Modularity of an open source software code base has been associated with growth of the software development community, the incentives for voluntary code contribution, and a reduction in the number of users who take code without contributing back to the community. As a theoretical construct, modularity links OSS to other domains of research, including organization theory, the economics of industry structure, and new product development. However, measuring the modularity of an OSS design has proven difficult, especially for large and complex systems. In this article, we describe some preliminary results of recent research at Carleton University that examines the evolving modularity of large-scale software systems. We describe a measurement method and a new modularity metric for comparing code bases of different size, introduce an open source toolkit that implements this method and metric, and provide an analysis of the evolution of the Apache Tomcat application server as an illustrative example of the insights gained from this approach. Although these results are preliminary, they open the door to further cross-discipline research that quantitatively links the concerns of business managers, entrepreneurs, policy-makers, and open source software developers.

  7. OpenFOAM: Open source CFD in research and industry

    Directory of Open Access Journals (Sweden)

    Hrvoje Jasak

    2009-12-01

    Full Text Available The current focus of development in industrial Computational Fluid Dynamics (CFD is integration of CFD into Computer-Aided product development, geometrical optimisation, robust design and similar. On the other hand, in CFD research aims to extend the boundaries of practical engineering use in “non-traditional” areas. Requirements of computational flexibility and code integration are contradictory: a change of coding paradigm, with object orientation, library components, equation mimicking is proposed as a way forward. This paper describes OpenFOAM, a C++ object oriented library for Computational Continuum Mechanics (CCM developed by the author. Efficient and flexible implementation of complex physical models is achieved by mimicking the form of partial differential equation in software, with code functionality provided in library form. Open Source deployment and development model allows the user to achieve desired versatility in physical modeling without the sacrifice of complex geometry support and execution efficiency.

  8. Open Plot Project: an open-source toolkit for 3-D structural data analysis

    Directory of Open Access Journals (Sweden)

    S. Tavani

    2011-05-01

    Full Text Available In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis.

    The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software.

    The software (for both Windows and Linux O.S., the User Manual, a set of example movies (complementary to the User Manual, and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

  9. 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

  10. Deep Learning in Open Source Learning Streams

    DEFF Research Database (Denmark)

    Kjærgaard, Thomas

    2016-01-01

    This chapter presents research on deep learning in a digital learning environment and raises the question if digital instructional designs can catalyze deeper learning than traditional classroom teaching. As a theoretical point of departure the notion of ‘situated learning’ is utilized...... and contrasted to the notion of functionalistic learning in a digital context. The mechanism that enables deep learning in this context is ‘The Open Source Learning Stream’. ‘The Open Source Learning Stream’ is the notion of sharing ‘learning instances’ in a digital space (discussion board, Facebook group......, Twitter hashtags etc.). The ‘learning instances’ are described as mediated signs of learning expressed through text in the stream that is further developed by peers and by the teacher. The expressions of ‘learning instances’ are analyzed and categorized according to whether it expresses prestructural...

  11. 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...

  12. 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...

  13. An Open-Source Microscopic Traffic Simulator

    CERN Document Server

    Treiber, Martin; 10.1109/MITS.2010.939208

    2010-01-01

    We present the interactive Java-based open-source traffic simulator available at www.traffic-simulation.de. In contrast to most closed-source commercial simulators, the focus is on investigating fundamental issues of traffic dynamics rather than simulating specific road networks. This includes testing theories for the spatiotemporal evolution of traffic jams, comparing and testing different microscopic traffic models, modeling the effects of driving styles and traffic rules on the efficiency and stability of traffic flow, and investigating novel ITS technologies such as adaptive cruise control, inter-vehicle and vehicle-infrastructure communication.

  14. Integrated open source mine workers compensation system

    CSIR Research Space (South Africa)

    Coetzee, L

    2006-08-01

    Full Text Available the solution using open-source technologies. Previously the department had already ADMINISTRATIO PUBLICA - VOL 14 NO 2 AUGUST 2006 126 invested heavily in Oracle as persistence store. It was therefore decided to continue with Oracle as back-end store, even... (the Oracle database) was obtained using JDBC. To support collaboration between the distributed users (each with different tasks and requirements) a role-based access control module was developed. Each registered user has various roles assigned...

  15. Datacube Services in Action, Using Open Source and Open Standards

    Science.gov (United States)

    Baumann, P.; Misev, D.

    2016-12-01

    Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

  16. Pentaho Business Analytics: a Business Intelligence Open Source Alternative

    Directory of Open Access Journals (Sweden)

    Diana TÂRNĂVEANU

    2012-10-01

    Full Text Available Most organizations strive to obtain fast, interactive and insightful analytics in order to fundament the most effective and profitable decisions. They need to incorporate huge amounts of data in order to run analysis based on queries and reports with collaborative capabilities. The large variety of Business Intelligence solutions on the market makes it very difficult for organizations to select one and evaluate the impact of the selected solution to the organization. The need of a strategy to help organization chose the best solution for investment emerges. In the past, Business Intelligence (BI market was dominated by closed source and commercial tools, but in the last years open source solutions developed everywhere. An Open Source Business Intelligence solution can be an option due to time-sensitive, sprawling requirements and tightening budgets. This paper presents a practical solution implemented in a suite of Open Source Business Intelligence products called Pentaho Business Analytics, which provides data integration, OLAP services, reporting, dashboarding, data mining and ETL capabilities. The study conducted in this paper suggests that the open source phenomenon could become a valid alternative to commercial platforms within the BI context.

  17. Data Analysis with Open Source Tools

    CERN Document Server

    Janert, Philipp

    2010-01-01

    Collecting data is relatively easy, but turning raw information into something useful requires that you know how to extract precisely what you need. With this insightful book, intermediate to experienced programmers interested in data analysis will learn techniques for working with data in a business environment. You'll learn how to look at data to discover what it contains, how to capture those ideas in conceptual models, and then feed your understanding back into the organization through business plans, metrics dashboards, and other applications. Along the way, you'll experiment with conce

  18. 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.

  19. 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.

  20. Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field.

    Science.gov (United States)

    Wójcikowski, Maciej; Zielenkiewicz, Piotr; Siedlecki, Pawel

    2015-01-01

    There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package. We here describe the Open Drug Discovery Toolkit (ODDT), which aims to fulfill the need for comprehensive and open source drug discovery software. The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. We here present three use cases for ODDT in common tasks in computer-aided drug discovery. Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT's source code, additional examples and documentation are available on GitHub (https://github.com/oddt/oddt).

  1. Search Analytics: Automated Learning, Analysis, and Search with Open Source

    Science.gov (United States)

    Hundman, K.; Mattmann, C. A.; Hyon, J.; Ramirez, P.

    2016-12-01

    The sheer volume of unstructured scientific data makes comprehensive human analysis impossible, resulting in missed opportunities to identify relationships, trends, gaps, and outliers. As the open source community continues to grow, tools like Apache Tika, Apache Solr, Stanford's DeepDive, and Data-Driven Documents (D3) can help address this challenge. With a focus on journal publications and conference abstracts often in the form of PDF and Microsoft Office documents, we've initiated an exploratory NASA Advanced Concepts project aiming to use the aforementioned open source text analytics tools to build a data-driven justification for the HyspIRI Decadal Survey mission. We call this capability Search Analytics, and it fuses and augments these open source tools to enable the automatic discovery and extraction of salient information. In the case of HyspIRI, a hyperspectral infrared imager mission, key findings resulted from the extractions and visualizations of relationships from thousands of unstructured scientific documents. The relationships include links between satellites (e.g. Landsat 8), domain-specific measurements (e.g. spectral coverage) and subjects (e.g. invasive species). Using the above open source tools, Search Analytics mined and characterized a corpus of information that would be infeasible for a human to process. More broadly, Search Analytics offers insights into various scientific and commercial applications enabled through missions and instrumentation with specific technical capabilities. For example, the following phrases were extracted in close proximity within a publication: "In this study, hyperspectral images…with high spatial resolution (1 m) were analyzed to detect cutleaf teasel in two areas. …Classification of cutleaf teasel reached a users accuracy of 82 to 84%." Without reading a single paper we can use Search Analytics to automatically identify that a 1 m spatial resolution provides a cutleaf teasel detection users accuracy of 82

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

    Science.gov (United States)

    Camargo Jr, Kenneth Rochel de; Coeli, Claudia Medina

    2015-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Kenneth Rochel de Camargo Jr.

    2015-02-01

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

  4. Deploying and Configuring the ODI Agent as a Windows Service by the Open Source Tools of YAJSW%使用开源工具YAJSW将ODIAgent发布为Windows系统服务

    Institute of Scientific and Technical Information of China (English)

    孙玮

    2015-01-01

    Considering the problems of starting ODI agent manually,such as the complex and cumbersome methods of starting up,and the lack of convenience for ODI data integration projects in need of full day operation and a lot of manual intervention,we proposed the use of open source tools YAJSW(Yet Another Java Service Wrapper),which can deploy the ODI agent as a windows service.In this way,we can start or stop the agent directly in the window,and the agent can be started up automatically when the server restarted.%针对在ODI中手动启动Agent的方法复杂、繁琐,对于需要全天运行的ODI数据集成项目来说非常不方便,需要大量的人工干预,本文提出了使用开源工具YAJSW(Yet Another Java Service Wrapper)将ODI Agent发布为Windows服务,直接在Windows的服务窗口中实现对所发布的Agent进行启停和系统重启后服务的自动启动。

  5. 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....

  6. Developing Open Source System Expertise in Europe

    DEFF Research Database (Denmark)

    Nyborg, Mads; Gustafsson, Finn; Christensen, Jørgen Erik

    2011-01-01

    are interested in knowing which factors play a role in information systems and what the similarities and differences between the various national approaches in open source software systems and techniques are. The event forms a unique opportunity in promoting active learning in an international environment....... Students get experience working in teams across country boundaries. In the paper we will describe the structure and our experiences from participating in this IP with relation to the CDIO initiative. Finally we draw conclusions and give our recommendations based on those....

  7. Google and Open Source (Keynote Talk)

    OpenAIRE

    DiBona, Chris

    2015-01-01

    In this talk Chris DiBona will review Google's use of open source projects and the history of prominent releases like Android, Chromium, Angular.js and some 3500 other projects (though not all of them will be surveyed!). Keeping such releases on track and efficient and, in some cases, retiring them has been his focus since he started at the company. He'll review the various ways Google supports the worldwide community of software developers that it has derived so much value from. Specifically...

  8. New Open Source E-Learning Book

    Directory of Open Access Journals (Sweden)

    TOJDE

    2004-04-01

    Full Text Available We would like to promote and introduce a new book that Terry Anderson and Fathi Elloumi have edited from Athabasca University. It is entitled Theory and Practice of Online Learning. The book is licensed for educational and non commercial use, download and printing under a Creative Commons license. We have released it as open source so that it can be more easily accessed by professionals and hopefully used in coursework by learners throughout the world. During the two weeks since its release in mid February over 4300 individual downloads were made of the whole book, in addition to many for individualchapters.

  9. Open Source Energy Simulation for Elementary School

    CERN Document Server

    Lye, Sze Yee

    2012-01-01

    With the interactivity and multiple representation features, computer simulations lend itself to the guided inquiry learning. However, these simulations are usually designed for post-elementary students. Thus, the aim of this study is to investigate how the use of guided inquiry approach with customized energy simulation can improve students' understanding of this topic. In this ongoing research, the case study is adopted. In the first phase of the study, we have modified open source energy simulation based on principles for reducing extraneous processing, existing energy simulation and guided inquiry approach. The modified simulation is sent to teachers for evaluation and the feedback is encouraging. In the next phase of the study, the guided inquiry lesson package involving the energy simulation would be designed and deployed in an elementary classroom. Multiple data sources would be collected to seek a deeper understanding on how this learning package can possibly impact students' understanding of the phys...

  10. MicMac GIS application: free open source

    Science.gov (United States)

    Duarte, L.; Moutinho, O.; Teodoro, A.

    2016-10-01

    The use of Remotely Piloted Aerial System (RPAS) for remote sensing applications is becoming more frequent as the technologies on on-board cameras and the platform itself are becoming a serious contender to satellite and airplane imagery. MicMac is a photogrammetric tool for image matching that can be used in different contexts. It is an open source software and it can be used as a command line or with a graphic interface (for each command). The main objective of this work was the integration of MicMac with QGIS, which is also an open source software, in order to create a new open source tool applied to photogrammetry/remote sensing. Python language was used to develop the application. This tool would be very useful in the manipulation and 3D modelling of a set of images. The main objective was to create a toolbar in QGIS with the basic functionalities with intuitive graphic interfaces. The toolbar is composed by three buttons: produce the points cloud, create the Digital Elevation Model (DEM) and produce the orthophoto of the study area. The application was tested considering 35 photos, a subset of images acquired by a RPAS in the Aguda beach area, Porto, Portugal. They were used in order to create a 3D terrain model and from this model obtain an orthophoto and the corresponding DEM. The code is open and can be modified according to the user requirements. This integration would be very useful in photogrammetry and remote sensing community combined with GIS capabilities.

  11. 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.

  12. An Evaluation Format for "Open" Software Tools.

    Science.gov (United States)

    Murphy, Cheryl A.

    1995-01-01

    Evaluates six "open" (empty of content and customized by users) software programs using the literature-based characteristics of documentation, learner control, branching capabilities, portability, ease of use, and cost-effectiveness. Interviewed computer-knowledgeable individuals to confirm the legitimacy of the evaluative characteristics. (LRW)

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

    Science.gov (United States)

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

    2014-01-01

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

  14. 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.

  15. Open Source Hardware for DIY Environmental Sensing

    Science.gov (United States)

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

    2014-12-01

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

  16. 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…

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

    Science.gov (United States)

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

    2014-12-01

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

  18. 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...

  19. 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...

  20. OSeMOSYS: The Open Source Energy Modeling System

    Energy Technology Data Exchange (ETDEWEB)

    Howells, Mark, E-mail: mark.i.howells@gmail.com [Royal Institute of Technology (KTH) (Sweden); Rogner, Holger [Planning and Economic Studies Section, International Atomic Energy Agency (Austria); Strachan, Neil [Energy Institute, University College London (United Kingdom); Heaps, Charles [Stockholm Environmental Institute (SEI) (United States); Huntington, Hillard [Stanford University (United States); Kypreos, Socrates [Paul Scherrer Institute (Switzerland); Hughes, Alison [Energy Research Centre, University of Cape Town (South Africa); Silveira, Semida [Royal Institute of Technology (KTH) (Sweden); DeCarolis, Joe [North Carolina State University (United States); Bazillian, Morgan [United Nations Industrial Development Organization (UNIDO) (Austria); Roehrl, Alexander [United Nations Department of Economic and Social Affairs (UNDESA) (United States)

    2011-10-15

    This paper discusses the design and development of the Open Source Energy Modeling System (OSeMOSYS). It describes the model's formulation in terms of a 'plain English' description, algebraic formulation, implementation-in terms of its full source code, as well as a detailed description of the model inputs, parameters, and outputs. A key feature of the OSeMOSYS implementation is that it is contained in less than five pages of documented, easily accessible code. Other existing energy system models that do not have this emphasis on compactness and openness makes the barrier to entry by new users much higher, as well as making the addition of innovative new functionality very difficult. The paper begins by describing the rationale for the development of OSeMOSYS and its structure. The current preliminary implementation of the model is then demonstrated for a discrete example. Next, we explain how new development efforts will build on the existing OSeMOSYS codebase. The paper closes with thoughts regarding the organization of the OSeMOSYS community, associated capacity development efforts, and linkages to other open source efforts including adding functionality to the LEAP model. - Highlights: > OSeMOSYS is a new free and open source energy systems. > This model is written in a simple, open, flexible and transparent manner to support teaching. > OSeMOSYS is based on free software and optimizes using a free solver. > This model replicates the results of many popular tools, such as MARKAL. > A link between OSeMOSYS and LEAP has been developed.

  1. SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

    Science.gov (United States)

    Updegrove, Adam; Wilson, Nathan M; Merkow, Jameson; Lan, Hongzhi; Marsden, Alison L; Shadden, Shawn C

    2017-03-01

    Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.

  2. 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…

  3. 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…

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

    Science.gov (United States)

    Wang, Jing

    2013-01-01

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

  5. 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...

  6. Evolution of an Open Source Strategy

    Directory of Open Access Journals (Sweden)

    Ronald Baecker

    2007-10-01

    Full Text Available On June 8th, 2005, we officially launched the ePresence (http://epresence.tv/ Interactive Media Open Source Consortium, at the Knowledge Media Design Institute (KMDI, University of Toronto (UofT. We had been researching and developing ePresence, our webcasting, webconferencing, and archiving software project for about five years. Throughout the early phase of the project we used the system to produce live webcasts of KMDI's annual lecture series. Eventually word spread about our webcasting system and other universities, such as Memorial University in Newfoundland, became interested. It was obvious that the time to share our project with the world had come, but what wasn't obvious to us at the time was how we were going to do that.

  7. The architecture of open source applications

    CERN Document Server

    Wilson, Greg

    2012-01-01

    Architects look at thousands of buildings during their training, and study critiques of those buildings written by masters. In contrast, most software developers only ever get to know a handful of large programs well - usually programs they wrote themselves - and never study the great programs of history. As a result, they repeat one another's mistakes rather than building on one another's successes. This book's goal is to change that. In it, the authors of twenty-five open source applications explain how their software is structured, and why. What are each program's major components? How do they interact? And what did their builders learn during their development? In answering these questions, the contributors to this book provide unique insights into how they think.

  8. An Affordable Open-Source Turbidimeter

    Science.gov (United States)

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

    2014-01-01

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

  9. 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.

  10. A identidade profissional no jornalismo open source

    Directory of Open Access Journals (Sweden)

    Ana Maria Brambilla

    2005-06-01

    Full Text Available Ao aprofundar o conceito de jornalismo open source e seus valores de aplicação na Internet, o presente artigo focaliza a preocupação despertada em jornalistas profissionais em um cenário onde cada cidadão é um repórter. Para ilustrar essa pesquisa foi estudado o noticiário coreano OhmyNews, online desde 2000, publicando artigos escritos por pessoas que não têm formação jornalística. A intenção desta reflexão é ampliar as discussões pela busca da reconfiguração do papel do jornalista em uma mídia que está cada vez mais sob domínio do público.

  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 open source business model for malaria.

    Science.gov (United States)

    Årdal, Christine; Røttingen, John-Arne

    2015-01-01

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

  13. An open source business model for malaria.

    Directory of Open Access Journals (Sweden)

    Christine Årdal

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

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

    Science.gov (United States)

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

    2016-04-01

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

  15. 事件驱动的面向云制造服务架构及其开源实现%Event-driven service-oriented architecture for cloud manufacturing and its implementation with open source tools

    Institute of Scientific and Technical Information of China (English)

    姚锡凡; 金鸿; 李彬; 张洁; 林颖; 周宏甫

    2013-01-01

    Internet-of-Things enabled Cloud Manufacturing faces the problems such as vertical collaboration between services via the Internet of Services, the horizontal collaboration between devices via the Internet of Things (IoT), and consequent Complex Event Processing (CEP) and Event-Driven Architecture (EDA). Therefore, Cloud Computing, CEP, Service-Oriented Architecture (SOA) and EDA were fused to propose Event-Driven SOA for Cloud Manufacturing (EDSOA4CM), and EDSOA4CM was implemented with open source tools. The proposed architecture was the extension of SOA for Cloud Manufacturing (SOA4CM), its service-oriented and event-driven functions were supported by the Enterprise Service Bus (ESB), and event pattern detection and event-driven business process were implemented via an event flow engine and a rule engine.%物联网使能的云制造面临在垂直方向上通过务联网协同各种服务、在水平方向上通过物联网协同各种设备以及由此引起的事件复杂处理和事件驱动架构问题.为此,融合云计算、复杂事件处理、面向服务架构与事件驱动架构,提出事件驱动的面向云制造服务架构,并用开源软件加以实现.该架构是面向云制造服务架构的延伸,能够通过企业服务总线实现面向服务与事件驱动功能,通过事件流引擎和规则引擎结合实现事件模式检测和事件驱动的业务流程.

  16. OPEN SOURCE ARCHITECTURE PER LA CITTÀ METROPOLITANA DI REGGIO CALABRIA

    Directory of Open Access Journals (Sweden)

    Gabriele Di Quarto

    2014-12-01

    Full Text Available The paper presents the role of the new Open Source technologies to encourage participation in the processes of incorporation of metropolitan cities established by the Italian legal system by Law 56 of 7 April 2014. Highlighted how technological innovation can provide useful tools to fill the competitive gap resulting from the physical conformation of the territory and from the delays in infrastructure of the future metropolitan city of Reggio Calabria. And is finally presented the experimental project of neighborhood of Archi CEP in Reggio Calabria.

  17. 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.

  18. Open Plot Project: an open-source toolkit for 3-D structural data analysis

    Directory of Open Access Journals (Sweden)

    S. Tavani

    2010-12-01

    Full Text Available In this work we present the Open Plot Project, a software for structural data analysis including a 3-D environment. This first alpha release represents a stand-alone toolkit for structural data analysis and, due to many import/export facilities and to the presence of a 3-D environment, also candidates as a tool to be incorporated in workflows for 3-D geological modelling.

    The software (for both Windows and Linux O.S., the User Manual, a set of example movies, and the source code are provided as Supplement. It is our purpose that the publication of the source code sets the base for the development of a public and free software that, hopefully, the structural geologists community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

  19. Open-Source Automated Mapping Four-Point Probe

    Directory of Open Access Journals (Sweden)

    Handy Chandra

    2017-01-01

    Full Text Available Scientists have begun using self-replicating rapid prototyper (RepRap 3-D printers to manufacture open source digital designs of scientific equipment. This approach is refined here to develop a novel instrument capable of performing automated large-area four-point probe measurements. The designs for conversion of a RepRap 3-D printer to a 2-D open source four-point probe (OS4PP measurement device are detailed for the mechanical and electrical systems. Free and open source software and firmware are developed to operate the tool. The OS4PP was validated against a wide range of discrete resistors and indium tin oxide (ITO samples of different thicknesses both pre- and post-annealing. The OS4PP was then compared to two commercial proprietary systems. Results of resistors from 10 to 1 MΩ show errors of less than 1% for the OS4PP. The 3-D mapping of sheet resistance of ITO samples successfully demonstrated the automated capability to measure non-uniformities in large-area samples. The results indicate that all measured values are within the same order of magnitude when compared to two proprietary measurement systems. In conclusion, the OS4PP system, which costs less than 70% of manual proprietary systems, is comparable electrically while offering automated 100 micron positional accuracy for measuring sheet resistance over larger areas.

  20. Open-Source Automated Mapping Four-Point Probe.

    Science.gov (United States)

    Chandra, Handy; Allen, Spencer W; Oberloier, Shane W; Bihari, Nupur; Gwamuri, Jephias; Pearce, Joshua M

    2017-01-26

    Scientists have begun using self-replicating rapid prototyper (RepRap) 3-D printers to manufacture open source digital designs of scientific equipment. This approach is refined here to develop a novel instrument capable of performing automated large-area four-point probe measurements. The designs for conversion of a RepRap 3-D printer to a 2-D open source four-point probe (OS4PP) measurement device are detailed for the mechanical and electrical systems. Free and open source software and firmware are developed to operate the tool. The OS4PP was validated against a wide range of discrete resistors and indium tin oxide (ITO) samples of different thicknesses both pre- and post-annealing. The OS4PP was then compared to two commercial proprietary systems. Results of resistors from 10 to 1 MΩ show errors of less than 1% for the OS4PP. The 3-D mapping of sheet resistance of ITO samples successfully demonstrated the automated capability to measure non-uniformities in large-area samples. The results indicate that all measured values are within the same order of magnitude when compared to two proprietary measurement systems. In conclusion, the OS4PP system, which costs less than 70% of manual proprietary systems, is comparable electrically while offering automated 100 micron positional accuracy for measuring sheet resistance over larger areas.

  1. 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.

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

    Science.gov (United States)

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

    2015-12-01

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

  3. Open source software engineering for geoscientific modeling applications

    Science.gov (United States)

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

    2012-12-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  6. 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.

  7. 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...

  8. 10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

    Science.gov (United States)

    2010-01-01

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

  9. An open-source laser electronics suite

    Science.gov (United States)

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

    2016-05-01

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

  10. 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.

  11. 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...

  12. The 2015 Bioinformatics Open Source Conference (BOSC 2015.

    Directory of Open Access Journals (Sweden)

    Nomi L Harris

    2016-02-01

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

  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. An Extensible Open-Source Compiler Infrastructure for Testing

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, D; Ur, S; Vuduc, R

    2005-12-09

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

  15. Introducing a new open source GIS user interface for the SWAT model

    Science.gov (United States)

    The Soil and Water Assessment Tool (SWAT) model is a robust watershed modelling tool. It typically uses the ArcSWAT interface to create its inputs. ArcSWAT is public domain software which works in the licensed ArcGIS environment. The aim of this paper was to develop an open source user interface ...

  16. 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.

  17. Open-Source Data and the Study of Homicide.

    Science.gov (United States)

    Parkin, William S; Gruenewald, Jeff

    2015-07-20

    To date, no discussion has taken place in the social sciences as to the appropriateness of using open-source data to augment, or replace, official data sources in homicide research. The purpose of this article is to examine whether open-source data have the potential to be used as a valid and reliable data source in testing theory and studying homicide. Official and open-source homicide data were collected as a case study in a single jurisdiction over a 1-year period. The data sets were compared to determine whether open-sources could recreate the population of homicides and variable responses collected in official data. Open-source data were able to replicate the population of homicides identified in the official data. Also, for every variable measured, the open-sources captured as much, or more, of the information presented in the official data. Also, variables not available in official data, but potentially useful for testing theory, were identified in open-sources. The results of the case study show that open-source data are potentially as effective as official data in identifying individual- and situational-level characteristics, provide access to variables not found in official homicide data, and offer geographic data that can be used to link macro-level characteristics to homicide events.

  18. Performances evaluation of different open source

    Directory of Open Access Journals (Sweden)

    Arun Patel

    2016-06-01

    Full Text Available In Open sources DEMs such as SRTM, ASTER and Cartosat-1, various factors affecting the accuracy of satellite based DEM such as errors during data collection, systematic errors and unknown errors that are geographically dependent on terrain conditions cannot be avoided. For these reasons it is very necessary to check and compare the performances and validation of the above mentioned different satellite based DEMs. Accuracy assessment of these DEM has been done using DGPS points. For these points proper interpolation of the surface was developed using different interpolation techniques. For the generation of the surface the first step was converting the satellite based DEMs height into linear interpolation contour maps of 1 m interval. Then came selecting random sample points on the contour line and generating the interpolated surface using different interpolation techniques such as IDW, GPI, RBF, OK and UK, LPI, TR and BI, which are commonly used in geomorphology research. This interpolated surface helps in proper representation of the terrain and was checked under different terrain surfaces. For validation of DGPS points the height was taken for ground control points and standard statistical tests such as ME and RMSE were applied. From above investigation, it is reveals that above mention DEMs which are used for study. Cartosat-1 (30 m data product is better than SRTM (90 m and ASTER (30 m because it had produced low RMSE of 3.49 m without applying the interpolation method. Investigation also reveals after applying the interpolation techniques on this data error can be reduced. In the case of Cartosat-1 and SRTM, low RMSE and ME were produced by the BI method, where Cartosat-1 DEM had an RMSE of 3.36 m with ME of −2.74 m, respectively. But in this case, RMSE and ME of SRTM is 2.73 m and −0.36 m, respectively. BI is designed for image processing and can be used for imagery were a maximum height variation in satellite DEM and terrain

  19. 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.

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

    Science.gov (United States)

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

    2014-05-01

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

  1. Digital Forensics Capabilities in an Open Source Framework

    Directory of Open Access Journals (Sweden)

    Cosmin Bubulean

    2015-06-01

    Full Text Available This article focus to establish a new perspective about digital forensics and how this technology could be used by more and more people. Nowadays, this term is not so popular between regular computer users. They don’t know what digital forensics is and how could they take advantage of this new technology. The tools available on the market are designated and used especially for legal authorities all over the world. Most of them are a company solution of the problem, premium software, and the development facilities are private, but they offer support and trainings that come with a price.  But for a regular user this isn’t very handy, because this software comes with high prices, or couldn’t be used at all, due to the fact that for a few products only the law enforcements units have this right. However, open-source solutions have now a rapid development, and the developer community behind them is a big plus. DDF – Digital Forensics Framework is an open-source framework, having great capabilities that empower a regular user with great investigations features.

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

    Science.gov (United States)

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

    2015-05-01

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

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

    Science.gov (United States)

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

    2015-07-08

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

  4. 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/).

  5. How Hard Can It Be? : Developing in Open Source

    Directory of Open Access Journals (Sweden)

    Rosalie Blake

    2009-06-01

    Full Text Available In 2000 a small public library system in New Zealand developed and released Koha, the world’s first open source library management system. This is the story of how that came to pass and why, and of the lessons learnt in their first foray into developing in open source.

  6. 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.

  7. Integrating an Automatic Judge into an Open Source LMS

    Science.gov (United States)

    Georgouli, Katerina; Guerreiro, Pedro

    2011-01-01

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

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

    Science.gov (United States)

    Glassman, Michael; Bartholomew, Mitchell; Jones, Travis

    2011-01-01

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

  9. Open Source Library Management Systems: A Multidimensional Evaluation

    Science.gov (United States)

    Balnaves, Edmund

    2008-01-01

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

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

    Science.gov (United States)

    Conner, Trey; Gresham, Morgan; McCracken, Jill

    2011-01-01

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

  11. Open Source Library Management Systems: A Multidimensional Evaluation

    Science.gov (United States)

    Balnaves, Edmund

    2008-01-01

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

  12. BOOK REVIEW: The Success of Open Source by Steven Weber

    Directory of Open Access Journals (Sweden)

    Eric Lease Morgan

    2007-12-01

    Full Text Available The Success of Open Source by Steven Weber details the history, process, motivations, and possible long-term effects of open source software (OSS. Weber’s book can be used as a set of guidelines – a description of a framework – for building software solutions for the computing problems facing libraries.

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

    Science.gov (United States)

    Hogan, P.

    2009-12-01

    . Spatial information intelligence is a global issue that will increasingly affect our ability to survive as a species. Collectively we must better appreciate the complex relationships that make life on Earth possible. Providing spatial information in its native context can accelerate our ability to process that information. To maximize this ability to process information, three basic elements are required: data delivery (server technology), data access (client technology), and data processing (information intelligence). NASA World Wind provides open source client and server technologies based on open standards. The possibilities for data processing and data sharing are enhanced by this inclusive infrastructure for geographic information. It is interesting that this open source and open standards approach, unfettered by proprietary constraints, simultaneously provides for entirely proprietary use of this same technology. 1. WHY WORLD WIND? NASA World Wind began as a single program with specific functionality, to deliver NASA content. But as the possibilities for virtual globe technology became more apparent, we found that while enabling a new class of information technology, we were also getting in the way. Researchers, developers and even users expressed their desire for World Wind functionality in ways that would service their specific needs. They want it in their web pages. They want to add their own features. They want to manage their own data. They told us that only with this kind of flexibility, could their objectives and the potential for this technology be truly realized. World Wind client technology is a set of development tools, a software development kit (SDK) that allows a software engineer to create applications requiring geographic visualization technology. 2. MODULAR COMPONENTRY Accelerated evolution of a technology requires that the essential elements of that technology be modular components such that each can advance independent of the other

  14. Open source system options for librarians and archivists

    CERN Document Server

    Tomer, Christinger

    2017-01-01

    The importance of open source systems in the context of libraries and archives is perhaps greater now than ever before. This book explains the essentials of open source systems to benefit academic and public librarians and archivists who have a vested interest in the future of integrated online library systems. Author Christinger Tomer, who has studied open source systems for more than two decades and used them extensively in both teaching and consulting, provides brief histories of both library automation and open source software, in the latter instance focusing on aspects that have more directly influenced library and archival computing. He then describes and analyzes key open source systems and critically compares them to commercial systems in terms of design, functionality, and ease of administration. The book concludes with an in-depth description of how these systems are currently being employed as well as insightful predictions about how this segment of the software environment is likely to evolve.

  15. 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.

  16. Institutional and pedagogical criteria for productive open source learning environments

    DEFF Research Database (Denmark)

    Svendsen, Brian Møller; Ryberg, Thomas; Semey, Ian Peter;

    2004-01-01

    In this article we present some institutional and pedagogical criteria for making an informed decision in relation to identifying and choosing a productive open source learning environment. We argue that three concepts (implementation, maintainability and further development) are important when...... considering the sustainability and cost efficiency of an open source system, and we outline a set of key points for evaluating an open source software in terms of cost of system adoption. Furthermore we identify a range of pedagogical concepts and criteria to emphasize the importance of considering...... the relation between the local pedagogical practice and the pedagogical design of the open source learning environment. This we illustrate through an analysis of an open source system and our own pedagogical practice at Aalborg University, Denmark (POPP)....

  17. Institutional and pedagogical criteria for productive open source learning environments

    DEFF Research Database (Denmark)

    Svendsen, Brian Møller; Ryberg, Thomas; Semey, Ian Peter

    2004-01-01

    In this article we present some institutional and pedagogical criteria for making an informed decision in relation to identifying and choosing a productive open source learning environment. We argue that three concepts (implementation, maintainability and further development) are important when...... considering the sustainability and cost efficiency of an open source system, and we outline a set of key points for evaluating an open source software in terms of cost of system adoption. Furthermore we identify a range of pedagogical concepts and criteria to emphasize the importance of considering...... the relation between the local pedagogical practice and the pedagogical design of the open source learning environment. This we illustrate through an analysis of an open source system and our own pedagogical practice at Aalborg University, Denmark (POPP)....

  18. 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.

  19. 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.

  20. Inexpensive Open-Source Data Logging in the Field

    Science.gov (United States)

    Wickert, A. D.

    2013-12-01

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

  1. Open source project to aid ionosphere physics research

    Science.gov (United States)

    Huba, J. D.; Joyce, G.

    In the past decade, the Open Source Model for software development has gained popularity and has had many major achievements: emacs, Linux, the Gimp, and Python, to name a few. The basic idea is to provide the source code of the model or application, a tutorial on its use, and a feedback mechanism with the community so that the model can be tested, improved, and archived. Given the success of the Open Source Model, it may prove valuable in the development of scientific research codes. With this in mind, we are "open sourcing" the SAMI2 low- to mid-latitude ionospheric model that was recently developed at the Naval Research Laboratory.

  2. Open Source Software Projects Needing Security Investments

    Science.gov (United States)

    2015-06-19

    Static Analysis Security Tools (e.g., Coverity Scan) ............... 2-19  2.  Lexically Scanning Static Analysis Security Tools (e.g., flawfinder and...ACCORDING TO [GHAPANCHI2011] User interest Traffic on the project Web site, downloads of the code, number of developers who have joined the project team...through hard work….” 3. “Establish a high-quality Web site to showcase and promote your project.” 4. “Create good documentation for your (potential) user

  3. ACToR Chemical Structure processing using Open Source ...

    Science.gov (United States)

    ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

  4. No Strings Attached: Open Source Solutions

    Science.gov (United States)

    Fredricks, Kathy

    2009-01-01

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

  5. No Strings Attached: Open Source Solutions

    Science.gov (United States)

    Fredricks, Kathy

    2009-01-01

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

  6. Meteorological Error Budget Using Open Source Data

    Science.gov (United States)

    2016-09-01

    VBA ) script was created that would read the model - based output and corresponding sounding data for each message type (METCM or METB3), output type...produce artillery MET error budget tables that account for expected errors when using MET model -based systems. Representatives of the US and other...nations within the North Atlantic Treaty Organization expressed a need for shareable model -based MET error budgets. Use of an openly available civilian

  7. OpenSesame : An open-source, graphical experiment builder for the social sciences

    NARCIS (Netherlands)

    Mathot, Sebastiaan; Schreij, Daniel; Theeuwes, Jan

    2012-01-01

    In the present article, we introduce OpenSesame, a graphical experiment builder for the social sciences. OpenSesame is free, open-source, and cross-platform. It features a comprehensive and intuitive graphical user interface and supports Python scripting for complex tasks. Additional functionality,

  8. 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

  9. OpenBook WordPress Plugin: Open Source Access to Bibliographic Data

    Directory of Open Access Journals (Sweden)

    John Miedema

    2008-09-01

    Full Text Available OpenBook is a WordPress PHP plugin that implements the Open Library APIs to insert book covers, titles, authors and publishers into web pages. The motive behind the development was to provide an easy alternative to the common practice of linking to Amazon. Open Library was selected as a data source because it is both open source and open data.The plugin is useful for book reviewers, library webmasters, anyone who wants to put book covers and data on their WordPress blog or website. The plugin also allows users to add links to publisher websites, a feature that was considered significant to independent publishers.

  10. 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.

  11. 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.

  12. Controlling open quantum systems: tools, achievements, and limitations

    Science.gov (United States)

    Koch, Christiane P.

    2016-06-01

    The advent of quantum devices, which exploit the two essential elements of quantum physics, coherence and entanglement, has sparked renewed interest in the control of open quantum systems. Successful implementations face the challenge of preserving relevant nonclassical features at the level of device operation. A major obstacle is decoherence, which is caused by interaction with the environment. Optimal control theory is a tool that can be used to identify control strategies in the presence of decoherence. Here we review recent advances in optimal control methodology that allow typical tasks in device operation for open quantum systems to be tackled and discuss examples of relaxation-optimized dynamics. Optimal control theory is also a useful tool to exploit the environment for control. We discuss examples and point out possible future extensions.

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

    Energy Technology Data Exchange (ETDEWEB)

    Doak, J.; Howell, J.A.

    1995-08-01

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

  14. Setting up of an Open Source based Private Cloud

    Directory of Open Access Journals (Sweden)

    G R Karpagam

    2011-05-01

    Full Text Available Cloud Computing is an attractive concept in IT field, since it allows the resources to be provisioned according to the user needs[11]. It provides services on virtual machines whereby the user can share resources, software and other devices on demand. Cloud services are supported both by Proprietary and Open Source Systems. As Proprietary products are very expensive, customers are not allowed to experiment on their product and security is a major issue in it, Open source systems helps in solving out these problems. Cloud Computing motivated many academic and non academic members to develop Open Source Cloud Setup, here the users are allowed to study the source code and experiment it. This paper describes the configuration of a private cloud using Eucalyptus. Eucalyptus an open source system has been used to implement a private cloud using the hardware and software without making any modification to it and provide various types of services to the cloud computing environment

  15. OpenSimulator Interoperability with DRDC Simulation Tools: Compatibility Study

    Science.gov (United States)

    2014-09-01

    conversion. iv These tools include Blender, AutoCAD , 3DS Max and SketchUp. Thus, DRDC use case (1) was demonstrated as feasible. However...supplementary support for the creation of content and resources compatible with OpenSimulator. These include programs such as Blender, GIMP, AutoCAD , 3DS MAX...support the PDS, PDMS, ACIS (.sat), MicroStation (.dgn), and AutoCAD (.dwg) formats, but not COLLADA directly [14]. An important limitation of

  16. IPMACC: Open Source OpenACC to CUDA/OpenCL Translator

    OpenAIRE

    Lashgar, Ahmad; Majidi, Alireza; Baniasadi, Amirali

    2014-01-01

    In this paper we introduce IPMACC, a framework for translating OpenACC applications to CUDA or OpenCL. IPMACC is composed of set of translators translating OpenACC for C applications to CUDA or OpenCL. The framework uses the system compiler (e.g. nvcc) for generating final accelerator's binary. The framework can be used for extending the OpenACC API, executing OpenACC applications, or obtaining CUDA or OpenCL code which is equivalent to OpenACC code. We verify correctness of our framework und...

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

    Science.gov (United States)

    Erdemir, Ahmet

    2016-01-01

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

  18. 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.

  19. Forks impacts and motivations in free and open source projects

    Directory of Open Access Journals (Sweden)

    R. Viseur

    2012-02-01

    Full Text Available Forking is a mechanism of splitting in a community and is typically found in the free and open source software field. As a failure of cooperation in a context of open innovation, forking is a practical and informative subject of study. In-depth researches concerning the fork phenomenon are uncommon. We therefore conducted a detailed study of 26 forks from popular free and open source projects. We created fact sheets, highlighting the impact and motivations to fork. We particularly point to the fact that the desire for greater technical differentiation and problems of project governance are major sources of conflict.

  20. Open source R&D - an anomaly in innovation management?

    DEFF Research Database (Denmark)

    Ulhøi, John Parm

    2004-01-01

    This paper addresses innovations based on the principle of open source or non-proprietary knowledge. Viewed through the lens of private property theory, such agency appears to be a true anomaly. However, by a further turn of the theoretical kaleidoscope, we will show that there may be perfectly...... justifiable reasons for not regarding open source innovations as anomalies. The paper has identified three generic cases of open source innovation, which is an offspring of contemporary theory made possible by combining elements of the model of private agency with those of the model of collective agency...

  1. 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...

  2. Open source R&D - an anomaly in innovation management?

    DEFF Research Database (Denmark)

    Ulhøi, John Parm

    2004-01-01

    This paper addresses innovations based on the principle of open source or non-proprietary knowledge. Viewed through the lens of private property theory, such agency appears to be a true anomaly. However, by a further turn of the theoretical kaleidoscope, we will show that there may be perfectly...... justifiable reasons for not regarding open source innovations as anomalies. The paper has identified three generic cases of open source innovation, which is an offspring of contemporary theory made possible by combining elements of the model of private agency with those of the model of collective agency...

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

    OpenAIRE

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

    2015-01-01

    Summary: The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched. Availabil...

  4. Integrating Free and Open Source Solutions into Geospatial Science Education

    Directory of Open Access Journals (Sweden)

    Vaclav Petras

    2015-06-01

    Full Text Available While free and open source software becomes increasingly important in geospatial research and industry, open science perspectives are generally less reflected in universities’ educational programs. We present an example of how free and open source software can be incorporated into geospatial education to promote open and reproducible science. Since 2008 graduate students at North Carolina State University have the opportunity to take a course on geospatial modeling and analysis that is taught with both proprietary and free and open source software. In this course, students perform geospatial tasks simultaneously in the proprietary package ArcGIS and the free and open source package GRASS GIS. By ensuring that students learn to distinguish between geospatial concepts and software specifics, students become more flexible and stronger spatial thinkers when choosing solutions for their independent work in the future. We also discuss ways to continually update and improve our publicly available teaching materials for reuse by teachers, self-learners and other members of the GIS community. Only when free and open source software is fully integrated into geospatial education, we will be able to encourage a culture of openness and, thus, enable greater reproducibility in research and development applications.

  5. 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.

  6. Contrasting Proprietary and Free/Open Source Game Development

    Directory of Open Access Journals (Sweden)

    Marco Zamarian

    2008-10-01

    Full Text Available Free/Libre Open Source Software (F/LOSS development practices are gaining momentum in the computer game industry. This traditionally proprietary industry is becoming more interested in the F/LOSS paradigm for developing complex software projects. Software practitioners, both managers and developers, need to understand the potential in order to benefit properly from incorporating F/LOSS practices into their proprietary production cycle. Comparisons between proprietary and F/LOSS software development processes are usually characterized in terms of the relationship between property rights, revenue distribution and power within a network of actors. By contrast, coordination and control practices, mediating artifacts and development tools, and the interactions between the different actors involved in the development are often neglected. Proprietary and F/LOSS development differ in terms of the knowledge exchanges between the relevant actors and the different strategies employed to overcome information asymmetries. Recognizing this difference is an essential step for evaluating how proprietary, closed-source software houses can benefit by integrating various F/LOSS practices into their development agenda.

  7. Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|Speedshop

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Barton

    2014-06-30

    Peta-scale computing environments pose significant challenges for both system and application developers and addressing them required more than simply scaling up existing tera-scale solutions. Performance analysis tools play an important role in gaining this understanding, but previous monolithic tools with fixed feature sets have not sufficed. Instead, this project worked on the design, implementation, and evaluation of a general, flexible tool infrastructure supporting the construction of performance tools as “pipelines” of high-quality tool building blocks. These tool building blocks provide common performance tool functionality, and are designed for scalability, lightweight data acquisition and analysis, and interoperability. For this project, we built on Open|SpeedShop, a modular and extensible open source performance analysis tool set. The design and implementation of such a general and reusable infrastructure targeted for petascale systems required us to address several challenging research issues. All components needed to be designed for scale, a task made more difficult by the need to provide general modules. The infrastructure needed to support online data aggregation to cope with the large amounts of performance and debugging data. We needed to be able to map any combination of tool components to each target architecture. And we needed to design interoperable tool APIs and workflows that were concrete enough to support the required functionality, yet provide the necessary flexibility to address a wide range of tools. A major result of this project is the ability to use this scalable infrastructure to quickly create tools that match with a machine architecture and a performance problem that needs to be understood. Another benefit is the ability for application engineers to use the highly scalable, interoperable version of Open|SpeedShop, which are reassembled from the tool building blocks into a flexible, multi-user interface set of tools. This set of

  8. Developing Healthcare Data Analytics APPs with Open Data Science Tools.

    Science.gov (United States)

    Hao, Bibo; Sun, Wen; Yu, Yiqin; Xie, Guotong

    2017-01-01

    Recent advances in big data analytics provide more flexible, efficient, and open tools for researchers to gain insight from healthcare data. Whilst many tools require researchers to develop programs with programming languages like Python, R and so on, which is not a skill set grasped by many researchers in the healthcare data analytics area. To make data science more approachable, we explored existing tools and developed a practice that can help data scientists convert existing analytics pipelines to user-friendly analytics APPs with rich interactions and features of real-time analysis. With this practice, data scientists can develop customized analytics pipelines as APPs in Jupyter Notebook and disseminate them to other researchers easily, and researchers can benefit from the shared notebook to perform analysis tasks or reproduce research results much more easily.

  9. 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

  10. Open source GIS for HIV/AIDS management

    Directory of Open Access Journals (Sweden)

    Ricketts Adam

    2008-10-01

    Full Text Available Abstract Background Reliable access to basic services can improve a community's resilience to HIV/AIDS. Accordingly, work is being done to upgrade the physical infrastructure in affected areas, often employing a strategy of decentralised service provision. Spatial characteristics are one of the major determinants in implementing services, even in the smaller municipal areas, and good quality spatial information is needed to inform decision making processes. However, limited funds, technical infrastructure and human resource capacity result in little or no access to spatial information for crucial infrastructure development decisions at local level. This research investigated whether it would be possible to develop a GIS for basic infrastructure planning and management at local level. Given the resource constraints of the local government context, particularly in small municipalities, it was decided that open source software should be used for the prototype system. Results The design and development of a prototype system illustrated that it is possible to develop an open source GIS system that can be used within the context of local information management. Usability tests show a high degree of usability for the system, which is important considering the heavy workload and high staff turnover that characterises local government in South Africa. Local infrastructure management stakeholders interviewed in a case study of a South African municipality see the potential for the use of GIS as a communication tool and are generally positive about the use of GIS for these purposes. They note security issues that may arise through the sharing of information, lack of skills and resource constraints as the major barriers to adoption. Conclusion The case study shows that spatial information is an identified need at local level. Open source GIS software can be used to develop a system to provide local-level stakeholders with spatial information. However, the

  11. 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.

  12. Towards the Adoption of Open Source and Open Access Electronic Health Record Systems

    Directory of Open Access Journals (Sweden)

    Ilias Maglogiannis

    2012-01-01

    Full Text Available As the Electronic Health Record (EHR systems constantly expand to support more clinical activities and their implementations in healthcare organizations become more widespread, several communities have been working intensively for several years to develop open access and open source EHR software, aiming at reducing the costs of EHR deployment and maintenance. In this paper, we describe and evaluate the most popular open source electronic medical records such as openEMR, openMRS and patientOS, providing their technical features and potentials. These systems are considered quite important due to their prevalence. The article presents the key features of each system and outlines the advantages and problems of Open Source Software (OSS Systems through a review of the literature, in order to demonstrate the possibility of their adoption in modern electronic healthcare systems. Also discussed are the future trends of OS EHRs in the context of the Personal Health Records and mobile computing paradigm.

  13. 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)

  14. Implementing a real estate management system using open source ...

    African Journals Online (AJOL)

    Implementing a real estate management system using open source GIS software. ... already gets most of the information without having to leave home or work. ... to provide the background on which the parcels of land (plots) are displayed.

  15. Open Source Radiation Hardened by Design Technology

    Science.gov (United States)

    Shuler, Robert

    2016-01-01

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

  16. Cognitive Readiness Assessment and Reporting: An Open Source Mobile Framework for Operational Decision Support and Performance Improvement

    Science.gov (United States)

    Heric, Matthew; Carter, Jenn

    2011-01-01

    Cognitive readiness (CR) and performance for operational time-critical environments are continuing points of focus for military and academic communities. In response to this need, we designed an open source interactive CR assessment application as a highly adaptive and efficient open source testing administration and analysis tool. It is capable…

  17. GRASS GIS: The first Open Source Temporal GIS

    Science.gov (United States)

    Gebbert, Sören; Leppelt, Thomas

    2015-04-01

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

  18. A FRAMEWORK FOR AN OPEN SOURCE GEOSPATIAL CERTIFICATION MODEL

    OpenAIRE

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

    2016-01-01

    The geospatial industry is forecasted to have an enormous growth in the forthcoming years and an extended need for well-educated workforce. Hence ongoing education and training play an important role in the professional life. Parallel, in the geospatial and IT arena as well in the political discussion and legislation Open Source solutions, open data proliferation, and the use of open standards have an increasing significance. Based on the Memorandum of Understanding between International Cart...

  19. Open Ephys electroencephalography (Open Ephys  +  EEG): a modular, low-cost, open-source solution to human neural recording

    Science.gov (United States)

    Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie

    2017-06-01

    Objective. Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Approach. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys  +  EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. Main results. The Open Ephys  +  EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys  +  EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Significance. Open Ephys  +  EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.

  20. Open Ephys electroencephalography (Open Ephys  +  EEG): a modular, low-cost, open-source solution to human neural recording.

    Science.gov (United States)

    Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie

    2017-06-01

    Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys  +  EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. The Open Ephys  +  EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys  +  EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Open Ephys  +  EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.

  1. 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…

  2. Open Source Solutions for Libraries: ABCD vs Koha

    Science.gov (United States)

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

    2013-01-01

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

  3. 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…

  4. A Survey Of Top 10 Open Source Learning Management Systems

    Directory of Open Access Journals (Sweden)

    Mohamed R. Elabnody

    2015-08-01

    Full Text Available Open Source LMSs are fully flexible and customizable so they can be designed in line with your schoolorganizations brand image. Open Source LMSs can also be converted to social learning platforms. You can create an online community through your LMS. This paper describes the most important features in learning management systems LMS that are critical to compare and contrast depend on your system requirements. Also represents a multiple LMS providers that are designed to use in university environment.

  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. Open source technologies for delivering historical maps online - case studies at the National Library of Scotland

    Directory of Open Access Journals (Sweden)

    Christopher Fleet

    2012-11-01

    Full Text Available Over the last four years, the National Library of Scotland has saved money and improved user access to online historical maps through the implementation of new open source technologies. These new tools include a new Viewer for MrSID images using OpenLayers, a collaborative Georeferencer application, new Tile Map Services for delivering georeferenced historical maps online, and a new GeoServer and OpenLayers application for accessing 44,000 series maps as clickable indexes. All of these applications were developed by Petr Pridal / Klokan Technologies, in collaboration with the National Library of Scotland, and all of them are easily extendible to other map libraries. These open source tools also provide an excellent basis for collaboration with other map libraries, sharing technology, experience and advice.

  7. Open source electronic health records and chronic disease management.

    Science.gov (United States)

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

    2014-02-01

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

  8. EPUB as publication format in Open Access journals: Tools and workflow

    Directory of Open Access Journals (Sweden)

    Trude Eikebrokk

    2014-04-01

    Full Text Available In this article, we present a case study of how the main publishing format of an Open Access journal was changed from PDF to EPUB by designing a new workflow using JATS as the basic XML source format. We state the reasons and discuss advantages for doing this, how we did it, and the costs of changing an established Microsoft Word workflow. As an example, we use one typical sociology article with tables, illustrations and references. We then follow the article from JATS markup through different transformations resulting in XHTML, EPUB and MOBI versions. In the end, we put everything together in an automated XProc pipeline. The process has been developed on free and open source tools, and we describe and evaluate these tools in the article. The workflow is suitable for non-professional publishers, and all code is attached and free for reuse by others.

  9. Industrial open source solutions for product life cycle management

    Directory of Open Access Journals (Sweden)

    Jaime Campos

    2014-12-01

    Full Text Available The authors go through the open source for product life cycle management (PLM and the efforts done from communities such as the open source initiative. The characteristics of the open source solutions are highlighted as well. Next, the authors go through the requirements for PLM. This is an area where more attention has been given as the manufacturers are competing with the quality and life cycle costs of their products. Especially, the need of companies to try to get a strong position in providing services for their products and thus to make themselves less vulnerable to changes in the market has led to high interest in product life cycle simulation. The potential of applying semantic data management to solve these problems discussed in the light of recent developments. In addition, a basic roadmap is presented as to how the above-described problems could be tackled with open software solutions.

  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. 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

  12. 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...

  13. 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

  14. A FRAMEWORK FOR AN OPEN SOURCE GEOSPATIAL CERTIFICATION MODEL

    Directory of Open Access Journals (Sweden)

    T. U. R. Khan

    2016-06-01

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

  15. a Framework for AN Open Source Geospatial Certification Model

    Science.gov (United States)

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

    2016-06-01

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

  16. 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

  17. 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....

  18. Open source identity management patterns and practices using OpenAM 10.x

    CERN Document Server

    Kenning, Waylon

    2013-01-01

    This is a Packt Mini in a tutorial format that provides multiple examples on Identity Management using OpenAM 10.x.Open Source Identity Management Patterns and Practices Using OpenAM 10.x is great for developers and architects who are new to Identity Management, and who want a brief overview of what's possible and how to quickly implement a prototype. It's assumed that you've had experience with web applications and some knowledge of Apache and Tomcat.

  19. Visualization and analysis of atomistic simulation data with OVITO-the Open Visualization Tool

    Science.gov (United States)

    Stukowski, Alexander

    2010-01-01

    The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/.

  20. 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...

  1. Secrecy versus openness: Internet security and the limits of open source and peer production

    NARCIS (Netherlands)

    Schmidt, A.

    2014-01-01

    Open source and peer production have been praised as organisational models that could change the world for the better. It is commonly asserted that almost any societal activity could benefit from distributed, bottom-up collaboration — by making societal interaction more open, more social, and more d

  2. An open source, wireless capable miniature microscope system

    Science.gov (United States)

    Liberti, William A., III; Perkins, L. Nathan; Leman, Daniel P.; Gardner, Timothy J.

    2017-08-01

    Objective. Fluorescence imaging through head-mounted microscopes in freely behaving animals is becoming a standard method to study neural circuit function. Flexible, open-source designs are needed to spur evolution of the method. Approach. We describe a miniature microscope for single-photon fluorescence imaging in freely behaving animals. The device is made from 3D printed parts and off-the-shelf components. These microscopes weigh less than 1.8 g, can be configured to image a variety of fluorophores, and can be used wirelessly or in conjunction with active commutators. Microscope control software, based in Swift for macOS, provides low-latency image processing capabilities for closed-loop, or BMI, experiments. Main results. Miniature microscopes were deployed in the songbird premotor region HVC (used as a proper name), in singing zebra finches. Individual neurons yield temporally precise patterns of calcium activity that are consistent over repeated renditions of song. Several cells were tracked over timescales of weeks and months, providing an opportunity to study learning related changes in HVC. Significance. 3D printed miniature microscopes, composed completely of consumer grade components, are a cost-effective, modular option for head-mounting imaging. These easily constructed and customizable tools provide access to cell-type specific neural ensembles over timescales of weeks.

  3. RF Wave Simulation Using the MFEM Open Source FEM Package

    Science.gov (United States)

    Stillerman, J.; Shiraiwa, S.; Bonoli, P. T.; Wright, J. C.; Green, D. L.; Kolev, T.

    2016-10-01

    A new plasma wave simulation environment based on the finite element method is presented. MFEM, a scalable open-source FEM library, is used as the basis for this capability. MFEM allows for assembling an FEM matrix of arbitrarily high order in a parallel computing environment. A 3D frequency domain RF physics layer was implemented using a python wrapper for MFEM and a cold collisional plasma model was ported. This physics layer allows for defining the plasma RF wave simulation model without user knowledge of the FEM weak-form formulation. A graphical user interface is built on πScope, a python-based scientific workbench, such that a user can build a model definition file interactively. Benchmark cases have been ported to this new environment, with results being consistent with those obtained using COMSOL multiphysics, GENRAY, and TORIC/TORLH spectral solvers. This work is a first step in bringing to bear the sophisticated computational tool suite that MFEM provides (e.g., adaptive mesh refinement, solver suite, element types) to the linear plasma-wave interaction problem, and within more complicated integrated workflows, such as coupling with core spectral solver, or incorporating additional physics such as an RF sheath potential model or kinetic effects. USDoE Awards DE-FC02-99ER54512, DE-FC02-01ER54648.

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

    Science.gov (United States)

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

    2016-07-01

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

  5. 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.

  6. Implementation of Reliable Open Source IRIS Recognition System

    Directory of Open Access Journals (Sweden)

    Dhananjay Ikhar

    2013-12-01

    Full Text Available RELIABLE automatic recognition of persons has long been an attractive goal. As in all pattern recognition problems, the key issue is the relation between inter-class and intra-class variability: objects can be reliably classified only if the variability among different instances of a given class is less than the variability between different classes.The objective of this paper is to implement an open-source iris recognition system in order to verify the claimed performance of the technology. The development tool used will be MATLAB, and emphasis will be only on the software for performing recognition and not hardware for capturing an eye image. A reliable application development approach will be employed in order to produce results quickly. MATLAB provides an excellent environment, with its image processing toolbox. To test the system, a database of 756 grayscale eye images courtesy of Chinese Academy of Sciences-Institute of Automation (CASIA is used. The system is to be composed of a number of sub-systems, which correspond to each stage of iris recognition. These stages are- image acquisition, segmentation, normalization and feature encoding. The input to the system will be an eye image, and the output will be an iris template, which will provide a mathematical representation of the iris region. Which conclude the objectives to design recognition system are- study of different biometrics and their features? Study of different recognition systems and their steps, selection of simple and efficient recognition algorithm for implementation, selection of fast and efficient tool for processing, apply the implemented algorithm to different database and find out performance factors.

  7. Improving hydropower choices via an online and open access tool.

    Science.gov (United States)

    Vilela, Thais; Reid, John

    2017-01-01

    This paper describes and validates the HydroCalculator Tool developed by Conservation Strategy Fund. The HydroCalculator Tool allows researchers, policy-makers and citizens to easily assess hydropower feasibility, by calculating traditional financial indicators, such as the levelized cost of energy, as well as greenhouse gas emissions and the economic net present value including emissions costs. Currently, people other than project developers have limited or no access to such information, which stifles informed public debate on electric energy options. Within this context, the use of the HydroCalculator Tool may contribute to the debate, by facilitating access to information. To validate the tool's greenhouse gas calculations, we replicate two peer-reviewed articles that estimate greenhouse gas emissions from different hydropower plants in the Amazon basin. The estimates calculated by the HydroCalculator Tool are similar to the ones found in both peer-reviewed articles. The results show that hydropower plants can lead to greenhouse gas emissions and that, in some cases, these emissions can be larger than those of alternative energy sources producing the same amount of electricity.

  8. Extraction Analysis and Creation of Three-Dimensional Road Profiles Using Matlab OpenCRG Tool

    Directory of Open Access Journals (Sweden)

    Rakesh Hari Borse

    2015-08-01

    Full Text Available In vehicle systems dynamics there are wide applications of simulation of vehicles on road surfaces. These simulation applications are related to vehicle handling ride comfort and durability. For accurate prediction of results there is a need for a reliable and efficient road representations. The efficient representation of road surface profiles is to represent them in three-dimensional space. This is made possible by the CRG Curved Regular Grid approach. OpenCRG is a completely open source project including a tool suite for the creation modification and evaluation of road surfaces. Its objective is to standardized detailed road surface description and it may be used for applications like tire models vibrations or driving simulation. The Matlab tool suite of OpenCRG provides powerful modification or creation tools and allows to visualize the 3D road data representation. The current research focuses on basic concepts of OpenCRG and its Matlab environment. The extraction of longitudinal two-dimensional road profiles from three-dimensional CRG format is researched. The creation of simple virtual three-dimensional roads has been programmed. A Matlab software tool to extract create and analyze the three-dimensional road profiles is to be developed.

  9. Open source drug discovery in practice: a case study.

    Directory of Open Access Journals (Sweden)

    Christine Årdal

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

  10. Open source drug discovery in practice: a case study.

    Science.gov (United States)

    Årdal, Christine; Røttingen, John-Arne

    2012-01-01

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

  11. An International Look at Women in Open Source

    Directory of Open Access Journals (Sweden)

    Cathy Malmrose

    2009-05-01

    Full Text Available When attending conferences, working with various open source teams, and generally interacting with people in the open source world, we see women as a small representative minority. The disparity leaves us wondering: "How to activate the other 50% of the population?". The question, "How do we include more women?" has been asked many times and answered in many ways. Cathy Malmrose, CEO of ZaReason, a Linux hardware company, stated, "possibly the most immediately effective solution is to showcase women internationally and their contributions. By simply talking about what women are doing all over the world, it creates an atmosphere of acceptance, encouraging more women to try contributing, no matter where they are located or what their situation is. Our goal is to normalize the experience of having women on open source projects". This issue of OSBR is a powerful effort to do just that. This article provides a glance at women in open source internationally. It is by no means comprehensive and is based solely on a random sampling of women who are currently contributing. The goal of this article is to give you a sense of the breadth and depth of women contributing to open source.

  12. Beginning Blender Open Source 3D Modeling, Animations, and Game Design

    CERN Document Server

    Flavell, L

    2010-01-01

    A new world of creative possibilities is opened by Blender, the most popular and powerful open source 3D and animation tool. Blender is not just free software; it is also an important professional tool used in animated shorts, television commercials, and shows, as well as in production for films like Spiderman 2. Lance Flavell's Beginning Blender will give you the skills to start shaping new worlds and virtual characters, and perhaps lead you down a new professional path. Beginning Blender covers the Blender 2.5 release in-depth. The book starts with the creation of simple figures using basic

  13. Near Real Time Discovery and Conversion of Open Source Information to a Reward Matrix

    Directory of Open Access Journals (Sweden)

    Mark Rahmes

    2014-02-01

    Full Text Available We describe a system model for determining decision making strategies based upon the ability to perform data mining and pattern discovery utilizing open source information to automatically predict the likelihood of reactions to specific events or situational awareness from multiple information sources. Within this paper, we discuss the development of a method for determining actionable information to efficiently propitiate manpower, equipment assets, or propaganda responses to multiple application case scenario experiments. In our experiments, we have integrated open source information linking to human sentiment and manipulated other user selectable interlinking relative probabilities for different reactions to different events based upon current knowledge generated from the situation or event. The goal of our solution, called GlobalSite, is to deliver trustworthy decision making analysis which evaluates situations and potential impacts of such decisions through acquired open source information becoming a vital tool for continuing mission operations, analyst information or other decision making scenarios.

  14. 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.

  15. Inspiring the Next Generation of Scientists: Building on 52 Years of Tradition in Diatom Research with Open-Source, Web-Based Collaboration Tools and Online Resources in a Field Course for High School Students

    Science.gov (United States)

    Howard, K. L.; Lee, S. S.

    2015-12-01

    Open-source, web-based forums and online resources can be used to develop a collaborative, active-learning approach for engaging and training students in the scientific process. We used the Diatoms of the United States website as an online resource for diatom taxonomy and developed a Google+ class community to serve as a platform for high school students to learn about research in diatom taxonomy, community ecology and diatom applications to the earth sciences. Ecology and Systematics of Diatoms is a field course that has been taught at the undergraduate and graduate levels at the Iowa Lakeside Lab field station for 52 years, beginning with the Diatom Clinic in 1963. Freshwater diatom education at Lakeside Lab has since evolved into a foundational training course attracting budding diatomists from all over the world, and has grown to include a week-long course for high school students. Successful since 2012, the high school course is now offered for college credit (University of Iowa), and covers methods of diatom specimen collection and preparation, microscopy, identification of diatom genera, diatom ecology, applications of diatom research, and an introduction to data analysis incorporating multivariate statistics (ordination) using the R statistical program, as well as primary scientific literature. During the 2015 course, students contributed to a Google+ class community where they posted images, data, and questions. The web-based platform allowed students to easily share information and to give and receive feedback from both peers and instructors. Students collaborated via the Google+ community and used the Diatoms of the United States website to develop a taxonomic reference for a field-based group research project, simulating how an actual diatom research program would develop a region or project-specific flora harmonized across analysts. Students investigated the taxonomy and ecology of diatom epiphytes on the green alga Cladophora from the littoral zone of

  16. 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

  17. 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...

  18. Open Source AV solution supporting In Situ Simulation

    DEFF Research Database (Denmark)

    Krogh, Kristian; Pociunas, Gintas; Dahl, Mads Ronald

    the software to meet our expectations for a portable AV system for VAD. The system would make use of “off the shelf” hardware components which are widely available and easily replaced or expanded. The developed AV software and coding is contracted to be available as Copyleft Open Source to ensure low cost...... a stable AV software that has be developed and implemented for an in situ simulation initiative. This version (1.3) is the first on released as Open Source (Copyleft) software (see QR tag). We have found that it is possible to deliver multi-camera video assisted debriefing in a mobile, in situ simulation...... environment using an AV system constructed from “off the shelf” components and Open Source software....

  19. Open Source Web Based Geospatial Processing with OMAR

    Directory of Open Access Journals (Sweden)

    Mark Lucas

    2009-01-01

    Full Text Available The availability of geospatial data sets is exploding. New satellites, aerial platforms, video feeds, global positioning system tagged digital photos, and traditional GIS information are dramatically increasing across the globe. These raw materials need to be dynamically processed, combined and correlated to generate value added information products to answer a wide range of questions. This article provides an overview of OMAR web based geospatial processing. OMAR is part of the Open Source Software Image Map project under the Open Source Geospatial Foundation. The primary contributors of OSSIM make their livings by providing professional services to US Government agencies and programs. OMAR provides one example that open source software solutions are increasingly being deployed in US government agencies. We will also summarize the capabilities of OMAR and its plans for near term development.

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

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

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

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

    Science.gov (United States)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

  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. 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.

  5. 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).

  6. Data from thermal testing of the Open Source Cryostage

    DEFF Research Database (Denmark)

    Buch, Johannes Lørup; Ramløv, Hans

    2016-01-01

    The data presented here is related to the research article "An open source cryostage and software analysis method for detection of antifreeze activity" (Buch and Ramløv, 2016) [1]. The design of the Open Source Cryostage (OSC) is tested in terms of thermal limits, thermal efficiency and electrical...... efficiency. This article furthermore includes an overview of the electrical circuitry and a flowchart of the software program controlling the temperature of the OSC. The thermal efficiency data is presented here as degrees per volt and maximum cooling capacity....

  7. 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.

  8. Open source and DIY hardware for DNA nanotechnology labs.

    Science.gov (United States)

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

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

  9. 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...

  10. Data from thermal testing of the Open Source Cryostage

    Directory of Open Access Journals (Sweden)

    Johannes Lørup Buch

    2016-09-01

    Full Text Available The data presented here is related to the research article “An open source cryostage and software analysis method for detection of antifreeze activity” (Buch and Ramløv, 2016 [1]. The design of the Open Source Cryostage (OSC is tested in terms of thermal limits, thermal efficiency and electrical efficiency. This article furthermore includes an overview of the electrical circuitry and a flowchart of the software program controlling the temperature of the OSC. The thermal efficiency data is presented here as degrees per volt and maximum cooling capacity.

  11. Open source and DIY hardware for DNA nanotechnology labs

    Directory of Open Access Journals (Sweden)

    Tulsi R. Damase

    2015-08-01

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

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

    Science.gov (United States)

    Marturano, Antonio

    2011-01-01

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

  13. 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

  14. OpenMC In Situ Source Convergence Detection

    Energy Technology Data Exchange (ETDEWEB)

    Aldrich, Garrett Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. of California, Davis, CA (United States); Dutta, Soumya [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); The Ohio State Univ., Columbus, OH (United States); Woodring, Jonathan Lee [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-07

    We designed and implemented an in situ version of particle source convergence for the OpenMC particle transport simulator. OpenMC is a Monte Carlo based-particle simulator for neutron criticality calculations. For the transport simulation to be accurate, source particles must converge on a spatial distribution. Typically, convergence is obtained by iterating the simulation by a user-settable, fixed number of steps, and it is assumed that convergence is achieved. We instead implement a method to detect convergence, using the stochastic oscillator for identifying convergence of source particles based on their accumulated Shannon Entropy. Using our in situ convergence detection, we are able to detect and begin tallying results for the full simulation once the proper source distribution has been confirmed. Our method ensures that the simulation is not started too early, by a user setting too optimistic parameters, or too late, by setting too conservative a parameter.

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

    Science.gov (United States)

    Mitternacht, Simon

    2016-01-01

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

  16. 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.

  17. 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.

  18. 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…

  19. 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

  20. 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....